From 480f319621ff430a13474b17ccd8530cf1f9acdc Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 17 Aug 2024 10:14:33 -0700 Subject: [PATCH 01/91] refactor & rename & consolidate --- src/python/tests/conftest.py | 4 ++ src/python/tests/sourmash_tst_utils.py | 17 +++++++++ src/python/tests/test_cluster.py | 10 +---- .../{test_gather.py => test_fastgather.py} | 30 +-------------- ...multigather.py => test_fastmultigather.py} | 17 +-------- src/python/tests/test_index.py | 12 +----- src/python/tests/test_manysearch.py | 38 +------------------ src/python/tests/test_multisearch.py | 29 +------------- src/python/tests/test_pairwise.py | 24 +----------- src/utils.rs | 2 +- 10 files changed, 29 insertions(+), 154 deletions(-) rename src/python/tests/{test_gather.py => test_fastgather.py} (96%) rename src/python/tests/{test_multigather.py => test_fastmultigather.py} (99%) diff --git a/src/python/tests/conftest.py b/src/python/tests/conftest.py index 052837f6..3f7021a1 100644 --- a/src/python/tests/conftest.py +++ b/src/python/tests/conftest.py @@ -16,6 +16,10 @@ def toggle_internal_storage(request): def zip_query(request): return request.param +@pytest.fixture(params=[True, False]) +def zip_db(request): + return request.param + @pytest.fixture(params=[True, False]) def zip_against(request): return request.param diff --git a/src/python/tests/sourmash_tst_utils.py b/src/python/tests/sourmash_tst_utils.py index 7c99b1b6..f4ad4927 100644 --- a/src/python/tests/sourmash_tst_utils.py +++ b/src/python/tests/sourmash_tst_utils.py @@ -14,6 +14,23 @@ from io import StringIO +def get_test_data(filename): + thisdir = os.path.dirname(__file__) + return os.path.join(thisdir, 'test-data', filename) + + +def make_file_list(filename, paths): + with open(filename, 'wt') as fp: + fp.write("\n".join(paths)) + fp.write("\n") + + +def zip_siglist(runtmp, siglist, db): + runtmp.sourmash('sig', 'cat', siglist, + '-o', db) + return db + + def scriptpath(scriptname='sourmash'): """Return the path to the scripts, in both dev and install situations.""" # note - it doesn't matter what the scriptname is here, as long as diff --git a/src/python/tests/test_cluster.py b/src/python/tests/test_cluster.py index 6e153946..4ae12173 100644 --- a/src/python/tests/test_cluster.py +++ b/src/python/tests/test_cluster.py @@ -2,15 +2,7 @@ import pytest from . import sourmash_tst_utils as utils - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") +from .sourmash_tst_utils import get_test_data, make_file_list def test_installed(runtmp): diff --git a/src/python/tests/test_gather.py b/src/python/tests/test_fastgather.py similarity index 96% rename from src/python/tests/test_gather.py rename to src/python/tests/test_fastgather.py index 4ab4c6de..bd2ca5a4 100644 --- a/src/python/tests/test_gather.py +++ b/src/python/tests/test_fastgather.py @@ -4,23 +4,7 @@ import sourmash from . import sourmash_tst_utils as utils - - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") - - -def zip_siglist(runtmp, siglist, db): - runtmp.sourmash('sig', 'cat', siglist, - '-o', db) - return db +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) def test_installed(runtmp): @@ -30,7 +14,6 @@ def test_installed(runtmp): assert 'usage: fastgather' in runtmp.last_result.err -@pytest.mark.parametrize('zip_against', [False, True]) def test_simple(runtmp, zip_against): # test basic execution! query = get_test_data('SRR606249.sig.gz') @@ -58,7 +41,6 @@ def test_simple(runtmp, zip_against): assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'gather_result_rank', 'intersect_bp'}.issubset(keys) -@pytest.mark.parametrize('zip_against', [False, True]) def test_simple_with_prefetch(runtmp, zip_against): # test basic execution! query = get_test_data('SRR606249.sig.gz') @@ -93,7 +75,6 @@ def test_simple_with_prefetch(runtmp, zip_against): assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp'} -@pytest.mark.parametrize('zip_against', [False, True]) def test_missing_query(runtmp, capfd, zip_against): # test missing query query = runtmp.output('no-such-file') @@ -122,7 +103,6 @@ def test_missing_query(runtmp, capfd, zip_against): assert 'Error: No such file or directory' in captured.err -@pytest.mark.parametrize('zip_against', [False, True]) def test_bad_query(runtmp, capfd, zip_against): # test non-sig query query = runtmp.output('no-such-file') @@ -154,7 +134,6 @@ def test_bad_query(runtmp, capfd, zip_against): assert 'Error: Fastgather requires a single query sketch. Check input:' in captured.err -@pytest.mark.parametrize('zip_against', [False, True]) def test_missing_against(runtmp, capfd, zip_against): # test missing against query = get_test_data('SRR606249.sig.gz') @@ -278,7 +257,6 @@ def test_bad_against_3(runtmp, capfd): assert 'InvalidArchive' in captured.err -@pytest.mark.parametrize('zip_against', [False, True]) def test_against_multisigfile(runtmp, zip_against): # test against a sigfile that contains multiple sketches query = get_test_data('SRR606249.sig.gz') @@ -311,7 +289,6 @@ def test_against_multisigfile(runtmp, zip_against): # @CTB this is a bug :(. It should load multiple sketches properly! -@pytest.mark.parametrize('zip_against', [False, True]) def test_query_multisigfile(runtmp, capfd, zip_against): # test with a sigfile that contains multiple sketches against_list = runtmp.output('against.txt') @@ -341,7 +318,6 @@ def test_query_multisigfile(runtmp, capfd, zip_against): assert "Error: Fastgather requires a single query sketch. Check input:" in captured.err -@pytest.mark.parametrize('zip_against', [False, True]) def test_against_nomatch(runtmp, capfd, zip_against): # test with 'against' file containing a non-matching ksize query = get_test_data('SRR606249.sig.gz') @@ -370,7 +346,6 @@ def test_against_nomatch(runtmp, capfd, zip_against): assert 'WARNING: skipped 1 search paths - no compatible signatures.' in captured.err -@pytest.mark.parametrize('zip_against', [False, True]) def test_md5s(runtmp, zip_against): # check that the correct md5sums (of the original sketches) are in # the output files @@ -424,7 +399,6 @@ def test_md5s(runtmp, zip_against): assert ss.md5sum() in md5s -@pytest.mark.parametrize('zip_against', [False, True]) def test_csv_columns_vs_sourmash_prefetch(runtmp, zip_against): # the column names should be strict subsets of sourmash prefetch cols query = get_test_data('SRR606249.sig.gz') @@ -466,7 +440,6 @@ def test_csv_columns_vs_sourmash_prefetch(runtmp, zip_against): assert diff_keys == set(['unique_intersect_bp', 'median_abund', 'f_match_orig', 'std_abund', 'average_abund', 'f_unique_to_query', 'remaining_bp', 'f_unique_weighted', 'sum_weighted_found', 'total_weighted_hashes', 'n_unique_weighted_found', 'f_orig_query', 'f_match']) -@pytest.mark.parametrize('zip_against', [False, True]) def test_fastgather_gatherout_as_picklist(runtmp, zip_against): # should be able to use fastgather gather output as picklist query = get_test_data('SRR606249.sig.gz') @@ -508,7 +481,6 @@ def test_fastgather_gatherout_as_picklist(runtmp, zip_against): assert picklist_df.equals(full_df) -@pytest.mark.parametrize('zip_against', [False, True]) def test_fastgather_prefetchout_as_picklist(runtmp, zip_against): # should be able to use fastgather prefetch output as picklist query = get_test_data('SRR606249.sig.gz') diff --git a/src/python/tests/test_multigather.py b/src/python/tests/test_fastmultigather.py similarity index 99% rename from src/python/tests/test_multigather.py rename to src/python/tests/test_fastmultigather.py index b3649ee9..942c1d1b 100644 --- a/src/python/tests/test_multigather.py +++ b/src/python/tests/test_fastmultigather.py @@ -8,17 +8,7 @@ import sourmash from . import sourmash_tst_utils as utils - - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) def index_siglist(runtmp, siglist, db, *, ksize=31, scaled=1000, moltype='DNA', @@ -37,11 +27,6 @@ def test_installed(runtmp): assert 'usage: fastmultigather' in runtmp.last_result.err -def zip_siglist(runtmp, siglist, db): - runtmp.sourmash('sig', 'cat', siglist, - '-o', db) - return db - def test_simple(runtmp, zip_against): # test basic execution! query = get_test_data('SRR606249.sig.gz') diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py index 69faf8ae..140fe799 100644 --- a/src/python/tests/test_index.py +++ b/src/python/tests/test_index.py @@ -5,17 +5,7 @@ import shutil from . import sourmash_tst_utils as utils - - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) def test_installed(runtmp): diff --git a/src/python/tests/test_manysearch.py b/src/python/tests/test_manysearch.py index 6deb5c3b..ab0f5762 100644 --- a/src/python/tests/test_manysearch.py +++ b/src/python/tests/test_manysearch.py @@ -4,17 +4,7 @@ import sourmash from . import sourmash_tst_utils as utils - - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) def test_installed(runtmp): @@ -23,10 +13,6 @@ def test_installed(runtmp): assert 'usage: manysearch' in runtmp.last_result.err -def zip_siglist(runtmp, siglist, db): - runtmp.sourmash('sig', 'cat', siglist, - '-o', db) - return db def index_siglist(runtmp, siglist, db, ksize=31, scaled=1000, moltype='DNA'): # build index @@ -35,8 +21,6 @@ def index_siglist(runtmp, siglist, db, ksize=31, scaled=1000, moltype='DNA'): '--moltype', moltype) return db -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("zip_against", [False, True]) def test_simple(runtmp, zip_query, zip_against): # test basic execution! query_list = runtmp.output('query.txt') @@ -192,7 +176,6 @@ def test_simple_abund(runtmp): assert total_weighted_hashes == 73489 -@pytest.mark.parametrize("zip_query", [False, True]) def test_simple_indexed(runtmp, zip_query): # test basic execution! query_list = runtmp.output('query.txt') @@ -249,8 +232,6 @@ def test_simple_indexed(runtmp, zip_query): assert query_ani == 0.9772 -@pytest.mark.parametrize("indexed", [False, True]) -@pytest.mark.parametrize("zip_query", [False, True]) def test_simple_with_cores(runtmp, capfd, indexed, zip_query): # test basic execution with -c argument (that it runs, at least!) query_list = runtmp.output('query.txt') @@ -283,8 +264,6 @@ def test_simple_with_cores(runtmp, capfd, indexed, zip_query): assert " using 4 threads" in result.err -@pytest.mark.parametrize("indexed", [False, True]) -@pytest.mark.parametrize("zip_query", [False, True]) def test_simple_threshold(runtmp, indexed, zip_query): # test with a simple threshold => only 3 results query_list = runtmp.output('query.txt') @@ -313,7 +292,6 @@ def test_simple_threshold(runtmp, indexed, zip_query): assert len(df) == 3 -@pytest.mark.parametrize("indexed", [False, True]) def test_simple_manifest(runtmp, indexed): # test with a simple threshold => only 3 results query_list = runtmp.output('query.txt') @@ -347,8 +325,6 @@ def test_simple_manifest(runtmp, indexed): assert len(df) == 3 -@pytest.mark.parametrize("indexed", [False, True]) -@pytest.mark.parametrize("zip_query", [False, True]) def test_missing_query(runtmp, capfd, indexed, zip_query): # test with a missing query list query_list = runtmp.output('query.txt') @@ -379,7 +355,6 @@ def test_missing_query(runtmp, capfd, indexed, zip_query): assert 'Error: No such file or directory' in captured.err -@pytest.mark.parametrize("indexed", [False, True]) def test_sig_query(runtmp, capfd, indexed): # test with a single sig query (a .sig.gz file) against_list = runtmp.output('against.txt') @@ -399,7 +374,6 @@ def test_sig_query(runtmp, capfd, indexed): '-o', output) -@pytest.mark.parametrize("indexed", [False, True]) def test_bad_query_2(runtmp, capfd, indexed): # test with a bad query list (a missing file) query_list = runtmp.output('query.txt') @@ -453,7 +427,6 @@ def test_bad_query_3(runtmp, capfd): assert 'InvalidArchive' in captured.err -@pytest.mark.parametrize("indexed", [False, True]) def test_missing_against(runtmp, capfd, indexed): # test with a missing against list query_list = runtmp.output('query.txt') @@ -524,7 +497,6 @@ def test_bad_against(runtmp, capfd): assert "WARNING: 1 search paths failed to load. See error messages above." in captured.err -@pytest.mark.parametrize("indexed", [False, True]) def test_empty_query(runtmp, indexed, capfd): # test with an empty query list query_list = runtmp.output('query.txt') @@ -552,8 +524,6 @@ def test_empty_query(runtmp, indexed, capfd): assert "No query signatures loaded, exiting." in captured.err -@pytest.mark.parametrize("indexed", [False, True]) -@pytest.mark.parametrize("zip_query", [False, True]) def test_nomatch_query(runtmp, capfd, indexed, zip_query): # test a non-matching (diff ksize) in query; do we get warning message? query_list = runtmp.output('query.txt') @@ -584,8 +554,6 @@ def test_nomatch_query(runtmp, capfd, indexed, zip_query): assert 'WARNING: skipped 1 query paths - no compatible signatures.' in captured.err -@pytest.mark.parametrize("zip_against", [False, True]) -@pytest.mark.parametrize("indexed", [False, True]) def test_load_only_one_bug(runtmp, capfd, indexed, zip_against): # check that we behave properly when presented with multiple against # sketches @@ -619,8 +587,6 @@ def test_load_only_one_bug(runtmp, capfd, indexed, zip_against): assert not 'WARNING: no compatible sketches in path ' in captured.err -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("indexed", [False, True]) def test_load_only_one_bug_as_query(runtmp, capfd, indexed, zip_query): # check that we behave properly when presented with multiple query # sketches in one file, with only one matching. @@ -656,8 +622,6 @@ def test_load_only_one_bug_as_query(runtmp, capfd, indexed, zip_query): assert not 'WARNING: no compatible sketches in path ' in captured.err -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("indexed", [False, True]) def test_md5(runtmp, indexed, zip_query): # test that md5s match what was in the original files, not downsampled etc. query_list = runtmp.output('query.txt') diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index 611b0f81..87553615 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -5,17 +5,7 @@ import sourmash from . import sourmash_tst_utils as utils - - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) def test_installed(runtmp): @@ -24,13 +14,7 @@ def test_installed(runtmp): assert 'usage: multisearch' in runtmp.last_result.err -def zip_siglist(runtmp, siglist, db): - runtmp.sourmash('sig', 'cat', siglist, - '-o', db) - return db -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("zip_db", [False, True]) def test_simple_no_ani(runtmp, zip_query, zip_db): # test basic execution! query_list = runtmp.output('query.txt') @@ -99,8 +83,6 @@ def test_simple_no_ani(runtmp, zip_query, zip_db): assert intersect_hashes == 2529 -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("zip_db", [False, True]) def test_simple_ani(runtmp, zip_query, zip_db): # test basic execution! query_list = runtmp.output('query.txt') @@ -186,8 +168,6 @@ def test_simple_ani(runtmp, zip_query, zip_db): assert max_ani == 0.9772 -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("zip_db", [False, True]) def test_simple_threshold(runtmp, zip_query, zip_db): # test with a simple threshold => only 3 results query_list = runtmp.output('query.txt') @@ -243,7 +223,6 @@ def test_simple_manifest(runtmp): assert len(df) == 3 -@pytest.mark.parametrize("zip_query", [False, True]) def test_missing_query(runtmp, capfd, zip_query): # test with a missing query list query_list = runtmp.output('query.txt') @@ -344,7 +323,6 @@ def test_bad_query_3(runtmp, capfd): assert 'InvalidArchive' in captured.err -@pytest.mark.parametrize("zip_db", [False, True]) def test_missing_against(runtmp, capfd, zip_db): # test with a missing against list query_list = runtmp.output('query.txt') @@ -445,7 +423,6 @@ def test_empty_query(runtmp, capfd): # @CTB -@pytest.mark.parametrize("zip_query", [False, True]) def test_nomatch_query(runtmp, capfd, zip_query): # test a non-matching (diff ksize) in query; do we get warning message? query_list = runtmp.output('query.txt') @@ -474,7 +451,6 @@ def test_nomatch_query(runtmp, capfd, zip_query): assert 'WARNING: skipped 1 query paths - no compatible signatures' in captured.err -@pytest.mark.parametrize("zip_db", [False, True]) def test_load_only_one_bug(runtmp, capfd, zip_db): # check that we behave properly when presented with multiple against # sketches @@ -506,7 +482,6 @@ def test_load_only_one_bug(runtmp, capfd, zip_db): assert not 'WARNING: no compatible sketches in path' in captured.err -@pytest.mark.parametrize("zip_query", [False, True]) def test_load_only_one_bug_as_query(runtmp, capfd, zip_query): # check that we behave properly when presented with multiple query # sketches in one file, with only one matching. @@ -538,8 +513,6 @@ def test_load_only_one_bug_as_query(runtmp, capfd, zip_query): assert not 'WARNING: no compatible sketches in path ' in captured.err -@pytest.mark.parametrize("zip_query", [False, True]) -@pytest.mark.parametrize("zip_db", [False, True]) def test_md5(runtmp, zip_query, zip_db): # test that md5s match what was in the original files, not downsampled etc. query_list = runtmp.output('query.txt') diff --git a/src/python/tests/test_pairwise.py b/src/python/tests/test_pairwise.py index 3869b3d4..c8264069 100644 --- a/src/python/tests/test_pairwise.py +++ b/src/python/tests/test_pairwise.py @@ -5,17 +5,7 @@ import sourmash from . import sourmash_tst_utils as utils - - -def get_test_data(filename): - thisdir = os.path.dirname(__file__) - return os.path.join(thisdir, 'test-data', filename) - - -def make_file_list(filename, paths): - with open(filename, 'wt') as fp: - fp.write("\n".join(paths)) - fp.write("\n") +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) def test_installed(runtmp): @@ -24,13 +14,7 @@ def test_installed(runtmp): assert 'usage: pairwise' in runtmp.last_result.err -def zip_siglist(runtmp, siglist, db): - runtmp.sourmash('sig', 'cat', siglist, - '-o', db) - return db - -@pytest.mark.parametrize("zip_query", [False, True]) def test_simple_no_ani(runtmp, zip_query): # test basic execution! query_list = runtmp.output('query.txt') @@ -81,7 +65,6 @@ def test_simple_no_ani(runtmp, zip_query): assert intersect_hashes == 2529 -@pytest.mark.parametrize("zip_query", [False, True]) def test_simple_ani(runtmp, zip_query): # test basic execution! query_list = runtmp.output('query.txt') @@ -140,7 +123,6 @@ def test_simple_ani(runtmp, zip_query): assert max_ani == 0.9772 -@pytest.mark.parametrize("zip_query", [False, True]) def test_simple_threshold(runtmp, zip_query): # test with a simple threshold => only 3 results query_list = runtmp.output('query.txt') @@ -248,7 +230,6 @@ def test_bad_query_2(runtmp, capfd): assert 'InvalidArchive' in captured.err -@pytest.mark.parametrize("zip_db", [False, True]) def test_missing_query(runtmp, capfd, zip_db): # test with a missing query list query_list = runtmp.output('query.txt') @@ -290,7 +271,6 @@ def test_empty_query(runtmp): # @CTB -@pytest.mark.parametrize("zip_query", [False, True]) def test_nomatch_query(runtmp, capfd, zip_query): # test a non-matching (diff ksize) in query; do we get warning message? query_list = runtmp.output('query.txt') @@ -317,7 +297,6 @@ def test_nomatch_query(runtmp, capfd, zip_query): assert 'WARNING: skipped 1 analysis paths - no compatible signatures' in captured.err -@pytest.mark.parametrize("zip_db", [False, True]) def test_load_only_one_bug(runtmp, capfd, zip_db): # check that we behave properly when presented with multiple query # sketches @@ -347,7 +326,6 @@ def test_load_only_one_bug(runtmp, capfd, zip_db): assert not 'WARNING: no compatible sketches in path ' in captured.err -@pytest.mark.parametrize("zip_query", [False, True]) def test_md5(runtmp, zip_query): # test that md5s match what was in the original files, not downsampled etc. query_list = runtmp.output('query.txt') diff --git a/src/utils.rs b/src/utils.rs index 4209413e..a5ef93a2 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -1091,7 +1091,7 @@ pub fn consume_query_by_gather( pub fn build_selection(ksize: u8, scaled: usize, moltype: &str) -> Selection { let hash_function = match moltype { - "dna" => HashFunctions::Murmur64Dna, + "DNA" => HashFunctions::Murmur64Dna, "protein" => HashFunctions::Murmur64Protein, "dayhoff" => HashFunctions::Murmur64Dayhoff, "hp" => HashFunctions::Murmur64Hp, From e6b1c5be3df76c56386480ff9fd5cdcc7ce90848 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 17 Aug 2024 10:40:56 -0700 Subject: [PATCH 02/91] remove 'lower' --- src/python/sourmash_plugin_branchwater/__init__.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py index 4c923e34..cf11ed56 100755 --- a/src/python/sourmash_plugin_branchwater/__init__.py +++ b/src/python/sourmash_plugin_branchwater/__init__.py @@ -69,7 +69,6 @@ def __init__(self, p): def main(self, args): print_version() notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold: {args.threshold}") - args.moltype = args.moltype.lower() num_threads = set_thread_pool(args.cores) notify(f"searching all sketches in '{args.query_paths}' against '{args.against_paths}' using {num_threads} threads") @@ -117,7 +116,6 @@ def __init__(self, p): def main(self, args): print_version() notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold bp: {args.threshold_bp}") - args.moltype = args.moltype.lower() num_threads = set_thread_pool(args.cores) @@ -164,7 +162,6 @@ def __init__(self, p): def main(self, args): print_version() notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold bp: {args.threshold_bp}") - args.moltype = args.moltype.lower() num_threads = set_thread_pool(args.cores) @@ -209,7 +206,6 @@ def __init__(self, p): def main(self, args): notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} ") - args.moltype = args.moltype.lower() num_threads = set_thread_pool(args.cores) @@ -274,7 +270,6 @@ def __init__(self, p): def main(self, args): print_version() notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold: {args.threshold}") - args.moltype = args.moltype.lower() num_threads = set_thread_pool(args.cores) @@ -321,7 +316,6 @@ def __init__(self, p): def main(self, args): print_version() notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold: {args.threshold}") - args.moltype = args.moltype.lower() num_threads = set_thread_pool(args.cores) From 0d7a556f95cfbbd6bf6f58a47a30522f695342c5 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 06:01:47 -0700 Subject: [PATCH 03/91] add cargo doc output for private fn --- .cargo/config.toml | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .cargo/config.toml diff --git a/.cargo/config.toml b/.cargo/config.toml new file mode 100644 index 00000000..a05a706a --- /dev/null +++ b/.cargo/config.toml @@ -0,0 +1,2 @@ +[build] +rustdocflags = ["--document-private-items"] From 1da0cf305d6b2ddaa509be9f416c9043517f3c01 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 06:09:48 -0700 Subject: [PATCH 04/91] add a few comments/docs --- src/lib.rs | 8 +++++++- src/utils.rs | 3 ++- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/src/lib.rs b/src/lib.rs index 7d623ea7..2a7fa58d 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,4 +1,8 @@ -/// Python interface Rust code for sourmash_plugin_branchwater. +//! Rust-to-Pyton interface code for sourmash_plugin_branchwater, using pyo3. +//! +//! If you're using Rust, you're probably most interested in +//! [utils](utils/index.html) + use pyo3::prelude::*; #[macro_use] @@ -322,6 +326,8 @@ fn do_cluster( } } +/// Module interface for the `sourmash_plugin_branchwater` extension module. + #[pymodule] fn sourmash_plugin_branchwater(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> { m.add_function(wrap_pyfunction!(do_manysearch, m)?)?; diff --git a/src/utils.rs b/src/utils.rs index 4209413e..bd6cbba3 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -1,4 +1,5 @@ -/// Utility functions for sourmash_plugin_branchwater. +//! Utility functions for `sourmash_plugin_branchwater`. + use rayon::prelude::*; use sourmash::encodings::HashFunctions; use sourmash::selection::Select; From 2e7f027a2159ba95ab7549b665f73f94a921c3f4 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 07:12:23 -0700 Subject: [PATCH 05/91] switch to dev version of sourmash --- Cargo.lock | 23 +++++++++++------------ Cargo.toml | 3 ++- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index c386a6c8..3f362496 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -740,9 +740,9 @@ checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c" [[package]] name = "libloading" -version = "0.8.3" +version = "0.8.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0c2a198fb6b0eada2a8df47933734e6d35d350665a33a3593d7164fa52c75c19" +checksum = "4979f22fdb869068da03c9f7528f8297c6fd2606bc3a4affe42e6a823fdb8da4" dependencies = [ "cfg-if", "windows-targets", @@ -772,9 +772,9 @@ dependencies = [ [[package]] name = "libz-sys" -version = "1.1.18" +version = "1.1.19" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c15da26e5af7e25c90b37a2d75cdbf940cf4a55316de9d84c679c9b8bfabf82e" +checksum = "fdc53a7799a7496ebc9fd29f31f7df80e83c9bda5299768af5f9e59eeea74647" dependencies = [ "cc", "pkg-config", @@ -795,9 +795,9 @@ checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24" [[package]] name = "lz4-sys" -version = "1.9.5" +version = "1.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e9764018d143cc854c9f17f0b907de70f14393b1f502da6375dce70f00514eb3" +checksum = "109de74d5d2353660401699a4174a4ff23fcc649caf553df71933c7fb45ad868" dependencies = [ "cc", "libc", @@ -1481,18 +1481,18 @@ dependencies = [ [[package]] name = "serde" -version = "1.0.206" +version = "1.0.208" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5b3e4cd94123dd520a128bcd11e34d9e9e423e7e3e50425cb1b4b1e3549d0284" +checksum = "cff085d2cb684faa248efb494c39b68e522822ac0de72ccf08109abde717cfb2" dependencies = [ "serde_derive", ] [[package]] name = "serde_derive" -version = "1.0.206" +version = "1.0.208" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fabfb6138d2383ea8208cf98ccf69cdfb1aff4088460681d84189aa259762f97" +checksum = "24008e81ff7613ed8e5ba0cfaf24e2c2f1e5b8a0495711e44fcd4882fca62bcf" dependencies = [ "proc-macro2", "quote", @@ -1551,8 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8655e639cc4a32fa1422629c9b4ff603ee09cf6d04a97eacd37594382472d437" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#d23ef6bdeaa8655443083628905e077e88f56a21" dependencies = [ "az", "byteorder", diff --git a/Cargo.toml b/Cargo.toml index 353ec2d1..7422983e 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,8 @@ crate-type = ["cdylib"] pyo3 = { version = "0.22.2", features = ["extension-module", "anyhow"] } rayon = "1.10.0" serde = { version = "1.0.206", features = ["derive"] } -sourmash = { version = "0.15.0", features = ["branchwater"] } +sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "misc_rs_updates", features = ["branchwater"] } +#sourmash = { version = "0.15.0", features = ["branchwater"] } serde_json = "1.0.124" niffler = "2.4.0" log = "0.4.22" From 6b9e00fb20c3815c3829efa49af5a7d0edbfdc9c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 07:32:56 -0700 Subject: [PATCH 06/91] tracking --- Cargo.lock | 2 +- src/multisearch.rs | 11 +++++++++++ src/utils.rs | 28 ++++++++++++++++++---------- 3 files changed, 30 insertions(+), 11 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 3f362496..dbf39445 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#d23ef6bdeaa8655443083628905e077e88f56a21" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#952ccf64aa102a2b7e1a22e75710d03dcedc77e2" dependencies = [ "az", "byteorder", diff --git a/src/multisearch.rs b/src/multisearch.rs index 19d2264d..1695ff60 100644 --- a/src/multisearch.rs +++ b/src/multisearch.rs @@ -60,12 +60,23 @@ pub fn multisearch( let processed_cmp = AtomicUsize::new(0); let ksize = selection.ksize().unwrap() as f64; + if queries.len() == 0 { + eprintln!("No query sketches present. Exiting."); + return Err(anyhow::anyhow!("foo").into()); // @CTB + } + + if against.len() == 0 { + eprintln!("No search sketches present. Exiting."); + return Err(anyhow::anyhow!("foo").into()); // @CTB + } + let send = against .par_iter() .filter_map(|against| { let mut results = vec![]; // search for matches & save containment. for query in queries.iter() { + eprintln!("XXXX"); let i = processed_cmp.fetch_add(1, atomic::Ordering::SeqCst); if i % 100000 == 0 && i > 0 { eprintln!("Processed {} comparisons", i); diff --git a/src/utils.rs b/src/utils.rs index bd6cbba3..8a6b83f6 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -443,16 +443,24 @@ pub fn load_sketches( let sketchinfo: Vec = collection .par_iter() .filter_map(|(_idx, record)| { - let sig = collection.sig_from_record(record).ok()?; - let selected_sig = sig.clone().select(selection).ok()?; - let minhash = selected_sig.minhash()?.clone(); - - Some(SmallSignature { - location: record.internal_location().to_string(), - name: sig.name(), - md5sum: sig.md5sum(), - minhash, - }) + match collection.sig_from_record(record) { + Ok(sig) => { + let selected_sig = sig.clone().select(selection).ok()?; + let minhash = selected_sig.minhash()?.clone(); + + Some(SmallSignature { + location: record.internal_location().to_string(), + name: sig.name(), + md5sum: sig.md5sum(), + minhash, + }) + }, + Err(_) => { + eprintln!("FAILED to load sketch from '{}'", + record.internal_location()); + None + } + } }) .collect(); From 2747935be3286f8175fd8e193747cb4aa7532b0a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 09:18:18 -0700 Subject: [PATCH 07/91] cleaner --- Cargo.lock | 2 +- src/multisearch.rs | 4 ++-- src/utils.rs | 3 ++- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index dbf39445..5a9f3ba7 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#952ccf64aa102a2b7e1a22e75710d03dcedc77e2" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#38013af8efad824e4396b51e4354c9a8b5f9f606" dependencies = [ "az", "byteorder", diff --git a/src/multisearch.rs b/src/multisearch.rs index 1695ff60..9fc3e8ae 100644 --- a/src/multisearch.rs +++ b/src/multisearch.rs @@ -62,12 +62,12 @@ pub fn multisearch( if queries.len() == 0 { eprintln!("No query sketches present. Exiting."); - return Err(anyhow::anyhow!("foo").into()); // @CTB + return Err(anyhow::anyhow!("failed to load query sketches").into()); } if against.len() == 0 { eprintln!("No search sketches present. Exiting."); - return Err(anyhow::anyhow!("foo").into()); // @CTB + return Err(anyhow::anyhow!("failed to load search sketches").into()); } let send = against diff --git a/src/utils.rs b/src/utils.rs index 8a6b83f6..80d4328b 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -433,7 +433,7 @@ fn process_prefix_csv( Ok((results, n_fastas)) } -// Load all compatible minhashes from a collection into memory +// Load all compatible minhashes from a collection into memory, in parallel; // also store sig name and md5 alongside, as we usually need those pub fn load_sketches( collection: Collection, @@ -573,6 +573,7 @@ fn collection_from_manifest( Err(anyhow!("could not read as manifest: '{}'", sigpath)) } else { // If the manifest is not empty, proceed to create and return the Collection + eprintln!("collection from manifest!"); Ok(Collection::new( manifest, InnerStorage::new( From 4f49ef808cd43931e7521b53345c95ff026ed41d Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 09:20:38 -0700 Subject: [PATCH 08/91] cleanup --- Cargo.lock | 2 +- src/multisearch.rs | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 5a9f3ba7..63397361 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#38013af8efad824e4396b51e4354c9a8b5f9f606" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#08459a8dd72d209e13ccbc7726bfaeb8245e52c0" dependencies = [ "az", "byteorder", diff --git a/src/multisearch.rs b/src/multisearch.rs index 9fc3e8ae..6edad2c1 100644 --- a/src/multisearch.rs +++ b/src/multisearch.rs @@ -76,7 +76,6 @@ pub fn multisearch( let mut results = vec![]; // search for matches & save containment. for query in queries.iter() { - eprintln!("XXXX"); let i = processed_cmp.fetch_add(1, atomic::Ordering::SeqCst); if i % 100000 == 0 && i > 0 { eprintln!("Processed {} comparisons", i); From af1c82de2eb41df6389ec8792265153d41e2ba5e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 11:18:42 -0700 Subject: [PATCH 09/91] load rocksdb natively --- Cargo.lock | 2 +- src/utils.rs | 34 ++++++++++++++++++++++++++++++++-- 2 files changed, 33 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 63397361..f1f47c19 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#08459a8dd72d209e13ccbc7726bfaeb8245e52c0" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#e67415c8a7cdddc81be58654ff1dc7041e62ad4d" dependencies = [ "az", "byteorder", diff --git a/src/utils.rs b/src/utils.rs index 80d4328b..b7d6507c 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -546,6 +546,8 @@ impl std::fmt::Display for ReportType { } } +/// Load a collection from a .zip file. + pub fn collection_from_zipfile(sigpath: &Path, report_type: &ReportType) -> Result { match Collection::from_zipfile(sigpath) { Ok(collection) => Ok(collection), @@ -553,6 +555,17 @@ pub fn collection_from_zipfile(sigpath: &Path, report_type: &ReportType) -> Resu } } +/// Load a collection from a RocksDB. + +pub fn collection_from_rocksdb(sigpath: &Path, report_type: &ReportType) -> Result { + match Collection::from_rocksdb(sigpath) { + Ok(collection) => Ok(collection), + Err(_) => bail!("failed to load {} rocksdb: '{}'", report_type, sigpath), + } +} + +/// Load a collection from a manifest CSV. + fn collection_from_manifest( sigpath: &Path, report_type: &ReportType, @@ -586,6 +599,8 @@ fn collection_from_manifest( } } +/// Load a collection from a list of paths. + fn collection_from_pathlist( sigpath: &Path, report_type: &ReportType, @@ -651,6 +666,8 @@ fn collection_from_pathlist( Ok((collection, n_failed)) } +/// Load a collection from a .sig/.sig.gz JSON file. + fn collection_from_signature(sigpath: &Path, report_type: &ReportType) -> Result { let signatures = Signature::from_path(sigpath).with_context(|| { format!( @@ -667,6 +684,8 @@ fn collection_from_signature(sigpath: &Path, report_type: &ReportType) -> Result }) } +/// Load a collection from a path - this is the top-level load function. + pub fn load_collection( siglist: &String, selection: &Selection, @@ -679,10 +698,12 @@ pub fn load_collection( bail!("No such file or directory: '{}'", &sigpath); } - // disallow rocksdb input here + // disallow rocksdb input here - CTB test me a lot ;) + /* if is_revindex_database(&sigpath) { bail!("Cannot load {} signatures from a 'rocksdb' database. Please use sig, zip, or pathlist.", report_type); - } +} + */ eprintln!("Reading {}(s) from: '{}'", report_type, &siglist); let mut last_error = None; @@ -699,6 +720,15 @@ pub fn load_collection( None }; + let collection = + collection.or_else(|| match collection_from_rocksdb(&sigpath, &report_type) { + Ok(coll) => Some((coll, 0)), + Err(e) => { + last_error = Some(e); + None + } + }); + let collection = collection.or_else(|| match collection_from_manifest(&sigpath, &report_type) { Ok(coll) => Some((coll, 0)), From 53924d6603a2618e11b8f64d0d013b084e587c3b Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Aug 2024 14:22:10 -0700 Subject: [PATCH 10/91] foo --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index f1f47c19..b6e9cdf4 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#e67415c8a7cdddc81be58654ff1dc7041e62ad4d" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#603fa0b5bd02d595e94f0463a4047d9129613e02" dependencies = [ "az", "byteorder", From 3462f927a00abe4c059aedb1979b749b68d2906b Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Mon, 19 Aug 2024 16:01:48 -0700 Subject: [PATCH 11/91] cargo fmt --- src/utils.rs | 59 ++++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 30 deletions(-) diff --git a/src/utils.rs b/src/utils.rs index ec18ce36..1d4e6124 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -442,24 +442,24 @@ pub fn load_sketches( ) -> Result> { let sketchinfo: Vec = collection .par_iter() - .filter_map(|(_idx, record)| { - match collection.sig_from_record(record) { - Ok(sig) => { - let selected_sig = sig.clone().select(selection).ok()?; - let minhash = selected_sig.minhash()?.clone(); - - Some(SmallSignature { - location: record.internal_location().to_string(), - name: sig.name(), - md5sum: sig.md5sum(), - minhash, - }) - }, - Err(_) => { - eprintln!("FAILED to load sketch from '{}'", - record.internal_location()); - None - } + .filter_map(|(_idx, record)| match collection.sig_from_record(record) { + Ok(sig) => { + let selected_sig = sig.clone().select(selection).ok()?; + let minhash = selected_sig.minhash()?.clone(); + + Some(SmallSignature { + location: record.internal_location().to_string(), + name: sig.name(), + md5sum: sig.md5sum(), + minhash, + }) + } + Err(_) => { + eprintln!( + "FAILED to load sketch from '{}'", + record.internal_location() + ); + None } }) .collect(); @@ -700,10 +700,10 @@ pub fn load_collection( // disallow rocksdb input here - CTB test me a lot ;) /* - if is_revindex_database(&sigpath) { - bail!("Cannot load {} signatures from a 'rocksdb' database. Please use sig, zip, or pathlist.", report_type); -} - */ + if is_revindex_database(&sigpath) { + bail!("Cannot load {} signatures from a 'rocksdb' database. Please use sig, zip, or pathlist.", report_type); + } + */ eprintln!("Reading {}(s) from: '{}'", report_type, &siglist); let mut last_error = None; @@ -720,14 +720,13 @@ pub fn load_collection( None }; - let collection = - collection.or_else(|| match collection_from_rocksdb(&sigpath, &report_type) { - Ok(coll) => Some((coll, 0)), - Err(e) => { - last_error = Some(e); - None - } - }); + let collection = collection.or_else(|| match collection_from_rocksdb(&sigpath, &report_type) { + Ok(coll) => Some((coll, 0)), + Err(e) => { + last_error = Some(e); + None + } + }); let collection = collection.or_else(|| match collection_from_manifest(&sigpath, &report_type) { From 9823ef6c98b19f0c7c8821e43802e6e335490681 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Mon, 19 Aug 2024 18:53:21 -0700 Subject: [PATCH 12/91] upd --- Cargo.lock | 31 ++++++++++++++++--------------- Cargo.toml | 2 +- src/utils.rs | 2 +- 3 files changed, 18 insertions(+), 17 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 45061cc0..3e9bc27e 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -713,9 +713,9 @@ dependencies = [ [[package]] name = "js-sys" -version = "0.3.69" +version = "0.3.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d" +checksum = "1868808506b929d7b0cfa8f75951347aa71bb21144b7791bae35d9bccfcfe37a" dependencies = [ "wasm-bindgen", ] @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=misc_rs_updates#603fa0b5bd02d595e94f0463a4047d9129613e02" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=more_rs_updates#affae94848a79a57b0b7cef801d41054e60458ee" dependencies = [ "az", "byteorder", @@ -1815,19 +1815,20 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" [[package]] name = "wasm-bindgen" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8" +checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5" dependencies = [ "cfg-if", + "once_cell", "wasm-bindgen-macro", ] [[package]] name = "wasm-bindgen-backend" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da" +checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b" dependencies = [ "bumpalo", "log", @@ -1840,9 +1841,9 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726" +checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf" dependencies = [ "quote", "wasm-bindgen-macro-support", @@ -1850,9 +1851,9 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro-support" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7" +checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836" dependencies = [ "proc-macro2", "quote", @@ -1863,15 +1864,15 @@ dependencies = [ [[package]] name = "wasm-bindgen-shared" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" +checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484" [[package]] name = "web-sys" -version = "0.3.69" +version = "0.3.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef" +checksum = "26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0" dependencies = [ "js-sys", "wasm-bindgen", diff --git a/Cargo.toml b/Cargo.toml index 61086ded..abc937f7 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,7 @@ crate-type = ["cdylib"] pyo3 = { version = "0.22.2", features = ["extension-module", "anyhow"] } rayon = "1.10.0" serde = { version = "1.0.208", features = ["derive"] } -sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "misc_rs_updates", features = ["branchwater"] } +sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "more_rs_updates", features = ["branchwater"] } #sourmash = { version = "0.15.0", features = ["branchwater"] } serde_json = "1.0.125" niffler = "2.4.0" diff --git a/src/utils.rs b/src/utils.rs index 1d4e6124..bec20457 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -442,7 +442,7 @@ pub fn load_sketches( ) -> Result> { let sketchinfo: Vec = collection .par_iter() - .filter_map(|(_idx, record)| match collection.sig_from_record(record) { + .filter_map(|(_idx, record)| match collection.sig_from_record2(record) { Ok(sig) => { let selected_sig = sig.clone().select(selection).ok()?; let minhash = selected_sig.minhash()?.clone(); From bfb5053fea322016d099d8c92e112b0eb32ca194 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 20 Aug 2024 10:32:15 -0700 Subject: [PATCH 13/91] upd --- src/fastmultigather.rs | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index 22b9efaa..4c5bb0ce 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -69,7 +69,10 @@ pub fn fastmultigather( let skipped_paths = AtomicUsize::new(0); let failed_paths = AtomicUsize::new(0); - query_collection.par_iter().for_each(|(_idx, record)| { + #[rustfmt::skip] + query_collection + .par_iter() + .for_each(|(_idx, record)| { // increment counter of # of queries. q: could we instead use the _idx from par_iter(), or will it vary based on thread? let _i = processed_queries.fetch_add(1, atomic::Ordering::SeqCst); // Load query sig (downsampling happens here) From c311a6984dbfb295cdcb43061eaeb267c8025687 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 20 Aug 2024 10:35:08 -0700 Subject: [PATCH 14/91] fix fmt --- src/fastmultigather.rs | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index 4c5bb0ce..22b9efaa 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -69,10 +69,7 @@ pub fn fastmultigather( let skipped_paths = AtomicUsize::new(0); let failed_paths = AtomicUsize::new(0); - #[rustfmt::skip] - query_collection - .par_iter() - .for_each(|(_idx, record)| { + query_collection.par_iter().for_each(|(_idx, record)| { // increment counter of # of queries. q: could we instead use the _idx from par_iter(), or will it vary based on thread? let _i = processed_queries.fetch_add(1, atomic::Ordering::SeqCst); // Load query sig (downsampling happens here) From 28b43d80ad6a57350a6a9a64ccdf6a5fd990255e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 20 Aug 2024 12:19:13 -0700 Subject: [PATCH 15/91] MRG: create `MultiCollection` for collections that span multiple files (#434) * preliminary victory * compiles and mostly runs * cleanup, split to new module * cleanup and comment * more cleanup of diff * cargo fmt * fix fmt * restore n_failed * comment failing test * cleanup and de-vec * create module/submodule structure * comment for later * get rid of vec * beg for help * cleanup and doc --- src/fastgather.rs | 2 +- src/fastmultigather.rs | 4 +- src/manysearch.rs | 4 +- src/mastiff_manygather.rs | 4 +- src/mastiff_manysearch.rs | 4 +- src/python/tests/test_fastgather.py | 3 +- src/{utils.rs => utils/mod.rs} | 234 +++++----------------------- src/utils/multicollection.rs | 229 +++++++++++++++++++++++++++ 8 files changed, 281 insertions(+), 203 deletions(-) rename src/{utils.rs => utils/mod.rs} (86%) create mode 100644 src/utils/multicollection.rs diff --git a/src/fastgather.rs b/src/fastgather.rs index 46512025..e4271249 100644 --- a/src/fastgather.rs +++ b/src/fastgather.rs @@ -33,7 +33,7 @@ pub fn fastgather( ) } // get single query sig and minhash - let query_sig = query_collection.sig_for_dataset(0)?; // need this for original md5sum + let query_sig = query_collection.get_first_sig().unwrap(); let query_sig_ds = query_sig.clone().select(selection)?; // downsample let query_mh = match query_sig_ds.minhash() { Some(query_mh) => query_mh, diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index 22b9efaa..0aa26adf 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -69,11 +69,11 @@ pub fn fastmultigather( let skipped_paths = AtomicUsize::new(0); let failed_paths = AtomicUsize::new(0); - query_collection.par_iter().for_each(|(_idx, record)| { + query_collection.par_iter().for_each(|(c, _idx, record)| { // increment counter of # of queries. q: could we instead use the _idx from par_iter(), or will it vary based on thread? let _i = processed_queries.fetch_add(1, atomic::Ordering::SeqCst); // Load query sig (downsampling happens here) - match query_collection.sig_from_record(record) { + match c.sig_from_record(record) { Ok(query_sig) => { let name = query_sig.name(); let prefix = name.split(' ').next().unwrap_or_default().to_string(); diff --git a/src/manysearch.rs b/src/manysearch.rs index a200b52d..5a585597 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -58,7 +58,7 @@ pub fn manysearch( let send = against_collection .par_iter() - .filter_map(|(_idx, record)| { + .filter_map(|(coll, _idx, record)| { let i = processed_sigs.fetch_add(1, atomic::Ordering::SeqCst); if i % 1000 == 0 && i > 0 { eprintln!("Processed {} search sigs", i); @@ -67,7 +67,7 @@ pub fn manysearch( let mut results = vec![]; // against downsampling happens here - match against_collection.sig_from_record(record) { + match coll.sig_from_record(record) { Ok(against_sig) => { if let Some(against_mh) = against_sig.minhash() { for query in query_sketchlist.iter() { diff --git a/src/mastiff_manygather.rs b/src/mastiff_manygather.rs index ea99153c..eb665cb6 100644 --- a/src/mastiff_manygather.rs +++ b/src/mastiff_manygather.rs @@ -54,12 +54,12 @@ pub fn mastiff_manygather( let send = query_collection .par_iter() - .filter_map(|(_idx, record)| { + .filter_map(|(coll, _idx, record)| { let threshold = threshold_bp / selection.scaled()? as usize; let ksize = selection.ksize()?; // query downsampling happens here - match query_collection.sig_from_record(record) { + match coll.sig_from_record(record) { Ok(query_sig) => { let mut results = vec![]; if let Some(query_mh) = query_sig.minhash() { diff --git a/src/mastiff_manysearch.rs b/src/mastiff_manysearch.rs index fac364c6..dee55e53 100644 --- a/src/mastiff_manysearch.rs +++ b/src/mastiff_manysearch.rs @@ -56,7 +56,7 @@ pub fn mastiff_manysearch( let send_result = query_collection .par_iter() - .filter_map(|(_idx, record)| { + .filter_map(|(coll, _idx, record)| { let i = processed_sigs.fetch_add(1, atomic::Ordering::SeqCst); if i % 1000 == 0 && i > 0 { eprintln!("Processed {} search sigs", i); @@ -64,7 +64,7 @@ pub fn mastiff_manysearch( let mut results = vec![]; // query downsample happens here - match query_collection.sig_from_record(record) { + match coll.sig_from_record(record) { Ok(query_sig) => { if let Some(query_mh) = query_sig.minhash() { let query_size = query_mh.size(); diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index bd2ca5a4..90d22786 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -604,7 +604,8 @@ def test_simple_hp(runtmp): def test_indexed_against(runtmp, capfd): - # do not accept rocksdb for now + return + # do not accept rocksdb for now @CTB we do now!! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') diff --git a/src/utils.rs b/src/utils/mod.rs similarity index 86% rename from src/utils.rs rename to src/utils/mod.rs index bec20457..3b958ef1 100644 --- a/src/utils.rs +++ b/src/utils/mod.rs @@ -1,10 +1,9 @@ //! Utility functions for `sourmash_plugin_branchwater`. - use rayon::prelude::*; use sourmash::encodings::HashFunctions; use sourmash::selection::Select; -use anyhow::{anyhow, Context, Result}; +use anyhow::{anyhow, Result}; use camino::Utf8Path as Path; use camino::Utf8PathBuf as PathBuf; use csv::Writer; @@ -13,7 +12,7 @@ use serde::{Deserialize, Serialize}; use std::cmp::{Ordering, PartialOrd}; use std::collections::BinaryHeap; use std::fs::{create_dir_all, File}; -use std::io::{BufRead, BufReader, BufWriter, Write}; +use std::io::{BufWriter, Write}; use std::panic; use std::sync::atomic; use std::sync::atomic::AtomicUsize; @@ -21,24 +20,18 @@ use zip::write::{ExtendedFileOptions, FileOptions, ZipWriter}; use zip::CompressionMethod; use sourmash::ani_utils::{ani_ci_from_containment, ani_from_containment}; -use sourmash::collection::Collection; use sourmash::manifest::{Manifest, Record}; use sourmash::selection::Selection; use sourmash::signature::{Signature, SigsTrait}; use sourmash::sketch::minhash::KmerMinHash; -use sourmash::storage::{FSStorage, InnerStorage, SigStore}; +use sourmash::storage::SigStore; use stats::{median, stddev}; use std::collections::{HashMap, HashSet}; -/// Track a name/minhash. -pub struct SmallSignature { - pub location: String, - pub name: String, - pub md5sum: String, - pub minhash: KmerMinHash, -} -/// Structure to hold overlap information from comparisons. +mod multicollection; +use multicollection::{MultiCollection, SmallSignature}; +/// Structure to hold overlap information from comparisons. pub struct PrefetchResult { pub name: String, pub md5sum: String, @@ -433,21 +426,24 @@ fn process_prefix_csv( Ok((results, n_fastas)) } +///////// + // Load all compatible minhashes from a collection into memory, in parallel; // also store sig name and md5 alongside, as we usually need those pub fn load_sketches( - collection: Collection, + multi: MultiCollection, selection: &Selection, _report_type: ReportType, ) -> Result> { - let sketchinfo: Vec = collection + let sketchinfo: Vec<_> = multi .par_iter() - .filter_map(|(_idx, record)| match collection.sig_from_record2(record) { + .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { Ok(sig) => { let selected_sig = sig.clone().select(selection).ok()?; let minhash = selected_sig.minhash()?.clone(); Some(SmallSignature { + collection: coll.clone(), // @CTB location: record.internal_location().to_string(), name: sig.name(), md5sum: sig.md5sum(), @@ -471,7 +467,7 @@ pub fn load_sketches( /// those with a minimum overlap. pub fn load_sketches_above_threshold( - against_collection: Collection, + against_collection: MultiCollection, query: &KmerMinHash, threshold_hashes: u64, ) -> Result<(BinaryHeap, usize, usize)> { @@ -480,10 +476,10 @@ pub fn load_sketches_above_threshold( let matchlist: BinaryHeap = against_collection .par_iter() - .filter_map(|(_idx, against_record)| { + .filter_map(|(coll, _idx, against_record)| { let mut results = Vec::new(); // Load against into memory - if let Ok(against_sig) = against_collection.sig_from_record(against_record) { + if let Ok(against_sig) = coll.sig_from_record(against_record) { if let Some(against_mh) = against_sig.minhash() { // downsample against_mh, but keep original md5sum let against_mh_ds = against_mh.downsample_scaled(query.scaled()).unwrap(); @@ -546,170 +542,25 @@ impl std::fmt::Display for ReportType { } } -/// Load a collection from a .zip file. - -pub fn collection_from_zipfile(sigpath: &Path, report_type: &ReportType) -> Result { - match Collection::from_zipfile(sigpath) { - Ok(collection) => Ok(collection), - Err(_) => bail!("failed to load {} zipfile: '{}'", report_type, sigpath), - } -} - -/// Load a collection from a RocksDB. - -pub fn collection_from_rocksdb(sigpath: &Path, report_type: &ReportType) -> Result { - match Collection::from_rocksdb(sigpath) { - Ok(collection) => Ok(collection), - Err(_) => bail!("failed to load {} rocksdb: '{}'", report_type, sigpath), - } -} - -/// Load a collection from a manifest CSV. - -fn collection_from_manifest( - sigpath: &Path, - report_type: &ReportType, -) -> Result { - let file = File::open(sigpath) - .with_context(|| format!("Failed to open {} file: '{}'", report_type, sigpath))?; - - let reader = BufReader::new(file); - let manifest = Manifest::from_reader(reader).with_context(|| { - format!( - "Failed to read {} manifest from: '{}'", - report_type, sigpath - ) - })?; - - if manifest.is_empty() { - // If the manifest is empty, return an error constructed with the anyhow! macro - Err(anyhow!("could not read as manifest: '{}'", sigpath)) - } else { - // If the manifest is not empty, proceed to create and return the Collection - eprintln!("collection from manifest!"); - Ok(Collection::new( - manifest, - InnerStorage::new( - FSStorage::builder() - .fullpath("".into()) - .subdir("".into()) - .build(), - ), - )) - } -} - -/// Load a collection from a list of paths. - -fn collection_from_pathlist( - sigpath: &Path, - report_type: &ReportType, -) -> Result<(Collection, usize), anyhow::Error> { - let file = File::open(sigpath).with_context(|| { - format!( - "Failed to open {} pathlist file: '{}'", - report_type, sigpath - ) - })?; - let reader = BufReader::new(file); - - // load list of paths - let lines: Vec<_> = reader - .lines() - .filter_map(|line| match line { - Ok(path) => Some(path), - Err(_err) => None, - }) - .collect(); - - // load sketches from paths in parallel. - let n_failed = AtomicUsize::new(0); - let records: Vec = lines - .par_iter() - .filter_map(|path| match Signature::from_path(path) { - Ok(signatures) => { - let recs: Vec = signatures - .into_iter() - .flat_map(|v| Record::from_sig(&v, path)) - .collect(); - Some(recs) - } - Err(err) => { - eprintln!("Sketch loading error: {}", err); - eprintln!("WARNING: could not load sketches from path '{}'", path); - let _ = n_failed.fetch_add(1, atomic::Ordering::SeqCst); - None - } - }) - .flatten() - .collect(); - - if records.is_empty() { - eprintln!( - "No valid signatures found in {} pathlist '{}'", - report_type, sigpath - ); - } - - let manifest: Manifest = records.into(); - let collection = Collection::new( - manifest, - InnerStorage::new( - FSStorage::builder() - .fullpath("".into()) - .subdir("".into()) - .build(), - ), - ); - let n_failed = n_failed.load(atomic::Ordering::SeqCst); - - Ok((collection, n_failed)) -} - -/// Load a collection from a .sig/.sig.gz JSON file. - -fn collection_from_signature(sigpath: &Path, report_type: &ReportType) -> Result { - let signatures = Signature::from_path(sigpath).with_context(|| { - format!( - "Failed to load {} signatures from: '{}'", - report_type, sigpath - ) - })?; - - Collection::from_sigs(signatures).with_context(|| { - format!( - "Loaded {} signatures but failed to load as collection: '{}'", - report_type, sigpath - ) - }) -} - -/// Load a collection from a path - this is the top-level load function. +/// Load a multi collection from a path - this is the new top-level load function. pub fn load_collection( siglist: &String, selection: &Selection, report_type: ReportType, allow_failed: bool, -) -> Result { +) -> Result { let sigpath = PathBuf::from(siglist); if !sigpath.exists() { bail!("No such file or directory: '{}'", &sigpath); } - // disallow rocksdb input here - CTB test me a lot ;) - /* - if is_revindex_database(&sigpath) { - bail!("Cannot load {} signatures from a 'rocksdb' database. Please use sig, zip, or pathlist.", report_type); - } - */ - eprintln!("Reading {}(s) from: '{}'", report_type, &siglist); let mut last_error = None; let collection = if sigpath.extension().map_or(false, |ext| ext == "zip") { - match collection_from_zipfile(&sigpath, &report_type) { + match MultiCollection::from_zipfile(&sigpath) { Ok(coll) => Some((coll, 0)), Err(e) => { last_error = Some(e); @@ -720,7 +571,7 @@ pub fn load_collection( None }; - let collection = collection.or_else(|| match collection_from_rocksdb(&sigpath, &report_type) { + let collection = collection.or_else(|| match MultiCollection::from_rocksdb(&sigpath) { Ok(coll) => Some((coll, 0)), Err(e) => { last_error = Some(e); @@ -728,32 +579,29 @@ pub fn load_collection( } }); - let collection = - collection.or_else(|| match collection_from_manifest(&sigpath, &report_type) { - Ok(coll) => Some((coll, 0)), - Err(e) => { - last_error = Some(e); - None - } - }); + let collection = collection.or_else(|| match MultiCollection::from_manifest(&sigpath) { + Ok(coll) => Some((coll, 0)), + Err(e) => { + last_error = Some(e); + None + } + }); - let collection = - collection.or_else(|| match collection_from_signature(&sigpath, &report_type) { - Ok(coll) => Some((coll, 0)), - Err(e) => { - last_error = Some(e); - None - } - }); + let collection = collection.or_else(|| match MultiCollection::from_signature(&sigpath) { + Ok(coll) => Some((coll, 0)), + Err(e) => { + last_error = Some(e); + None + } + }); - let collection = - collection.or_else(|| match collection_from_pathlist(&sigpath, &report_type) { - Ok((coll, n_failed)) => Some((coll, n_failed)), - Err(e) => { - last_error = Some(e); - None - } - }); + let collection = collection.or_else(|| match MultiCollection::from_pathlist(&sigpath) { + Ok((coll, n_failed)) => Some((coll, n_failed)), + Err(e) => { + last_error = Some(e); + None + } + }); match collection { Some((coll, n_failed)) => { @@ -805,7 +653,7 @@ pub fn load_collection( /// Returns an error if: /// * No signatures were successfully loaded. pub fn report_on_collection_loading( - collection: &Collection, + collection: &MultiCollection, skipped_paths: usize, failed_paths: usize, report_type: ReportType, diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs new file mode 100644 index 00000000..7804c021 --- /dev/null +++ b/src/utils/multicollection.rs @@ -0,0 +1,229 @@ +//! MultiCollection implementation to handle sketches coming from multiple files. + +use rayon::prelude::*; + +use anyhow::{anyhow, Context, Result}; +use camino::Utf8Path as Path; +use log::debug; +use std::fs::File; +use std::io::{BufRead, BufReader}; +use std::sync::atomic; +use std::sync::atomic::AtomicUsize; + +use sourmash::collection::{Collection, CollectionSet}; +use sourmash::encodings::Idx; +use sourmash::errors::SourmashError; +use sourmash::manifest::{Manifest, Record}; +use sourmash::selection::{Select, Selection}; +use sourmash::signature::Signature; +use sourmash::sketch::minhash::KmerMinHash; +use sourmash::storage::{FSStorage, InnerStorage, SigStore}; + +/// A collection of sketches, potentially stored in multiple files. +pub struct MultiCollection { + collections: Vec, +} + +impl MultiCollection { + fn new(collections: Vec) -> Self { + Self { collections } + } + + /// Build from a standalone manifest + pub fn from_manifest(sigpath: &Path) -> Result { + debug!("multi from manifest!"); + let file = + File::open(sigpath).with_context(|| format!("Failed to open file: '{}'", sigpath))?; + + let reader = BufReader::new(file); + let manifest = Manifest::from_reader(reader) + .with_context(|| format!("Failed to read manifest from: '{}'", sigpath))?; + + if manifest.is_empty() { + Err(anyhow!("could not read as manifest: '{}'", sigpath)) + } else { + let coll = Collection::new( + manifest, + InnerStorage::new( + FSStorage::builder() + .fullpath("".into()) + .subdir("".into()) + .build(), + ), + ); + Ok(MultiCollection::new(vec![coll])) + } + } + + /// Load a collection from a .zip file. + pub fn from_zipfile(sigpath: &Path) -> Result { + debug!("multi from zipfile!"); + match Collection::from_zipfile(sigpath) { + Ok(collection) => Ok(MultiCollection::new(vec![collection])), + Err(_) => bail!("failed to load zipfile: '{}'", sigpath), + } + } + + /// Load a collection from a RocksDB. + pub fn from_rocksdb(sigpath: &Path) -> Result { + debug!("multi from rocksdb!"); + match Collection::from_rocksdb(sigpath) { + Ok(collection) => Ok(MultiCollection::new(vec![collection])), + Err(_) => bail!("failed to load rocksdb: '{}'", sigpath), + } + } + + /// Load a collection from a list of paths. + pub fn from_pathlist(sigpath: &Path) -> Result<(Self, usize)> { + debug!("multi from pathlist!"); + let file = File::open(sigpath) + .with_context(|| format!("Failed to open pathlist file: '{}'", sigpath))?; + let reader = BufReader::new(file); + + // load list of paths + let lines: Vec<_> = reader + .lines() + .filter_map(|line| match line { + Ok(path) => Some(path), + Err(_err) => None, + }) + .collect(); + + // load sketches from paths in parallel. + let n_failed = AtomicUsize::new(0); + let records: Vec = lines + .par_iter() + .filter_map(|path| match Signature::from_path(path) { + Ok(signatures) => { + let recs: Vec = signatures + .into_iter() + .flat_map(|v| Record::from_sig(&v, path)) + .collect(); + Some(recs) + } + Err(err) => { + eprintln!("Sketch loading error: {}", err); + eprintln!("WARNING: could not load sketches from path '{}'", path); + let _ = n_failed.fetch_add(1, atomic::Ordering::SeqCst); + None + } + }) + .flatten() + .collect(); + + if records.is_empty() { + eprintln!("No valid signatures found in pathlist '{}'", sigpath); + } + + let manifest: Manifest = records.into(); + let collection = Collection::new( + manifest, + InnerStorage::new( + FSStorage::builder() + .fullpath("".into()) + .subdir("".into()) + .build(), + ), + ); + let n_failed = n_failed.load(atomic::Ordering::SeqCst); + + Ok((MultiCollection::new(vec![collection]), n_failed)) + } + + // Load from a sig file + pub fn from_signature(sigpath: &Path) -> Result { + debug!("multi from signature!"); + let signatures = Signature::from_path(sigpath) + .with_context(|| format!("Failed to load signatures from: '{}'", sigpath))?; + + let coll = Collection::from_sigs(signatures).with_context(|| { + format!( + "Loaded signatures but failed to load as collection: '{}'", + sigpath + ) + })?; + Ok(MultiCollection::new(vec![coll])) + } + + pub fn len(&self) -> usize { + let val: usize = self.collections.iter().map(|c| c.len()).sum(); + val + } + pub fn is_empty(&self) -> bool { + let val: usize = self.collections.iter().map(|c| c.len()).sum(); + if val > 0 { + false + } else { + true + } + } + + pub fn iter(&self) -> impl Iterator { + self.collections.iter() + } + + // iterate over tuples + pub fn item_iter(&self) -> impl Iterator { + // CTB: request review by Rust expert pls :). Does this make + // unnecessary copies?? + let s: Vec<_> = self + .iter() + .map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) + .flatten() + .collect(); + s.into_iter() + } + + pub fn par_iter(&self) -> impl IndexedParallelIterator { + // CTB: request review by Rust expert - why can't I use item_iter here? + // i.e. self.item_iter().into_par_iter()? + let s: Vec<_> = self + .iter() + .map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) + .flatten() + .collect(); + s.into_par_iter() + } + + pub fn get_first_sig(&self) -> Option { + if !self.is_empty() { + let query_item = self.item_iter().next().unwrap(); + let (coll, _, _) = query_item; + Some(coll.sig_for_dataset(0).ok()?) + } else { + None + } + } +} + +impl Select for MultiCollection { + fn select(mut self, selection: &Selection) -> Result { + // CTB: request review by Rust expert! Is the clone necessary? + self.collections = self + .iter() + .filter_map(|c| c.clone().select(selection).ok()) + .collect(); + Ok(self) + } +} + +impl TryFrom for CollectionSet { + type Error = SourmashError; + + fn try_from(multi: MultiCollection) -> Result { + // CTB: request review by Rust expert! Is the clone necessary? + let coll = multi.iter().next().unwrap().clone(); + let cs: CollectionSet = coll.try_into()?; + Ok(cs) + } +} + +/// Track a name/minhash. +pub struct SmallSignature { + // CTB: request help - can we/should we use references & lifetimes here? + pub collection: Collection, + pub location: String, + pub name: String, + pub md5sum: String, + pub minhash: KmerMinHash, +} From a1b19aec753d859661cff2441d7bec239eca9198 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 20 Aug 2024 12:24:25 -0700 Subject: [PATCH 16/91] clippy fixes --- src/fastmultigather.rs | 2 +- src/lib.rs | 1 + src/multisearch.rs | 4 ++-- src/utils/mod.rs | 8 ++++---- src/utils/multicollection.rs | 12 +++--------- 5 files changed, 11 insertions(+), 16 deletions(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index 0aa26adf..07dc22d2 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -133,7 +133,7 @@ pub fn fastmultigather( if let Ok(mut file) = File::create(&sig_filename) { let unique_hashes: HashSet = hashes.into_iter().collect(); let mut new_mh = KmerMinHash::new( - query_mh.scaled().try_into().unwrap(), + query_mh.scaled(), query_mh.ksize().try_into().unwrap(), query_mh.hash_function().clone(), query_mh.seed(), diff --git a/src/lib.rs b/src/lib.rs index 2a7fa58d..194bfae8 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -110,6 +110,7 @@ fn do_fastgather( } #[pyfunction] +#[allow(clippy::too_many_arguments)] #[pyo3(signature = (query_filenames, siglist_path, threshold_bp, ksize, scaled, moltype, output_path=None, save_matches=false))] fn do_fastmultigather( query_filenames: String, diff --git a/src/multisearch.rs b/src/multisearch.rs index 6edad2c1..17f8dfaf 100644 --- a/src/multisearch.rs +++ b/src/multisearch.rs @@ -60,12 +60,12 @@ pub fn multisearch( let processed_cmp = AtomicUsize::new(0); let ksize = selection.ksize().unwrap() as f64; - if queries.len() == 0 { + if queries.is_empty() { eprintln!("No query sketches present. Exiting."); return Err(anyhow::anyhow!("failed to load query sketches").into()); } - if against.len() == 0 { + if against.is_empty() { eprintln!("No search sketches present. Exiting."); return Err(anyhow::anyhow!("failed to load search sketches").into()); } diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 3b958ef1..a6ff9f23 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -853,7 +853,7 @@ pub fn consume_query_by_gather( } let query_md5sum: String = orig_query_mh.md5sum().clone(); let query_name = query.name().clone(); - let query_scaled = orig_query_mh.scaled().clone() as usize; //query_mh.scaled() as usize + let query_scaled = orig_query_mh.scaled() as usize; let mut query_mh = orig_query_mh.clone(); let mut orig_query_ds = orig_query_mh.clone().downsample_scaled(scaled)?; @@ -924,11 +924,11 @@ pub fn consume_query_by_gather( query_filename: query.filename(), query_name: query_name.clone(), query_md5: query_md5sum.clone(), - query_bp: query_bp.clone(), + query_bp, ksize, moltype: query_moltype.clone(), - scaled: query_scaled.clone(), - query_n_hashes: query_n_hashes, + scaled: query_scaled, + query_n_hashes, query_abundance: query_mh.track_abundance(), query_containment_ani: match_.query_containment_ani, match_containment_ani: match_.match_containment_ani, diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 7804c021..d0b66425 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -151,11 +151,7 @@ impl MultiCollection { } pub fn is_empty(&self) -> bool { let val: usize = self.collections.iter().map(|c| c.len()).sum(); - if val > 0 { - false - } else { - true - } + val == 0 } pub fn iter(&self) -> impl Iterator { @@ -168,8 +164,7 @@ impl MultiCollection { // unnecessary copies?? let s: Vec<_> = self .iter() - .map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) - .flatten() + .flat_map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) .collect(); s.into_iter() } @@ -179,8 +174,7 @@ impl MultiCollection { // i.e. self.item_iter().into_par_iter()? let s: Vec<_> = self .iter() - .map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) - .flatten() + .flat_map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) .collect(); s.into_par_iter() } From 51a14ac42ca70ce3eb5e461296ce815683f16e92 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 20 Aug 2024 13:51:01 -0700 Subject: [PATCH 17/91] compiling again --- src/utils/mod.rs | 2 +- src/utils/multicollection.rs | 109 +++++++++++++++++++---------------- 2 files changed, 60 insertions(+), 51 deletions(-) diff --git a/src/utils/mod.rs b/src/utils/mod.rs index a6ff9f23..8e60ac63 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -579,7 +579,7 @@ pub fn load_collection( } }); - let collection = collection.or_else(|| match MultiCollection::from_manifest(&sigpath) { + let collection = collection.or_else(|| match MultiCollection::from_standalone_manifest(&sigpath) { Ok(coll) => Some((coll, 0)), Err(e) => { last_error = Some(e); diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index d0b66425..42a1088f 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -9,6 +9,7 @@ use std::fs::File; use std::io::{BufRead, BufReader}; use std::sync::atomic; use std::sync::atomic::AtomicUsize; +use std::collections::HashSet; use sourmash::collection::{Collection, CollectionSet}; use sourmash::encodings::Idx; @@ -29,9 +30,49 @@ impl MultiCollection { Self { collections } } + // Turn a set of paths into list of Collections. + fn load_set_of_paths(paths: HashSet) -> (Vec, usize) { + let n_failed = AtomicUsize::new(0); + + let colls: Vec<_> = paths + .par_iter() + .filter_map(|iloc| match iloc { + // could just use a variant of load_collection here? + x if x.ends_with(".zip") => { + debug!("loading sigs from zipfile {}", x); + Some(Collection::from_zipfile(x).unwrap()) + }, + _ => { + debug!("loading sigs from sigfile {}", iloc); + let signatures = match Signature::from_path(iloc) { + Ok(signatures) => Some(signatures), + Err(err) => { + eprintln!("Sketch loading error: {}", err); + None + } + }; + + match signatures { + Some(signatures) => { + Some(Collection::from_sigs(signatures).unwrap()) + }, + None => { + eprintln!("WARNING: could not load sketches from path '{}'", iloc); + let _ = n_failed.fetch_add(1, atomic::Ordering::SeqCst); + None + } + } + } + }) + .collect(); + + let n_failed = n_failed.load(atomic::Ordering::SeqCst); + (colls, n_failed) + } + /// Build from a standalone manifest - pub fn from_manifest(sigpath: &Path) -> Result { - debug!("multi from manifest!"); + pub fn from_standalone_manifest(sigpath: &Path) -> Result { + debug!("multi from standalone manifest!"); let file = File::open(sigpath).with_context(|| format!("Failed to open file: '{}'", sigpath))?; @@ -42,16 +83,15 @@ impl MultiCollection { if manifest.is_empty() { Err(anyhow!("could not read as manifest: '{}'", sigpath)) } else { - let coll = Collection::new( - manifest, - InnerStorage::new( - FSStorage::builder() - .fullpath("".into()) - .subdir("".into()) - .build(), - ), - ); - Ok(MultiCollection::new(vec![coll])) + let ilocs: HashSet<_> = manifest + .internal_locations() + .map(|s| String::from(s)) + .collect(); + + let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); + let colls = colls.into_iter().collect(); + + Ok(MultiCollection::new(colls)) } } @@ -80,8 +120,8 @@ impl MultiCollection { .with_context(|| format!("Failed to open pathlist file: '{}'", sigpath))?; let reader = BufReader::new(file); - // load list of paths - let lines: Vec<_> = reader + // load set of paths + let lines: HashSet<_> = reader .lines() .filter_map(|line| match line { Ok(path) => Some(path), @@ -89,45 +129,14 @@ impl MultiCollection { }) .collect(); - // load sketches from paths in parallel. - let n_failed = AtomicUsize::new(0); - let records: Vec = lines - .par_iter() - .filter_map(|path| match Signature::from_path(path) { - Ok(signatures) => { - let recs: Vec = signatures - .into_iter() - .flat_map(|v| Record::from_sig(&v, path)) - .collect(); - Some(recs) - } - Err(err) => { - eprintln!("Sketch loading error: {}", err); - eprintln!("WARNING: could not load sketches from path '{}'", path); - let _ = n_failed.fetch_add(1, atomic::Ordering::SeqCst); - None - } - }) - .flatten() - .collect(); + let num_to_load = lines.len(); - if records.is_empty() { - eprintln!("No valid signatures found in pathlist '{}'", sigpath); - } + let (colls, n_failed) = MultiCollection::load_set_of_paths(lines); + let colls: Vec<_> = colls.into_iter().collect(); - let manifest: Manifest = records.into(); - let collection = Collection::new( - manifest, - InnerStorage::new( - FSStorage::builder() - .fullpath("".into()) - .subdir("".into()) - .build(), - ), - ); - let n_failed = n_failed.load(atomic::Ordering::SeqCst); + let n_missing = num_to_load - colls.len(); - Ok((MultiCollection::new(vec![collection]), n_failed)) + Ok((MultiCollection::new(colls), n_missing)) } // Load from a sig file From 99bd174cd4fcd3a936d7778656f0c79416d91a8a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 20 Aug 2024 13:58:23 -0700 Subject: [PATCH 18/91] cleanup --- src/utils/multicollection.rs | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 42a1088f..02118a1d 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -18,7 +18,7 @@ use sourmash::manifest::{Manifest, Record}; use sourmash::selection::{Select, Selection}; use sourmash::signature::Signature; use sourmash::sketch::minhash::KmerMinHash; -use sourmash::storage::{FSStorage, InnerStorage, SigStore}; +use sourmash::storage::SigStore; /// A collection of sketches, potentially stored in multiple files. pub struct MultiCollection { @@ -129,14 +129,10 @@ impl MultiCollection { }) .collect(); - let num_to_load = lines.len(); - let (colls, n_failed) = MultiCollection::load_set_of_paths(lines); let colls: Vec<_> = colls.into_iter().collect(); - let n_missing = num_to_load - colls.len(); - - Ok((MultiCollection::new(colls), n_missing)) + Ok((MultiCollection::new(colls), n_failed)) } // Load from a sig file From 36d33a513d704f5b3c8f39f1d83ae4caf5a3317b Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 06:27:57 -0700 Subject: [PATCH 19/91] bump sourmash to v0.15.1 --- Cargo.lock | 33 +++++++++++++++++---------------- Cargo.toml | 2 +- 2 files changed, 18 insertions(+), 17 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 8a17ac00..0d3b3611 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -713,9 +713,9 @@ dependencies = [ [[package]] name = "js-sys" -version = "0.3.69" +version = "0.3.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d" +checksum = "1868808506b929d7b0cfa8f75951347aa71bb21144b7791bae35d9bccfcfe37a" dependencies = [ "wasm-bindgen", ] @@ -1550,9 +1550,9 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" -version = "0.15.0" +version = "0.15.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8655e639cc4a32fa1422629c9b4ff603ee09cf6d04a97eacd37594382472d437" +checksum = "defabd52b7cb3212887b0f213f68133672ed0d85796136525da454f2b19cd320" dependencies = [ "az", "byteorder", @@ -1816,19 +1816,20 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" [[package]] name = "wasm-bindgen" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8" +checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5" dependencies = [ "cfg-if", + "once_cell", "wasm-bindgen-macro", ] [[package]] name = "wasm-bindgen-backend" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da" +checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b" dependencies = [ "bumpalo", "log", @@ -1841,9 +1842,9 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726" +checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf" dependencies = [ "quote", "wasm-bindgen-macro-support", @@ -1851,9 +1852,9 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro-support" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7" +checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836" dependencies = [ "proc-macro2", "quote", @@ -1864,15 +1865,15 @@ dependencies = [ [[package]] name = "wasm-bindgen-shared" -version = "0.2.92" +version = "0.2.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" +checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484" [[package]] name = "web-sys" -version = "0.3.69" +version = "0.3.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef" +checksum = "26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0" dependencies = [ "js-sys", "wasm-bindgen", diff --git a/Cargo.toml b/Cargo.toml index 15188b44..103808d5 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,7 @@ crate-type = ["cdylib"] pyo3 = { version = "0.22.2", features = ["extension-module", "anyhow"] } rayon = "1.10.0" serde = { version = "1.0.208", features = ["derive"] } -sourmash = { version = "0.15.0", features = ["branchwater"] } +sourmash = { version = "0.15.1", features = ["branchwater"] } serde_json = "1.0.125" niffler = "2.4.0" log = "0.4.22" From 7f0b0107d22ec82da9554837ecc8cc0d314fea1c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 06:46:59 -0700 Subject: [PATCH 20/91] check if is rocksdb --- src/utils/multicollection.rs | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 02118a1d..38c06fcb 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -10,6 +10,7 @@ use std::io::{BufRead, BufReader}; use std::sync::atomic; use std::sync::atomic::AtomicUsize; use std::collections::HashSet; +use camino::Utf8PathBuf; use sourmash::collection::{Collection, CollectionSet}; use sourmash::encodings::Idx; @@ -107,9 +108,25 @@ impl MultiCollection { /// Load a collection from a RocksDB. pub fn from_rocksdb(sigpath: &Path) -> Result { debug!("multi from rocksdb!"); - match Collection::from_rocksdb(sigpath) { - Ok(collection) => Ok(MultiCollection::new(vec![collection])), - Err(_) => bail!("failed to load rocksdb: '{}'", sigpath), + // duplicate logic from is_revindex_database + let path: Utf8PathBuf = sigpath.into(); + + let mut is_rocksdb = false; + + if path.is_dir() { + let current_file = path.join("CURRENT"); + if current_file.exists() && current_file.is_file() { + is_rocksdb = true; + } + } + + if is_rocksdb { + match Collection::from_rocksdb(sigpath) { + Ok(collection) => Ok(MultiCollection::new(vec![collection])), + Err(_) => bail!("failed to load rocksdb: '{}'", sigpath), + } + } else { + bail!("not a rocksdb: '{}'", sigpath) } } From 55619118a315f3f8f71b4db3a830bb664405247a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 07:21:30 -0700 Subject: [PATCH 21/91] weird error --- src/utils/multicollection.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 38c06fcb..c13de46c 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -203,7 +203,7 @@ impl MultiCollection { pub fn get_first_sig(&self) -> Option { if !self.is_empty() { - let query_item = self.item_iter().next().unwrap(); + let query_item = self.item_iter().next()?; let (coll, _, _) = query_item; Some(coll.sig_for_dataset(0).ok()?) } else { From dfe56d30c204a6c02785eefbd97447abbc6c74c6 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 07:22:36 -0700 Subject: [PATCH 22/91] use remove_unwrap branch of sourmash --- Cargo.lock | 3 +-- Cargo.toml | 3 ++- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 0d3b3611..fd48d99f 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,8 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "defabd52b7cb3212887b0f213f68133672ed0d85796136525da454f2b19cd320" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#45b1a8ff2f24e4742c9457bc388b5e9a1fd637f9" dependencies = [ "az", "byteorder", diff --git a/Cargo.toml b/Cargo.toml index 103808d5..c1ddaba7 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,8 @@ crate-type = ["cdylib"] pyo3 = { version = "0.22.2", features = ["extension-module", "anyhow"] } rayon = "1.10.0" serde = { version = "1.0.208", features = ["derive"] } -sourmash = { version = "0.15.1", features = ["branchwater"] } +#sourmash = { version = "0.15.1", features = ["branchwater"] } +sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "remove_unwrap", features = ["branchwater"] } serde_json = "1.0.125" niffler = "2.4.0" log = "0.4.22" From e6e80f3f4050f7927013e647f78e918c0aeef67e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 08:53:07 -0700 Subject: [PATCH 23/91] get index to work with MultiCollection --- Cargo.lock | 2 +- Cargo.toml | 2 +- src/index.rs | 10 +++++- src/mastiff_manysearch.rs | 4 +++ src/utils/mod.rs | 30 ++--------------- src/utils/multicollection.rs | 62 ++++++++++++++++++++++++++++++++++-- 6 files changed, 78 insertions(+), 32 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index fd48d99f..41169f9a 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#45b1a8ff2f24e4742c9457bc388b5e9a1fd637f9" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#53bcf0274f4b7bdec81077b44591af3a932a0270" dependencies = [ "az", "byteorder", diff --git a/Cargo.toml b/Cargo.toml index c1ddaba7..733d3aa2 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -17,7 +17,7 @@ sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "rem serde_json = "1.0.125" niffler = "2.4.0" log = "0.4.22" -env_logger = { version = "0.11.5", optional = true } +env_logger = { version = "0.11.5" } simple-error = "0.3.1" anyhow = "1.0.86" zip = { version = "2.0", default-features = false } diff --git a/src/index.rs b/src/index.rs index 0cb6a97d..dd786a49 100644 --- a/src/index.rs +++ b/src/index.rs @@ -1,9 +1,12 @@ +use log::debug; use sourmash::index::revindex::RevIndex; use sourmash::index::revindex::RevIndexOps; use sourmash::prelude::*; use std::path::Path; use crate::utils::{load_collection, ReportType}; +use crate::utils::multicollection::MultiCollection; +use sourmash::collection::Collection; pub fn index>( siglist: String, @@ -22,9 +25,14 @@ pub fn index>( allow_failed_sigpaths, )?; + debug!("loaded collection from '{}' with len {}", siglist, collection.len()); + + let sigs = collection.load_sigs()?; // @CTB load into memory :sob: + let coll = Collection::from_sigs(sigs)?; + let mut index = RevIndex::create( output.as_ref(), - collection.select(selection)?.try_into()?, + coll.select(selection)?.try_into()?, colors, )?; diff --git a/src/mastiff_manysearch.rs b/src/mastiff_manysearch.rs index dee55e53..950e977d 100644 --- a/src/mastiff_manysearch.rs +++ b/src/mastiff_manysearch.rs @@ -1,5 +1,6 @@ /// mastiff_manysearch: mastiff-indexed version of manysearch. use anyhow::Result; +use log::debug; use camino::Utf8PathBuf as PathBuf; use rayon::prelude::*; use std::sync::atomic; @@ -26,6 +27,7 @@ pub fn mastiff_manysearch( bail!("'{}' is not a valid RevIndex database", index); } // Open database once + debug!("Opened revindex: '{index}')"); let db = RevIndex::open(index, true, None)?; println!("Loaded DB"); @@ -73,6 +75,8 @@ pub fn mastiff_manysearch( db.matches_from_counter(counter, minimum_containment as usize); // filter the matches for containment + debug!("FOUND: {} matches for {:?}", matches.len(), + query_sig); for (path, overlap) in matches { let containment = overlap as f64 / query_size as f64; if containment >= minimum_containment { diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 8e60ac63..7e95e406 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -28,7 +28,7 @@ use sourmash::storage::SigStore; use stats::{median, stddev}; use std::collections::{HashMap, HashSet}; -mod multicollection; +pub mod multicollection; use multicollection::{MultiCollection, SmallSignature}; /// Structure to hold overlap information from comparisons. @@ -430,37 +430,13 @@ fn process_prefix_csv( // Load all compatible minhashes from a collection into memory, in parallel; // also store sig name and md5 alongside, as we usually need those +// @CTB switch to using load_sketches method directly! pub fn load_sketches( multi: MultiCollection, selection: &Selection, _report_type: ReportType, ) -> Result> { - let sketchinfo: Vec<_> = multi - .par_iter() - .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { - Ok(sig) => { - let selected_sig = sig.clone().select(selection).ok()?; - let minhash = selected_sig.minhash()?.clone(); - - Some(SmallSignature { - collection: coll.clone(), // @CTB - location: record.internal_location().to_string(), - name: sig.name(), - md5sum: sig.md5sum(), - minhash, - }) - } - Err(_) => { - eprintln!( - "FAILED to load sketch from '{}'", - record.internal_location() - ); - None - } - }) - .collect(); - - Ok(sketchinfo) + multi.load_sketches(selection) } /// Load a collection of sketches from a file, filtering to keep only diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index c13de46c..a90cd500 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -19,9 +19,10 @@ use sourmash::manifest::{Manifest, Record}; use sourmash::selection::{Select, Selection}; use sourmash::signature::Signature; use sourmash::sketch::minhash::KmerMinHash; -use sourmash::storage::SigStore; +use sourmash::storage::{ SigStore, MemStorage, InnerStorage }; /// A collection of sketches, potentially stored in multiple files. +#[derive(Clone)] pub struct MultiCollection { collections: Vec, } @@ -122,7 +123,10 @@ impl MultiCollection { if is_rocksdb { match Collection::from_rocksdb(sigpath) { - Ok(collection) => Ok(MultiCollection::new(vec![collection])), + Ok(collection) => { + debug!("...rocksdb successful!"); + Ok(MultiCollection::new(vec![collection])) + } Err(_) => bail!("failed to load rocksdb: '{}'", sigpath), } } else { @@ -210,6 +214,56 @@ impl MultiCollection { None } } + + // Load all sketches into memory, using SmallSignature to track original + // signature metadata. + pub fn load_sketches(&self, selection: &Selection) -> Result> { + let sketchinfo: Vec<_> = self + .par_iter() + .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { + Ok(sig) => { + let selected_sig = sig.clone().select(selection).ok()?; + let minhash = selected_sig.minhash()?.clone(); + + Some(SmallSignature { + collection: coll.clone(), // @CTB + location: record.internal_location().to_string(), + name: sig.name(), + md5sum: sig.md5sum(), + minhash, + }) + } + Err(_) => { + eprintln!( + "FAILED to load sketch from '{}'", + record.internal_location() + ); + None + } + }) + .collect(); + + Ok(sketchinfo) + } + + // Load all signatures into memory. + pub fn load_sigs(&self) -> Result> { + let sigs: Vec<_> = self + .par_iter() + .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { + Ok(sigstore) => Some(sigstore.into()), + Err(_) => { + eprintln!( + "FAILED to load sketch from '{}'", + record.internal_location() + ); + None + } + }) + .collect(); + + Ok(sigs) + } } impl Select for MultiCollection { @@ -223,16 +277,20 @@ impl Select for MultiCollection { } } +/* impl TryFrom for CollectionSet { type Error = SourmashError; fn try_from(multi: MultiCollection) -> Result { // CTB: request review by Rust expert! Is the clone necessary? +// @CTB need to do something better than just getting the first CS! :sob: +// @CTB could fail if more than one? let coll = multi.iter().next().unwrap().clone(); let cs: CollectionSet = coll.try_into()?; Ok(cs) } } +*/ /// Track a name/minhash. pub struct SmallSignature { From fed4db34ffc1e6085e5329dcf9ad69691f4a305c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 09:26:44 -0700 Subject: [PATCH 24/91] old bug now fixed --- src/python/tests/test_fastgather.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index 90d22786..3ec65326 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -280,13 +280,8 @@ def test_against_multisigfile(runtmp, zip_against): '-o', g_output, '--output-prefetch', p_output, '-s', '100000') df = pandas.read_csv(g_output) - if zip_against: - assert len(df) == 3 - print(df) - else: - print(df) - assert len(df) == 1 - # @CTB this is a bug :(. It should load multiple sketches properly! + assert len(df) == 3 + print(df) def test_query_multisigfile(runtmp, capfd, zip_against): From f5331ef6839788bbddb9ab5b803c77458aa0eeef Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 10:04:38 -0700 Subject: [PATCH 25/91] clippy, format, and fix --- src/index.rs | 13 ++++++------- src/mastiff_manysearch.rs | 5 ++--- src/utils/mod.rs | 18 +++++++++++------- src/utils/multicollection.rs | 31 +++++++++++++++++++++++-------- 4 files changed, 42 insertions(+), 25 deletions(-) diff --git a/src/index.rs b/src/index.rs index dd786a49..75c31c9d 100644 --- a/src/index.rs +++ b/src/index.rs @@ -5,7 +5,6 @@ use sourmash::prelude::*; use std::path::Path; use crate::utils::{load_collection, ReportType}; -use crate::utils::multicollection::MultiCollection; use sourmash::collection::Collection; pub fn index>( @@ -25,16 +24,16 @@ pub fn index>( allow_failed_sigpaths, )?; - debug!("loaded collection from '{}' with len {}", siglist, collection.len()); + debug!( + "loaded collection from '{}' with len {}", + siglist, + collection.len() + ); let sigs = collection.load_sigs()?; // @CTB load into memory :sob: let coll = Collection::from_sigs(sigs)?; - let mut index = RevIndex::create( - output.as_ref(), - coll.select(selection)?.try_into()?, - colors, - )?; + let mut index = RevIndex::create(output.as_ref(), coll.select(selection)?.try_into()?, colors)?; if use_internal_storage { index.internalize_storage()?; diff --git a/src/mastiff_manysearch.rs b/src/mastiff_manysearch.rs index 950e977d..158dded1 100644 --- a/src/mastiff_manysearch.rs +++ b/src/mastiff_manysearch.rs @@ -1,7 +1,7 @@ /// mastiff_manysearch: mastiff-indexed version of manysearch. use anyhow::Result; -use log::debug; use camino::Utf8PathBuf as PathBuf; +use log::debug; use rayon::prelude::*; use std::sync::atomic; use std::sync::atomic::AtomicUsize; @@ -75,8 +75,7 @@ pub fn mastiff_manysearch( db.matches_from_counter(counter, minimum_containment as usize); // filter the matches for containment - debug!("FOUND: {} matches for {:?}", matches.len(), - query_sig); + debug!("FOUND: {} matches for {:?}", matches.len(), query_sig); for (path, overlap) in matches { let containment = overlap as f64 / query_size as f64; if containment >= minimum_containment { diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 7e95e406..01ff4d6c 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -1,5 +1,6 @@ //! Utility functions for `sourmash_plugin_branchwater`. use rayon::prelude::*; + use sourmash::encodings::HashFunctions; use sourmash::selection::Select; @@ -555,13 +556,16 @@ pub fn load_collection( } }); - let collection = collection.or_else(|| match MultiCollection::from_standalone_manifest(&sigpath) { - Ok(coll) => Some((coll, 0)), - Err(e) => { - last_error = Some(e); - None - } - }); + let collection = + collection.or_else( + || match MultiCollection::from_standalone_manifest(&sigpath) { + Ok(coll) => Some((coll, 0)), + Err(e) => { + last_error = Some(e); + None + } + }, + ); let collection = collection.or_else(|| match MultiCollection::from_signature(&sigpath) { Ok(coll) => Some((coll, 0)), diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index a90cd500..462de3a0 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -4,22 +4,22 @@ use rayon::prelude::*; use anyhow::{anyhow, Context, Result}; use camino::Utf8Path as Path; +use camino::Utf8PathBuf; use log::debug; +use std::collections::HashSet; use std::fs::File; use std::io::{BufRead, BufReader}; use std::sync::atomic; use std::sync::atomic::AtomicUsize; -use std::collections::HashSet; -use camino::Utf8PathBuf; -use sourmash::collection::{Collection, CollectionSet}; +use sourmash::collection::Collection; use sourmash::encodings::Idx; use sourmash::errors::SourmashError; use sourmash::manifest::{Manifest, Record}; use sourmash::selection::{Select, Selection}; use sourmash::signature::Signature; use sourmash::sketch::minhash::KmerMinHash; -use sourmash::storage::{ SigStore, MemStorage, InnerStorage }; +use sourmash::storage::{FSStorage, InnerStorage, SigStore}; /// A collection of sketches, potentially stored in multiple files. #[derive(Clone)] @@ -43,7 +43,7 @@ impl MultiCollection { x if x.ends_with(".zip") => { debug!("loading sigs from zipfile {}", x); Some(Collection::from_zipfile(x).unwrap()) - }, + } _ => { debug!("loading sigs from sigfile {}", iloc); let signatures = match Signature::from_path(iloc) { @@ -56,8 +56,23 @@ impl MultiCollection { match signatures { Some(signatures) => { - Some(Collection::from_sigs(signatures).unwrap()) - }, + let records: Vec<_> = signatures + .into_iter() + .flat_map(|v| Record::from_sig(&v, iloc)) + .collect(); + + let manifest: Manifest = records.into(); + let collection = Collection::new( + manifest, + InnerStorage::new( + FSStorage::builder() + .fullpath("".into()) + .subdir("".into()) + .build(), + ), + ); + Some(collection) + } None => { eprintln!("WARNING: could not load sketches from path '{}'", iloc); let _ = n_failed.fetch_add(1, atomic::Ordering::SeqCst); @@ -87,7 +102,7 @@ impl MultiCollection { } else { let ilocs: HashSet<_> = manifest .internal_locations() - .map(|s| String::from(s)) + .map(String::from) .collect(); let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); From 8f901299c01a1de035155e17fb1a71ad84fb38b7 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 10:14:45 -0700 Subject: [PATCH 26/91] make names clearer --- src/index.rs | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/index.rs b/src/index.rs index 75c31c9d..f4bfe639 100644 --- a/src/index.rs +++ b/src/index.rs @@ -17,7 +17,7 @@ pub fn index>( ) -> Result<(), Box> { println!("Loading siglist"); - let collection = load_collection( + let multi = load_collection( &siglist, selection, ReportType::General, @@ -25,12 +25,12 @@ pub fn index>( )?; debug!( - "loaded collection from '{}' with len {}", + "loaded multicollection from '{}' with len {}", siglist, - collection.len() + multi.len() ); - let sigs = collection.load_sigs()?; // @CTB load into memory :sob: + let sigs = multi.load_sigs()?; // @CTB load into memory :sob: let coll = Collection::from_sigs(sigs)?; let mut index = RevIndex::create(output.as_ref(), coll.select(selection)?.try_into()?, colors)?; From 45113472a9266b8bdb19b0a05b344f308bf2a54f Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 10:48:05 -0700 Subject: [PATCH 27/91] ditch MultiCollection for index, at least for now --- src/index.rs | 49 +++++++++++++++++++++++++++++++++++-------------- 1 file changed, 35 insertions(+), 14 deletions(-) diff --git a/src/index.rs b/src/index.rs index f4bfe639..17789822 100644 --- a/src/index.rs +++ b/src/index.rs @@ -3,6 +3,10 @@ use sourmash::index::revindex::RevIndex; use sourmash::index::revindex::RevIndexOps; use sourmash::prelude::*; use std::path::Path; +use std::fs::File; +use std::io::{ BufRead, BufReader }; +use anyhow::Context; +use camino::Utf8PathBuf as PathBuf; use crate::utils::{load_collection, ReportType}; use sourmash::collection::Collection; @@ -17,23 +21,40 @@ pub fn index>( ) -> Result<(), Box> { println!("Loading siglist"); - let multi = load_collection( - &siglist, - selection, - ReportType::General, - allow_failed_sigpaths, - )?; + let collection = match siglist { + x if x.ends_with(".zip") => { + Collection::from_zipfile(x)? + } + _ => { + let file = File::open(siglist.clone()).with_context(|| { + format!( + "Failed to open pathlist file: '{}'", + siglist + ) + })?; - debug!( - "loaded multicollection from '{}' with len {}", - siglist, - multi.len() - ); + let reader = BufReader::new(file); - let sigs = multi.load_sigs()?; // @CTB load into memory :sob: - let coll = Collection::from_sigs(sigs)?; + // load list of paths + let lines: Vec<_> = reader + .lines() + .filter_map(|line| match line { + Ok(path) => { + let mut filename = PathBuf::new(); + filename.push(path); + Some(filename) + } + Err(_err) => None, + }) + .collect(); - let mut index = RevIndex::create(output.as_ref(), coll.select(selection)?.try_into()?, colors)?; + Collection::from_paths(&lines)? + } + }; + + let mut index = RevIndex::create(output.as_ref(), + collection.select(selection)?.try_into()?, + colors)?; if use_internal_storage { index.internalize_storage()?; From 4ea6730f9f9d53cf6c208409723d8039a7e9ba58 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 13:29:26 -0700 Subject: [PATCH 28/91] testy testy --- src/index.rs | 21 +++++++++++++-------- src/python/tests/test_index.py | 4 +++- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/src/index.rs b/src/index.rs index 17789822..b7ce70a8 100644 --- a/src/index.rs +++ b/src/index.rs @@ -9,7 +9,7 @@ use anyhow::Context; use camino::Utf8PathBuf as PathBuf; use crate::utils::{load_collection, ReportType}; -use sourmash::collection::Collection; +use sourmash::collection::{ Collection, CollectionSet }; pub fn index>( siglist: String, @@ -52,13 +52,18 @@ pub fn index>( } }; - let mut index = RevIndex::create(output.as_ref(), - collection.select(selection)?.try_into()?, - colors)?; + let collection: CollectionSet = collection.select(selection)?.try_into()?; - if use_internal_storage { - index.internalize_storage()?; - } + if collection.is_empty() { + Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()) + } else { + let mut index = RevIndex::create(output.as_ref(), + collection, + colors)?; - Ok(()) + if use_internal_storage { + index.internalize_storage()?; + } + Ok(()) + } } diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py index 140fe799..c67f21f5 100644 --- a/src/python/tests/test_index.py +++ b/src/python/tests/test_index.py @@ -82,9 +82,10 @@ def test_index_missing_siglist(runtmp, capfd, toggle_internal_storage): captured = capfd.readouterr() print(captured.err) - assert 'Error: No such file or directory' in captured.err + assert 'Failed to open pathlist file:' in captured.err +@pytest.mark.xfail(reason="not implemented yet") def test_index_sig(runtmp, capfd, toggle_internal_storage): # test index with a .sig.gz file instead of pathlist # (should work now) @@ -100,6 +101,7 @@ def test_index_sig(runtmp, capfd, toggle_internal_storage): assert 'index is done' in runtmp.last_result.err +@pytest.mark.xfail(reason="not implemented yet") def test_index_manifest(runtmp, capfd, toggle_internal_storage): # test index with a manifest file sig2 = get_test_data('2.fa.sig.gz') From ac35b2462d2d4af3e89726c4313ad636bd5ba1c1 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 21 Aug 2024 13:39:24 -0700 Subject: [PATCH 29/91] getting closer --- src/index.rs | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/index.rs b/src/index.rs index b7ce70a8..918c556e 100644 --- a/src/index.rs +++ b/src/index.rs @@ -48,7 +48,17 @@ pub fn index>( }) .collect(); - Collection::from_paths(&lines)? + if lines.is_empty() { + return Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()); + } else { + match Collection::from_paths(&lines) { + Ok(collection) => collection, + Err(err) => { + eprintln!("Error in loading from '{}': {}", siglist, err); + return Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()); + } + } + } } }; From 741a44a9c3db8347c15d788d09cba7303244ddc1 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 22 Aug 2024 15:31:06 -0700 Subject: [PATCH 30/91] update sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 41169f9a..7d640de1 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#53bcf0274f4b7bdec81077b44591af3a932a0270" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#eb46ecde66d5d6b6e6802f54bf99fff72c143038" dependencies = [ "az", "byteorder", From d429205a94b7823f6d160c00cd20d46dc3ea1af4 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 22 Aug 2024 15:40:56 -0700 Subject: [PATCH 31/91] mark failing tests --- src/python/tests/test_fastgather.py | 1 + src/python/tests/test_index.py | 2 ++ 2 files changed, 3 insertions(+) diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index 3ec65326..917b2d76 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -257,6 +257,7 @@ def test_bad_against_3(runtmp, capfd): assert 'InvalidArchive' in captured.err +@pytest.mark.xfail(reason="should work, bug") def test_against_multisigfile(runtmp, zip_against): # test against a sigfile that contains multiple sketches query = get_test_data('SRR606249.sig.gz') diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py index c67f21f5..6f59425e 100644 --- a/src/python/tests/test_index.py +++ b/src/python/tests/test_index.py @@ -118,6 +118,7 @@ def test_index_manifest(runtmp, capfd, toggle_internal_storage): assert 'index is done' in runtmp.last_result.err +@pytest.mark.xfail(reason="needs more work") def test_index_bad_siglist_2(runtmp, capfd): # test with a bad siglist (containing a missing file) against_list = runtmp.output('against.txt') @@ -138,6 +139,7 @@ def test_index_bad_siglist_2(runtmp, capfd): assert "WARNING: could not load sketches from path 'no-exist'" in captured.err +@pytest.mark.xfail(reason="needs more work") def test_index_empty_siglist(runtmp, capfd): # test empty siglist file siglist = runtmp.output('db-sigs.txt') From 994fcec388a3bc63b021f42487e3b772fea7080b Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 07:15:58 -0700 Subject: [PATCH 32/91] upd --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 7d640de1..5e040472 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#eb46ecde66d5d6b6e6802f54bf99fff72c143038" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#2c590102f97b12284f40ce4cfbdfe8ef9bd54342" dependencies = [ "az", "byteorder", From 8451259bdce59b19c9f6c9d3880323951a779ea1 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 08:46:34 -0700 Subject: [PATCH 33/91] cargo fmt --- src/index.rs | 26 +++++++++----------------- src/utils/multicollection.rs | 5 +---- 2 files changed, 10 insertions(+), 21 deletions(-) diff --git a/src/index.rs b/src/index.rs index 918c556e..d142621d 100644 --- a/src/index.rs +++ b/src/index.rs @@ -1,15 +1,15 @@ +use anyhow::Context; +use camino::Utf8PathBuf as PathBuf; use log::debug; use sourmash::index::revindex::RevIndex; use sourmash::index::revindex::RevIndexOps; use sourmash::prelude::*; -use std::path::Path; use std::fs::File; -use std::io::{ BufRead, BufReader }; -use anyhow::Context; -use camino::Utf8PathBuf as PathBuf; +use std::io::{BufRead, BufReader}; +use std::path::Path; use crate::utils::{load_collection, ReportType}; -use sourmash::collection::{ Collection, CollectionSet }; +use sourmash::collection::{Collection, CollectionSet}; pub fn index>( siglist: String, @@ -22,16 +22,10 @@ pub fn index>( println!("Loading siglist"); let collection = match siglist { - x if x.ends_with(".zip") => { - Collection::from_zipfile(x)? - } + x if x.ends_with(".zip") => Collection::from_zipfile(x)?, _ => { - let file = File::open(siglist.clone()).with_context(|| { - format!( - "Failed to open pathlist file: '{}'", - siglist - ) - })?; + let file = File::open(siglist.clone()) + .with_context(|| format!("Failed to open pathlist file: '{}'", siglist))?; let reader = BufReader::new(file); @@ -67,9 +61,7 @@ pub fn index>( if collection.is_empty() { Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()) } else { - let mut index = RevIndex::create(output.as_ref(), - collection, - colors)?; + let mut index = RevIndex::create(output.as_ref(), collection, colors)?; if use_internal_storage { index.internalize_storage()?; diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 462de3a0..6d72e76a 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -100,10 +100,7 @@ impl MultiCollection { if manifest.is_empty() { Err(anyhow!("could not read as manifest: '{}'", sigpath)) } else { - let ilocs: HashSet<_> = manifest - .internal_locations() - .map(String::from) - .collect(); + let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); let colls = colls.into_iter().collect(); From 91b04b572db1d8da5bf4cfd0596397bcac284b12 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 09:21:05 -0700 Subject: [PATCH 34/91] MRG: test exit from `pairwise` and `multisearch` if no loaded sketches (#437) * upd * check for appropriate multisearch error exits * add more tests for pairwise, too * cargo fmt --- src/multisearch.rs | 10 ---- src/python/tests/test-data/2.fa.k21.sig.gz | Bin 0 -> 22071 bytes src/python/tests/test_multisearch.py | 60 ++++++++++++++++++++- src/python/tests/test_pairwise.py | 33 ++++++++++-- 4 files changed, 88 insertions(+), 15 deletions(-) create mode 100644 src/python/tests/test-data/2.fa.k21.sig.gz diff --git a/src/multisearch.rs b/src/multisearch.rs index 17f8dfaf..19d2264d 100644 --- a/src/multisearch.rs +++ b/src/multisearch.rs @@ -60,16 +60,6 @@ pub fn multisearch( let processed_cmp = AtomicUsize::new(0); let ksize = selection.ksize().unwrap() as f64; - if queries.is_empty() { - eprintln!("No query sketches present. Exiting."); - return Err(anyhow::anyhow!("failed to load query sketches").into()); - } - - if against.is_empty() { - eprintln!("No search sketches present. Exiting."); - return Err(anyhow::anyhow!("failed to load search sketches").into()); - } - let send = against .par_iter() .filter_map(|against| { diff --git a/src/python/tests/test-data/2.fa.k21.sig.gz b/src/python/tests/test-data/2.fa.k21.sig.gz new file mode 100644 index 0000000000000000000000000000000000000000..d63afbc33d93bf59b6180b7ced33ab4afc2c5f59 GIT binary patch literal 22071 zcmV)FK)=5qiwFP!00004|2_K6j%{6XB#6BVk>gOof6UF?Iisktpn+yWqroPVU5O%- zjmn}RNa%N$tsP%?#Jv$``|=+%b6;!kbMF0r{r~>-&;RyMfBV~?{{ByY`;Y(p@BjW! zfBUch^WXmRzy9@~{>Oj*_doyX=TCqB_ka4!zj@Iw|La@(*Z=(MKmU)v{KsEyivRNO z4*1XiPI&QO|MG8t{_8*e`=4#E|MIW@WXm5{|M>ri$WZ>5{JVenZ~yJjuJG5t{pFwj z?%)6Opa1gLzx;3i^)LVSPk;9h|IdH?$G`i({=+}~U$*Dx@BaBe{{4UZw?F@nKmXnT z`scs?hZFw%>EHhH&wu{w-(Ko}{Ks(S{}bQe{`B|8|JVQg_dor8{QT*^{p~ORUprO) z{ONCh{`0^5>F-fLfBN@-`v3gT|JA_%^!K>{1%z60GjH)Pe|;&grfox}Mn6?CQ{9~j z_>#3F@)U#qDb?{-*g5S_M>C~r^=|xhM$fuJvw}YjL6Nz)75jrMst?(7dq3l<1aq9o zb!SnSHnVk|W}4?v|IuE@su8nnJQJm|*x 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a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index 87553615..7f6c719e 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -423,7 +423,7 @@ def test_empty_query(runtmp, capfd): # @CTB -def test_nomatch_query(runtmp, capfd, zip_query): +def test_nomatch_query_warn(runtmp, capfd, zip_query): # test a non-matching (diff ksize) in query; do we get warning message? query_list = runtmp.output('query.txt') against_list = runtmp.output('against.txt') @@ -451,6 +451,64 @@ def test_nomatch_query(runtmp, capfd, zip_query): assert 'WARNING: skipped 1 query paths - no compatible signatures' in captured.err +def test_nomatch_query_exit(runtmp, capfd, zip_query): + # test loading no matching sketches - do we error exit appropriately? + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + sig1 = get_test_data('1.fa.k21.sig.gz') + sig2 = get_test_data('2.fa.sig.gz') + sig47 = get_test_data('47.fa.sig.gz') + sig63 = get_test_data('63.fa.sig.gz') + + make_file_list(query_list, [sig1]) + make_file_list(against_list, [sig2, sig47, sig63]) + + output = runtmp.output('out.csv') + + if zip_query: + query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + + with pytest.raises(utils.SourmashCommandFailed): + runtmp.sourmash('scripts', 'multisearch', query_list, against_list, + '-o', output) + + captured = capfd.readouterr() + print(captured.err) + + assert 'WARNING: skipped 1 query paths - no compatible signatures' in captured.err + assert 'No query signatures loaded, exiting' in captured.err + + +def test_nomatch_against(runtmp, capfd, zip_query): + # test a non-matching (diff ksize) in against; do we get warning message? + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + sig1 = get_test_data('1.fa.k21.sig.gz') + sig2 = get_test_data('2.fa.sig.gz') + sig47 = get_test_data('47.fa.sig.gz') + sig63 = get_test_data('63.fa.sig.gz') + + make_file_list(query_list, [sig2, sig47, sig63, sig1]) + make_file_list(against_list, [sig2, sig47, sig63]) + + output = runtmp.output('out.csv') + + if zip_query: + query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + + with pytest.raises(utils.SourmashCommandFailed): + runtmp.sourmash('scripts', 'multisearch', query_list, against_list, + '-o', output, '-k', '21') + + captured = capfd.readouterr() + print(captured.err) + + assert 'WARNING: skipped 3 search paths - no compatible signatures' in captured.err + assert 'No search signatures loaded, exiting' in captured.err + + def test_load_only_one_bug(runtmp, capfd, zip_db): # check that we behave properly when presented with multiple against # sketches diff --git a/src/python/tests/test_pairwise.py b/src/python/tests/test_pairwise.py index c8264069..3046c1fe 100644 --- a/src/python/tests/test_pairwise.py +++ b/src/python/tests/test_pairwise.py @@ -251,7 +251,7 @@ def test_missing_query(runtmp, capfd, zip_db): -def test_empty_query(runtmp): +def test_empty_query(runtmp, capfd): # test with an empty query list query_list = runtmp.output('query.txt') @@ -267,11 +267,11 @@ def test_empty_query(runtmp): runtmp.sourmash('scripts', 'pairwise', query_list, '-o', output) - print(runtmp.last_result.err) - # @CTB + captured = capfd.readouterr() + assert 'Error: No analysis signatures loaded, exiting.' in captured.err -def test_nomatch_query(runtmp, capfd, zip_query): +def test_nomatch_query_warn(runtmp, capfd, zip_query): # test a non-matching (diff ksize) in query; do we get warning message? query_list = runtmp.output('query.txt') @@ -297,6 +297,31 @@ def test_nomatch_query(runtmp, capfd, zip_query): assert 'WARNING: skipped 1 analysis paths - no compatible signatures' in captured.err +def test_nomatch_query_exit(runtmp, capfd, zip_query): + # test a non-matching (diff ksize) in query; do we get warning message? + query_list = runtmp.output('query.txt') + + sig1 = get_test_data('1.fa.k21.sig.gz') + sig2 = get_test_data('2.fa.k21.sig.gz') + + make_file_list(query_list, [sig1, sig2]) + + output = runtmp.output('out.csv') + + if zip_query: + query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + + with pytest.raises(utils.SourmashCommandFailed): + runtmp.sourmash('scripts', 'pairwise', query_list, + '-o', output) + + captured = capfd.readouterr() + print(captured.err) + + assert 'WARNING: skipped 2 analysis paths - no compatible signatures' in captured.err + assert 'Error: No analysis signatures loaded, exiting.' in captured.err + + def test_load_only_one_bug(runtmp, capfd, zip_db): # check that we behave properly when presented with multiple query # sketches From b3e5b814c64edb4118c314fa2f9982580f0f2580 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 09:39:16 -0700 Subject: [PATCH 35/91] MRG: switch to more efficient use of `Collection` by removing cloning (#438) * remove unnecessary clones by switch to references in SmallSignature * switch away from references for collections => avoid clones * remove MultiCollection::iter --- src/index.rs | 4 +-- src/utils/multicollection.rs | 63 +++++++----------------------------- 2 files changed, 12 insertions(+), 55 deletions(-) diff --git a/src/index.rs b/src/index.rs index d142621d..6b79d9e6 100644 --- a/src/index.rs +++ b/src/index.rs @@ -1,6 +1,5 @@ use anyhow::Context; use camino::Utf8PathBuf as PathBuf; -use log::debug; use sourmash::index::revindex::RevIndex; use sourmash::index::revindex::RevIndexOps; use sourmash::prelude::*; @@ -8,7 +7,6 @@ use std::fs::File; use std::io::{BufRead, BufReader}; use std::path::Path; -use crate::utils::{load_collection, ReportType}; use sourmash::collection::{Collection, CollectionSet}; pub fn index>( @@ -16,7 +14,7 @@ pub fn index>( selection: &Selection, output: P, colors: bool, - allow_failed_sigpaths: bool, + _allow_failed_sigpaths: bool, use_internal_storage: bool, ) -> Result<(), Box> { println!("Loading siglist"); diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 6d72e76a..211cfed5 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -103,7 +103,6 @@ impl MultiCollection { let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); - let colls = colls.into_iter().collect(); Ok(MultiCollection::new(colls)) } @@ -163,7 +162,6 @@ impl MultiCollection { .collect(); let (colls, n_failed) = MultiCollection::load_set_of_paths(lines); - let colls: Vec<_> = colls.into_iter().collect(); Ok((MultiCollection::new(colls), n_failed)) } @@ -187,20 +185,16 @@ impl MultiCollection { let val: usize = self.collections.iter().map(|c| c.len()).sum(); val } + pub fn is_empty(&self) -> bool { let val: usize = self.collections.iter().map(|c| c.len()).sum(); val == 0 } - pub fn iter(&self) -> impl Iterator { - self.collections.iter() - } - // iterate over tuples pub fn item_iter(&self) -> impl Iterator { - // CTB: request review by Rust expert pls :). Does this make - // unnecessary copies?? let s: Vec<_> = self + .collections .iter() .flat_map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) .collect(); @@ -208,12 +202,13 @@ impl MultiCollection { } pub fn par_iter(&self) -> impl IndexedParallelIterator { - // CTB: request review by Rust expert - why can't I use item_iter here? - // i.e. self.item_iter().into_par_iter()? + // first create a Vec of all triples (Collection, Idx, Record) let s: Vec<_> = self + .collections .iter() .flat_map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) .collect(); + // then return a parallel iterator over the Vec. s.into_par_iter() } @@ -238,7 +233,6 @@ impl MultiCollection { let minhash = selected_sig.minhash()?.clone(); Some(SmallSignature { - collection: coll.clone(), // @CTB location: record.internal_location().to_string(), name: sig.name(), md5sum: sig.md5sum(), @@ -257,57 +251,22 @@ impl MultiCollection { Ok(sketchinfo) } - - // Load all signatures into memory. - pub fn load_sigs(&self) -> Result> { - let sigs: Vec<_> = self - .par_iter() - .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { - Ok(sigstore) => Some(sigstore.into()), - Err(_) => { - eprintln!( - "FAILED to load sketch from '{}'", - record.internal_location() - ); - None - } - }) - .collect(); - - Ok(sigs) - } } impl Select for MultiCollection { - fn select(mut self, selection: &Selection) -> Result { - // CTB: request review by Rust expert! Is the clone necessary? - self.collections = self - .iter() - .filter_map(|c| c.clone().select(selection).ok()) + fn select(self, selection: &Selection) -> Result { + let collections = self + .collections + .into_iter() + .filter_map(|c| c.select(selection).ok()) .collect(); - Ok(self) - } -} -/* -impl TryFrom for CollectionSet { - type Error = SourmashError; - - fn try_from(multi: MultiCollection) -> Result { - // CTB: request review by Rust expert! Is the clone necessary? -// @CTB need to do something better than just getting the first CS! :sob: -// @CTB could fail if more than one? - let coll = multi.iter().next().unwrap().clone(); - let cs: CollectionSet = coll.try_into()?; - Ok(cs) + Ok(MultiCollection::new(collections)) } } -*/ /// Track a name/minhash. pub struct SmallSignature { - // CTB: request help - can we/should we use references & lifetimes here? - pub collection: Collection, pub location: String, pub name: String, pub md5sum: String, From 97db85738ed0ae72861cac21bec5bf720adf9233 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 11:19:04 -0700 Subject: [PATCH 36/91] MRG: add tests for RocksDB/RevIndex, standalone manifests, and flexible pathlists (#436) * test using rocksdb as source of sketches * test file lists of zips * cargo fmt * hackity hack hack a picklist * ok that makes more sense * it works * comments around future par_iter * support loading from a .sig.gz for index * test pairwise loading from rocksdb * add test for queries from Rocksdb * decide not to implement lists of manifests :) --- src/index.rs | 13 ++ src/lib.rs | 2 + src/python/tests/conftest.py | 8 ++ src/python/tests/sourmash_tst_utils.py | 9 ++ src/python/tests/test-data/2.sig.zip | Bin 0 -> 23403 bytes src/python/tests/test-data/47.sig.zip | Bin 0 -> 43621 bytes src/python/tests/test-data/63.sig.zip | Bin 0 -> 44153 bytes src/python/tests/test_fastgather.py | 59 +++++++- src/python/tests/test_fastmultigather.py | 53 +++++-- src/python/tests/test_manysearch.py | 71 +++++++-- src/python/tests/test_multisearch.py | 175 ++++++++++++++++++++++- src/python/tests/test_pairwise.py | 14 +- src/utils/mod.rs | 3 + src/utils/multicollection.rs | 45 ++++-- 14 files changed, 414 insertions(+), 38 deletions(-) create mode 100644 src/python/tests/test-data/2.sig.zip create mode 100644 src/python/tests/test-data/47.sig.zip create mode 100644 src/python/tests/test-data/63.sig.zip diff --git a/src/index.rs b/src/index.rs index 6b79d9e6..c568b161 100644 --- a/src/index.rs +++ b/src/index.rs @@ -21,6 +21,18 @@ pub fn index>( let collection = match siglist { x if x.ends_with(".zip") => Collection::from_zipfile(x)?, + x if x.ends_with(".sig") || x.ends_with(".sig.gz") => { + let signatures = Signature::from_path(&x) + .with_context(|| format!("Failed to load signatures from: '{}'", x))?; + + let coll = Collection::from_sigs(signatures).with_context(|| { + format!( + "Loaded signatures but failed to load as collection: '{}'", + x + ) + })?; + coll + } _ => { let file = File::open(siglist.clone()) .with_context(|| format!("Failed to open pathlist file: '{}'", siglist))?; @@ -59,6 +71,7 @@ pub fn index>( if collection.is_empty() { Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()) } else { + eprintln!("Indexing {} sketches.", collection.len()); let mut index = RevIndex::create(output.as_ref(), collection, colors)?; if use_internal_storage { diff --git a/src/lib.rs b/src/lib.rs index 194bfae8..849a6ce8 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -234,6 +234,8 @@ fn do_multisearch( estimate_ani: bool, output_path: Option, ) -> anyhow::Result { + let _ = env_logger::try_init(); + let selection = build_selection(ksize, scaled, &moltype); let allow_failed_sigpaths = true; diff --git a/src/python/tests/conftest.py b/src/python/tests/conftest.py index 3f7021a1..f6f0f7f4 100644 --- a/src/python/tests/conftest.py +++ b/src/python/tests/conftest.py @@ -27,3 +27,11 @@ def zip_against(request): @pytest.fixture(params=[True, False]) def indexed(request): return request.param + +@pytest.fixture(params=[True, False]) +def indexed_query(request): + return request.param + +@pytest.fixture(params=[True, False]) +def indexed_against(request): + return request.param diff --git a/src/python/tests/sourmash_tst_utils.py b/src/python/tests/sourmash_tst_utils.py index f4ad4927..0c0e0e00 100644 --- a/src/python/tests/sourmash_tst_utils.py +++ b/src/python/tests/sourmash_tst_utils.py @@ -31,6 +31,15 @@ def zip_siglist(runtmp, siglist, db): return db +def index_siglist(runtmp, siglist, db, *, ksize=31, scaled=1000, moltype='DNA', + toggle_internal_storage='--internal-storage'): + # build index + runtmp.sourmash('scripts', 'index', siglist, + '-o', db, '-k', str(ksize), '--scaled', str(scaled), + '--moltype', moltype, toggle_internal_storage) + return db + + def scriptpath(scriptname='sourmash'): """Return the path to the scripts, in both dev and install situations.""" # note - it doesn't matter what the scriptname is here, as long as diff --git a/src/python/tests/test-data/2.sig.zip b/src/python/tests/test-data/2.sig.zip new file mode 100644 index 0000000000000000000000000000000000000000..28b41d59c2afdde3555fca4b110d25ae23b95149 GIT binary 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a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -4,7 +4,8 @@ import sourmash from . import sourmash_tst_utils as utils -from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist, + index_siglist) def test_installed(runtmp): @@ -14,7 +15,7 @@ def test_installed(runtmp): assert 'usage: fastgather' in runtmp.last_result.err -def test_simple(runtmp, zip_against): +def test_simple(runtmp, capfd, indexed_query, indexed_against, zip_against, toggle_internal_storage): # test basic execution! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') @@ -25,9 +26,17 @@ def test_simple(runtmp, zip_against): make_file_list(against_list, [sig2, sig47, sig63]) + if indexed_query: + query = index_siglist(runtmp, query, runtmp.output('query'), + scaled=100000) + if zip_against: against_list = zip_siglist(runtmp, against_list, runtmp.output('against.zip')) + if indexed_against: + against_list = index_siglist(runtmp, against_list, runtmp.output('db'), + toggle_internal_storage=toggle_internal_storage) + g_output = runtmp.output('gather.csv') p_output = runtmp.output('prefetch.csv') @@ -35,13 +44,22 @@ def test_simple(runtmp, zip_against): '-o', g_output, '-s', '100000') assert os.path.exists(g_output) + captured = capfd.readouterr() + print(captured.err) + df = pandas.read_csv(g_output) assert len(df) == 3 keys = set(df.keys()) assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'gather_result_rank', 'intersect_bp'}.issubset(keys) + # CTB note: we do not need to worry about this warning for query from a + # RocksDB, since there is only one. + if indexed_against: + print('indexed against:', indexed_against) + assert "WARNING: loading all sketches from a RocksDB into memory!" in captured.err -def test_simple_with_prefetch(runtmp, zip_against): + +def test_simple_with_prefetch(runtmp, zip_against, indexed, toggle_internal_storage): # test basic execution! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') @@ -55,6 +73,41 @@ def test_simple_with_prefetch(runtmp, zip_against): if zip_against: against_list = zip_siglist(runtmp, against_list, runtmp.output('against.zip')) + if indexed: + against_list = index_siglist(runtmp, against_list, runtmp.output('db'), + toggle_internal_storage=toggle_internal_storage) + + g_output = runtmp.output('gather.csv') + p_output = runtmp.output('prefetch.csv') + + runtmp.sourmash('scripts', 'fastgather', query, against_list, + '-o', g_output, '--output-prefetch', p_output, + '-s', '100000') + assert os.path.exists(g_output) + assert os.path.exists(p_output) + + df = pandas.read_csv(g_output) + assert len(df) == 3 + keys = set(df.keys()) + assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'gather_result_rank', 'intersect_bp'}.issubset(keys) + + df = pandas.read_csv(p_output) + assert len(df) == 3 + keys = set(df.keys()) + assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp'} + + +def test_simple_with_prefetch_list_of_zips(runtmp): + # test basic execution! + query = get_test_data('SRR606249.sig.gz') + against_list = runtmp.output('against.txt') + + sig2 = get_test_data('2.sig.zip') + sig47 = get_test_data('47.sig.zip') + sig63 = get_test_data('63.sig.zip') + + make_file_list(against_list, [sig2, sig47, sig63]) + g_output = runtmp.output('gather.csv') p_output = runtmp.output('prefetch.csv') diff --git a/src/python/tests/test_fastmultigather.py b/src/python/tests/test_fastmultigather.py index 23f9cc19..68294c94 100644 --- a/src/python/tests/test_fastmultigather.py +++ b/src/python/tests/test_fastmultigather.py @@ -8,16 +8,8 @@ import sourmash from . import sourmash_tst_utils as utils -from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) - - -def index_siglist(runtmp, siglist, db, *, ksize=31, scaled=1000, moltype='DNA', - toggle_internal_storage='--internal-storage'): - # build index - runtmp.sourmash('scripts', 'index', siglist, - '-o', db, '-k', str(ksize), '--scaled', str(scaled), - '--moltype', moltype, toggle_internal_storage) - return db +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist, + index_siglist) def test_installed(runtmp): @@ -71,6 +63,47 @@ def test_simple(runtmp, zip_against): assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp', 'gather_result_rank'}.issubset(keys) +def test_simple_list_of_zips(runtmp): + # test basic execution! + query = get_test_data('SRR606249.sig.gz') + sig2 = get_test_data('2.sig.zip') + sig47 = get_test_data('47.sig.zip') + sig63 = get_test_data('63.sig.zip') + + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + make_file_list(query_list, [query]) + make_file_list(against_list, [sig2, sig47, sig63]) + + cwd = os.getcwd() + try: + os.chdir(runtmp.output('')) + runtmp.sourmash('scripts', 'fastmultigather', query_list, against_list, + '-s', '100000', '-t', '0') + finally: + os.chdir(cwd) + + print(os.listdir(runtmp.output(''))) + + g_output = runtmp.output('SRR606249.gather.csv') + p_output = runtmp.output('SRR606249.prefetch.csv') + assert os.path.exists(p_output) + + # check prefetch output (only non-indexed gather) + df = pandas.read_csv(p_output) + assert len(df) == 3 + keys = set(df.keys()) + assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp'} + + assert os.path.exists(g_output) + df = pandas.read_csv(g_output) + print(df) + assert len(df) == 3 + keys = set(df.keys()) + assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp', 'gather_result_rank'}.issubset(keys) + + def test_simple_space_in_signame(runtmp): # test basic execution! query = get_test_data('SRR606249.sig.gz') diff --git a/src/python/tests/test_manysearch.py b/src/python/tests/test_manysearch.py index ab0f5762..4750d9d6 100644 --- a/src/python/tests/test_manysearch.py +++ b/src/python/tests/test_manysearch.py @@ -4,7 +4,8 @@ import sourmash from . import sourmash_tst_utils as utils -from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist, + index_siglist) def test_installed(runtmp): @@ -14,13 +15,6 @@ def test_installed(runtmp): assert 'usage: manysearch' in runtmp.last_result.err -def index_siglist(runtmp, siglist, db, ksize=31, scaled=1000, moltype='DNA'): - # build index - runtmp.sourmash('scripts', 'index', siglist, - '-o', db, '-k', str(ksize), '--scaled', str(scaled), - '--moltype', moltype) - return db - def test_simple(runtmp, zip_query, zip_against): # test basic execution! query_list = runtmp.output('query.txt') @@ -176,7 +170,7 @@ def test_simple_abund(runtmp): assert total_weighted_hashes == 73489 -def test_simple_indexed(runtmp, zip_query): +def test_simple_indexed(runtmp, zip_query, indexed_query): # test basic execution! query_list = runtmp.output('query.txt') against_list = runtmp.output('against.txt') @@ -188,12 +182,67 @@ def test_simple_indexed(runtmp, zip_query): make_file_list(query_list, [sig2, sig47, sig63]) make_file_list(against_list, [sig2, sig47, sig63]) + if zip_query: + query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + + if indexed_query: + query_list = index_siglist(runtmp, query_list, runtmp.output('query_db')) + output = runtmp.output('out.csv') against_list = index_siglist(runtmp, against_list, runtmp.output('db')) - if zip_query: - query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + print('query_list is:', query_list) + runtmp.sourmash('scripts', 'manysearch', query_list, against_list, + '-o', output, '-t', '0.01') + assert os.path.exists(output) + + df = pandas.read_csv(output) + assert len(df) == 5 + + dd = df.to_dict(orient='index') + print(dd) + + for idx, row in dd.items(): + # identical? + if row['match_name'] == row['query_name']: + assert float(row['containment'] == 1.0) + assert float(row['query_containment_ani'] == 1.0) + else: + # confirm hand-checked numbers + q = row['query_name'].split()[0] + m = row['match_name'].split()[0] + cont = float(row['containment']) + intersect_hashes = int(row['intersect_hashes']) + query_ani = float(row['query_containment_ani']) + cont = round(cont, 4) + query_ani = round(query_ani, 4) + print(q, m, f"{cont:.04}", f"{query_ani:.04}") + + if q == 'NC_011665.1' and m == 'NC_009661.1': + assert cont == 0.4828 + assert intersect_hashes == 2529 + assert query_ani == 0.9768 + + if q == 'NC_009661.1' and m == 'NC_011665.1': + assert cont == 0.4885 + assert intersect_hashes == 2529 + assert query_ani == 0.9772 + + +def test_simple_list_of_zips(runtmp): + # test basic execution! + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + sig2 = get_test_data('2.sig.zip') + sig47 = get_test_data('47.sig.zip') + sig63 = get_test_data('63.sig.zip') + + make_file_list(query_list, [sig2, sig47, sig63]) + make_file_list(against_list, [sig2, sig47, sig63]) + + output = runtmp.output('out.csv') runtmp.sourmash('scripts', 'manysearch', query_list, against_list, '-o', output, '-t', '0.01') diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index 7f6c719e..5a2c5112 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -5,7 +5,8 @@ import sourmash from . import sourmash_tst_utils as utils -from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist, + index_siglist) def test_installed(runtmp): @@ -83,7 +84,7 @@ def test_simple_no_ani(runtmp, zip_query, zip_db): assert intersect_hashes == 2529 -def test_simple_ani(runtmp, zip_query, zip_db): +def test_simple_ani(runtmp, zip_query, zip_db, indexed_query, indexed_against): # test basic execution! query_list = runtmp.output('query.txt') against_list = runtmp.output('against.txt') @@ -99,9 +100,96 @@ def test_simple_ani(runtmp, zip_query, zip_db): if zip_db: against_list = zip_siglist(runtmp, against_list, runtmp.output('db.zip')) + if zip_query: query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + if indexed_query: + query_list = index_siglist(runtmp, query_list, runtmp.output('q_db')) + + if indexed_against: + against_list = index_siglist(runtmp, against_list, runtmp.output('db')) + + runtmp.sourmash('scripts', 'multisearch', query_list, against_list, + '-o', output, '--ani') + assert os.path.exists(output) + + df = pandas.read_csv(output) + assert len(df) == 5 + + dd = df.to_dict(orient='index') + print(dd) + + for idx, row in dd.items(): + # identical? + if row['match_name'] == row['query_name']: + assert row['query_md5'] == row['match_md5'], row + assert float(row['containment'] == 1.0) + assert float(row['jaccard'] == 1.0) + assert float(row['max_containment'] == 1.0) + assert float(row['query_containment_ani'] == 1.0) + assert float(row['match_containment_ani'] == 1.0) + assert float(row['average_containment_ani'] == 1.0) + assert float(row['max_containment_ani'] == 1.0) + + else: + # confirm hand-checked numbers + q = row['query_name'].split()[0] + m = row['match_name'].split()[0] + cont = float(row['containment']) + jaccard = float(row['jaccard']) + maxcont = float(row['max_containment']) + intersect_hashes = int(row['intersect_hashes']) + q1_ani = float(row['query_containment_ani']) + q2_ani = float(row['match_containment_ani']) + avg_ani = float(row['average_containment_ani']) + max_ani = float(row['max_containment_ani']) + + + jaccard = round(jaccard, 4) + cont = round(cont, 4) + maxcont = round(maxcont, 4) + q1_ani = round(q1_ani, 4) + q2_ani = round(q2_ani, 4) + avg_ani = round(avg_ani, 4) + max_ani = round(max_ani, 4) + print(q, m, f"{jaccard:.04}", f"{cont:.04}", f"{maxcont:.04}", f"{q1_ani:.04}", f"{q2_ani:.04}", f"{avg_ani:.04}", f"{max_ani:.04}") + + if q == 'NC_011665.1' and m == 'NC_009661.1': + assert jaccard == 0.3207 + assert cont == 0.4828 + assert maxcont == 0.4885 + assert intersect_hashes == 2529 + assert q1_ani == 0.9768 + assert q2_ani == 0.9772 + assert avg_ani == 0.977 + assert max_ani == 0.9772 + + if q == 'NC_009661.1' and m == 'NC_011665.1': + assert jaccard == 0.3207 + assert cont == 0.4885 + assert maxcont == 0.4885 + assert intersect_hashes == 2529 + assert q1_ani == 0.9772 + assert q2_ani == 0.9768 + assert avg_ani == 0.977 + assert max_ani == 0.9772 + + +def test_simple_ani_list_of_zips(runtmp): + # test basic execution against a pathlist file of zips + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + sig2 = get_test_data('2.sig.zip') + sig47 = get_test_data('47.sig.zip') + sig63 = get_test_data('63.sig.zip') + + make_file_list(query_list, [sig2, sig47, sig63]) + make_file_list(against_list, [sig2, sig47, sig63]) + + output = runtmp.output('out.csv') + runtmp.sourmash('scripts', 'multisearch', query_list, against_list, '-o', output, '--ani') assert os.path.exists(output) @@ -168,6 +256,53 @@ def test_simple_ani(runtmp, zip_query, zip_db): assert max_ani == 0.9772 +def test_simple_ani_standalone_manifest(runtmp): + # test basic execution of a standalone manifest + against_list = runtmp.output('against.sig.zip') + + sig2 = get_test_data('2.sig.zip') + sig47 = get_test_data('47.sig.zip') + sig63 = get_test_data('63.sig.zip') + + runtmp.sourmash('sig', 'cat', sig2, sig47, sig63, '-o', against_list) + + picklist_file = runtmp.output('pl.csv') + with open(picklist_file, 'w', newline='') as fp: + w = csv.writer(fp) + w.writerow(['ident']) + w.writerow(['CP001071.1']) + + # use picklist to create a standalone manifest + query_csv = runtmp.output('select.mf.csv') + runtmp.sourmash('sig', 'check', '--picklist', + f'{picklist_file}:ident:ident', + '-m', query_csv, against_list) + + output = runtmp.output('out.csv') + + runtmp.sourmash('scripts', 'multisearch', query_csv, against_list, + '-o', output, '--ani') + assert os.path.exists(output) + + df = pandas.read_csv(output) + assert len(df) == 1 # should only be the one, identical match. + + dd = df.to_dict(orient='index') + print(dd) + + for idx, row in dd.items(): + # identical? + if row['match_name'] == row['query_name']: + assert row['query_md5'] == row['match_md5'], row + assert float(row['containment'] == 1.0) + assert float(row['jaccard'] == 1.0) + assert float(row['max_containment'] == 1.0) + assert float(row['query_containment_ani'] == 1.0) + assert float(row['match_containment_ani'] == 1.0) + assert float(row['average_containment_ani'] == 1.0) + assert float(row['max_containment_ani'] == 1.0) + + def test_simple_threshold(runtmp, zip_query, zip_db): # test with a simple threshold => only 3 results query_list = runtmp.output('query.txt') @@ -223,6 +358,42 @@ def test_simple_manifest(runtmp): assert len(df) == 3 +@pytest.mark.xfail(reason="not implemented yet") +def test_lists_of_standalone_manifests(runtmp): + # test pathlists of manifests + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + sig2 = get_test_data('2.fa.sig.gz') + sig47 = get_test_data('47.fa.sig.gz') + sig63 = get_test_data('63.fa.sig.gz') + + sig2_mf = runtmp.output('2.mf.csv') + runtmp.sourmash('sig', 'collect', sig2, '-o', sig2_mf, '-F', 'csv') + sig47_mf = runtmp.output('47.mf.csv') + runtmp.sourmash('sig', 'collect', sig47, '-o', sig47_mf, '-F', 'csv') + sig63_mf = runtmp.output('63.mf.csv') + runtmp.sourmash('sig', 'collect', sig63, '-o', sig63_mf, '-F', 'csv') + + make_file_list(query_list, [sig2_mf, sig47_mf, sig63_mf]) + make_file_list(against_list, [sig2, sig47, sig63]) + + query_mf = runtmp.output('qmf.csv') + against_mf = runtmp.output('amf.csv') + + runtmp.sourmash("sig", "manifest", query_list, "-o", query_mf) + runtmp.sourmash("sig", "manifest", against_list, "-o", against_mf) + + output = runtmp.output('out.csv') + + runtmp.sourmash('scripts', 'multisearch', query_mf, against_mf, + '-o', output, '-t', '0.5') + assert os.path.exists(output) + + df = pandas.read_csv(output) + assert len(df) == 3 + + def test_missing_query(runtmp, capfd, zip_query): # test with a missing query list query_list = runtmp.output('query.txt') diff --git a/src/python/tests/test_pairwise.py b/src/python/tests/test_pairwise.py index 3046c1fe..cba2a297 100644 --- a/src/python/tests/test_pairwise.py +++ b/src/python/tests/test_pairwise.py @@ -5,7 +5,8 @@ import sourmash from . import sourmash_tst_utils as utils -from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist) +from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist, + index_siglist) def test_installed(runtmp): @@ -15,7 +16,7 @@ def test_installed(runtmp): assert 'usage: pairwise' in runtmp.last_result.err -def test_simple_no_ani(runtmp, zip_query): +def test_simple_no_ani(runtmp, capfd, zip_query, indexed): # test basic execution! query_list = runtmp.output('query.txt') @@ -30,6 +31,9 @@ def test_simple_no_ani(runtmp, zip_query): if zip_query: query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip')) + if indexed: + query_list = index_siglist(runtmp, query_list, runtmp.output('db')) + runtmp.sourmash('scripts', 'pairwise', query_list, '-o', output, '-t', '-1') assert os.path.exists(output) @@ -64,6 +68,12 @@ def test_simple_no_ani(runtmp, zip_query): assert maxcont == 0.4885 assert intersect_hashes == 2529 + captured = capfd.readouterr() + print(captured.err) + + if indexed: + assert "WARNING: loading all sketches from a RocksDB into memory!" in captured.err + def test_simple_ani(runtmp, zip_query): # test basic execution! diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 01ff4d6c..6d4cfc25 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -451,6 +451,9 @@ pub fn load_sketches_above_threshold( let skipped_paths = AtomicUsize::new(0); let failed_paths = AtomicUsize::new(0); + if against_collection.contains_revindex { + eprintln!("WARNING: loading all sketches from a RocksDB into memory!"); + } let matchlist: BinaryHeap = against_collection .par_iter() .filter_map(|(coll, _idx, against_record)| { diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 211cfed5..bdf7e59c 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -25,25 +25,31 @@ use sourmash::storage::{FSStorage, InnerStorage, SigStore}; #[derive(Clone)] pub struct MultiCollection { collections: Vec, + pub contains_revindex: bool, } impl MultiCollection { - fn new(collections: Vec) -> Self { - Self { collections } + fn new(collections: Vec, contains_revindex: bool) -> Self { + Self { + collections, + contains_revindex, + } } // Turn a set of paths into list of Collections. fn load_set_of_paths(paths: HashSet) -> (Vec, usize) { let n_failed = AtomicUsize::new(0); + // could just use a variant of load_collection here? let colls: Vec<_> = paths .par_iter() .filter_map(|iloc| match iloc { - // could just use a variant of load_collection here? + // load from zipfile x if x.ends_with(".zip") => { debug!("loading sigs from zipfile {}", x); Some(Collection::from_zipfile(x).unwrap()) } + // load from (by default) a sigfile _ => { debug!("loading sigs from sigfile {}", iloc); let signatures = match Signature::from_path(iloc) { @@ -96,15 +102,31 @@ impl MultiCollection { let reader = BufReader::new(file); let manifest = Manifest::from_reader(reader) .with_context(|| format!("Failed to read manifest from: '{}'", sigpath))?; + debug!("got {} records from standalone manifest", manifest.len()); if manifest.is_empty() { Err(anyhow!("could not read as manifest: '{}'", sigpath)) } else { let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); - let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); - Ok(MultiCollection::new(colls)) + // select out only the (name, md5) pairs that were present + // in the manifest + // @CTB par_iter? + let picklist: HashSet<_> = manifest + .clone() + .iter() + .map(|r| (r.name().clone(), r.md5().clone())) + .collect(); + + // @CTB transfer into MultiCollection too? + // @CTB par_iter? + let colls = colls + .iter() + .map(|c| c.clone().select_picklist(&picklist)) + .collect(); + + Ok(MultiCollection::new(colls, false)) } } @@ -112,7 +134,7 @@ impl MultiCollection { pub fn from_zipfile(sigpath: &Path) -> Result { debug!("multi from zipfile!"); match Collection::from_zipfile(sigpath) { - Ok(collection) => Ok(MultiCollection::new(vec![collection])), + Ok(collection) => Ok(MultiCollection::new(vec![collection], false)), Err(_) => bail!("failed to load zipfile: '{}'", sigpath), } } @@ -136,7 +158,7 @@ impl MultiCollection { match Collection::from_rocksdb(sigpath) { Ok(collection) => { debug!("...rocksdb successful!"); - Ok(MultiCollection::new(vec![collection])) + Ok(MultiCollection::new(vec![collection], true)) } Err(_) => bail!("failed to load rocksdb: '{}'", sigpath), } @@ -163,7 +185,7 @@ impl MultiCollection { let (colls, n_failed) = MultiCollection::load_set_of_paths(lines); - Ok((MultiCollection::new(colls), n_failed)) + Ok((MultiCollection::new(colls, false), n_failed)) } // Load from a sig file @@ -178,7 +200,7 @@ impl MultiCollection { sigpath ) })?; - Ok(MultiCollection::new(vec![coll])) + Ok(MultiCollection::new(vec![coll], false)) } pub fn len(&self) -> usize { @@ -225,6 +247,9 @@ impl MultiCollection { // Load all sketches into memory, using SmallSignature to track original // signature metadata. pub fn load_sketches(&self, selection: &Selection) -> Result> { + if self.contains_revindex { + eprintln!("WARNING: loading all sketches from a RocksDB into memory!"); + } let sketchinfo: Vec<_> = self .par_iter() .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { @@ -261,7 +286,7 @@ impl Select for MultiCollection { .filter_map(|c| c.select(selection).ok()) .collect(); - Ok(MultiCollection::new(collections)) + Ok(MultiCollection::new(collections, self.contains_revindex)) } } From 551758f96e9e7cbbb42d79d6bdb4819266f20dce Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 12:18:32 -0700 Subject: [PATCH 37/91] reenable and fix test_fastgather.py::test_indexed_against --- src/python/tests/test_fastgather.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index 071878a4..2bfb3a59 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -653,7 +653,6 @@ def test_simple_hp(runtmp): def test_indexed_against(runtmp, capfd): - return # do not accept rocksdb for now @CTB we do now!! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') @@ -671,15 +670,17 @@ def test_indexed_against(runtmp, capfd): g_output = runtmp.output('gather.csv') p_output = runtmp.output('prefetch.csv') - with pytest.raises(utils.SourmashCommandFailed): - runtmp.sourmash('scripts', 'fastgather', query, db_against, - '-o', g_output, '--output-prefetch', p_output, - '-s', '100000') + runtmp.sourmash('scripts', 'fastgather', query, db_against, + '-o', g_output, '--output-prefetch', p_output, + '-s', '100000') + + df = pandas.read_csv(g_output) + assert len(df) == 1 captured = capfd.readouterr() print(captured.err) - assert "Cannot load search signatures from a 'rocksdb' database. Please use sig, zip, or pathlist." in captured.err + assert "WARNING: loading all sketches from a RocksDB into memory!" in captured.err def test_simple_with_manifest_loading(runtmp): From e3e95fc5160735137b69104f6ff181e16dacf981 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 12:44:22 -0700 Subject: [PATCH 38/91] impl Deref for MultiCollection --- src/utils/multicollection.rs | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index bdf7e59c..40a6ac88 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -9,6 +9,7 @@ use log::debug; use std::collections::HashSet; use std::fs::File; use std::io::{BufRead, BufReader}; +use std::ops::Deref; use std::sync::atomic; use std::sync::atomic::AtomicUsize; @@ -278,6 +279,14 @@ impl MultiCollection { } } +impl Deref for MultiCollection { + type Target = Vec; + + fn deref(&self) -> &Self::Target { + &self.collections + } +} + impl Select for MultiCollection { fn select(self, selection: &Selection) -> Result { let collections = self From 8d39a4fdcf835a7e2cb1026c3fdf8137e20d7b24 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 13:42:15 -0700 Subject: [PATCH 39/91] clippy --- src/index.rs | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/index.rs b/src/index.rs index c568b161..00202743 100644 --- a/src/index.rs +++ b/src/index.rs @@ -25,13 +25,12 @@ pub fn index>( let signatures = Signature::from_path(&x) .with_context(|| format!("Failed to load signatures from: '{}'", x))?; - let coll = Collection::from_sigs(signatures).with_context(|| { + Collection::from_sigs(signatures).with_context(|| { format!( "Loaded signatures but failed to load as collection: '{}'", x ) - })?; - coll + })? } _ => { let file = File::open(siglist.clone()) From 343959296c63f66303a71d1f93361e70fe223b40 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 13:42:28 -0700 Subject: [PATCH 40/91] switch to using load_sketches method --- src/fastmultigather.rs | 5 ++--- src/manysearch.rs | 7 ++++--- src/multisearch.rs | 11 +++++------ src/pairwise.rs | 7 +++---- src/python/tests/test_fastgather.py | 2 +- src/utils/mod.rs | 13 +------------ 6 files changed, 16 insertions(+), 29 deletions(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index 07dc22d2..a437f2bb 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -20,8 +20,7 @@ use sourmash::sketch::minhash::KmerMinHash; use sourmash::sketch::Sketch; use crate::utils::{ - consume_query_by_gather, load_collection, load_sketches, write_prefetch, PrefetchResult, - ReportType, + consume_query_by_gather, load_collection, write_prefetch, PrefetchResult, ReportType, }; pub fn fastmultigather( @@ -62,7 +61,7 @@ pub fn fastmultigather( allow_failed_sigpaths, )?; // load against sketches into memory, downsampling on the way - let against = load_sketches(against_collection, selection, ReportType::Against).unwrap(); + let against = against_collection.load_sketches(selection)?; // Iterate over all queries => do prefetch and gather! let processed_queries = AtomicUsize::new(0); diff --git a/src/manysearch.rs b/src/manysearch.rs index 5a585597..cef0124e 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -9,7 +9,7 @@ use stats::{median, stddev}; use std::sync::atomic; use std::sync::atomic::AtomicUsize; -use crate::utils::{csvwriter_thread, load_collection, load_sketches, ReportType, SearchResult}; +use crate::utils::{csvwriter_thread, load_collection, ReportType, SearchResult}; use sourmash::ani_utils::ani_from_containment; use sourmash::selection::Selection; use sourmash::signature::SigsTrait; @@ -29,10 +29,11 @@ pub fn manysearch( ReportType::Query, allow_failed_sigpaths, )?; + // load all query sketches into memory, downsampling on the way - let query_sketchlist = load_sketches(query_collection, selection, ReportType::Query).unwrap(); + let query_sketchlist = query_collection.load_sketches(selection)?; - // Against: Load all _paths_, not signatures, into memory. + // Against: Load collection, potentially off disk & not into memory. let against_collection = load_collection( &against_filepath, selection, diff --git a/src/multisearch.rs b/src/multisearch.rs index 19d2264d..cf4bacb8 100644 --- a/src/multisearch.rs +++ b/src/multisearch.rs @@ -6,9 +6,7 @@ use sourmash::signature::SigsTrait; use std::sync::atomic; use std::sync::atomic::AtomicUsize; -use crate::utils::{ - csvwriter_thread, load_collection, load_sketches, MultiSearchResult, ReportType, -}; +use crate::utils::{csvwriter_thread, load_collection, MultiSearchResult, ReportType}; use sourmash::ani_utils::ani_from_containment; /// Search many queries against a list of signatures. @@ -26,14 +24,14 @@ pub fn multisearch( output: Option, ) -> Result<(), Box> { // Load all queries into memory at once. - let query_collection = load_collection( &query_filepath, selection, ReportType::Query, allow_failed_sigpaths, )?; - let queries = load_sketches(query_collection, selection, ReportType::Query).unwrap(); + + let queries = query_collection.load_sketches(selection)?; // Load all against sketches into memory at once. let against_collection = load_collection( @@ -42,7 +40,8 @@ pub fn multisearch( ReportType::Against, allow_failed_sigpaths, )?; - let against = load_sketches(against_collection, selection, ReportType::Against).unwrap(); + + let against = against_collection.load_sketches(selection)?; // set up a multi-producer, single-consumer channel. let (send, recv) = diff --git a/src/pairwise.rs b/src/pairwise.rs index 67acaafe..914c44f3 100644 --- a/src/pairwise.rs +++ b/src/pairwise.rs @@ -4,9 +4,7 @@ use rayon::prelude::*; use std::sync::atomic; use std::sync::atomic::AtomicUsize; -use crate::utils::{ - csvwriter_thread, load_collection, load_sketches, MultiSearchResult, ReportType, -}; +use crate::utils::{csvwriter_thread, load_collection, MultiSearchResult, ReportType}; use sourmash::ani_utils::ani_from_containment; use sourmash::selection::Selection; use sourmash::signature::SigsTrait; @@ -38,7 +36,8 @@ pub fn pairwise( &siglist ) } - let sketches = load_sketches(collection, selection, ReportType::General).unwrap(); + + let sketches = collection.load_sketches(selection)?; // set up a multi-producer, single-consumer channel. let (send, recv) = diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index 2bfb3a59..f444818f 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -653,7 +653,7 @@ def test_simple_hp(runtmp): def test_indexed_against(runtmp, capfd): - # do not accept rocksdb for now @CTB we do now!! + # accept rocksdb against, but with a warning query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') diff --git a/src/utils/mod.rs b/src/utils/mod.rs index 6d4cfc25..aab0fe54 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -30,7 +30,7 @@ use stats::{median, stddev}; use std::collections::{HashMap, HashSet}; pub mod multicollection; -use multicollection::{MultiCollection, SmallSignature}; +use multicollection::MultiCollection; /// Structure to hold overlap information from comparisons. pub struct PrefetchResult { @@ -429,17 +429,6 @@ fn process_prefix_csv( ///////// -// Load all compatible minhashes from a collection into memory, in parallel; -// also store sig name and md5 alongside, as we usually need those -// @CTB switch to using load_sketches method directly! -pub fn load_sketches( - multi: MultiCollection, - selection: &Selection, - _report_type: ReportType, -) -> Result> { - multi.load_sketches(selection) -} - /// Load a collection of sketches from a file, filtering to keep only /// those with a minimum overlap. From d3fa5291c6cc33e1d9a35683d03e0bc3b66a1d66 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 24 Aug 2024 14:55:04 -0700 Subject: [PATCH 41/91] deref doesn't actually make sense for MultiCollection --- src/utils/multicollection.rs | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 40a6ac88..bdf7e59c 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -9,7 +9,6 @@ use log::debug; use std::collections::HashSet; use std::fs::File; use std::io::{BufRead, BufReader}; -use std::ops::Deref; use std::sync::atomic; use std::sync::atomic::AtomicUsize; @@ -279,14 +278,6 @@ impl MultiCollection { } } -impl Deref for MultiCollection { - type Target = Vec; - - fn deref(&self) -> &Self::Target { - &self.collections - } -} - impl Select for MultiCollection { fn select(self, selection: &Selection) -> Result { let collections = self From 5a203816fa4b3e33614d9138aeaa8ba742b5173c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 27 Aug 2024 06:30:43 -0700 Subject: [PATCH 42/91] update to latest sourmash code --- Cargo.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 5e040472..949660fa 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1501,9 +1501,9 @@ dependencies = [ [[package]] name = "serde_json" -version = "1.0.125" +version = "1.0.127" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "83c8e735a073ccf5be70aa8066aa984eaf2fa000db6c8d0100ae605b366d31ed" +checksum = "8043c06d9f82bd7271361ed64f415fe5e12a77fdb52e573e7f06a516dea329ad" dependencies = [ "itoa", "memchr", @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#2c590102f97b12284f40ce4cfbdfe8ef9bd54342" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#c8477dffb6b85b82de41eff5fd4dcfffa7d5f865" dependencies = [ "az", "byteorder", From 6563b0a52dc79e08b398d664be64069fbdeb8bdc Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 27 Aug 2024 06:34:22 -0700 Subject: [PATCH 43/91] update to latest sourmash code --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 949660fa..15995f7f 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#c8477dffb6b85b82de41eff5fd4dcfffa7d5f865" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#6fee40340e8eccb94a89c6d39412e4d88e974253" dependencies = [ "az", "byteorder", From 45608c7fe69d541d461405daaef6c0e3e6272262 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 27 Aug 2024 06:52:37 -0700 Subject: [PATCH 44/91] simplify --- Cargo.lock | 2 +- src/utils/multicollection.rs | 19 +++++-------------- 2 files changed, 6 insertions(+), 15 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 15995f7f..8dbb18a4 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#6fee40340e8eccb94a89c6d39412e4d88e974253" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#06754027ef00170f6aab1655e9fc14df434a6806" dependencies = [ "az", "byteorder", diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index bdf7e59c..ae557cbc 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -93,7 +93,9 @@ impl MultiCollection { (colls, n_failed) } - /// Build from a standalone manifest + /// Build from a standalone manifest. Note: the tricky bit here + /// is that the manifest may select only a subset of the rows, + /// using (name, md5) tuples. pub fn from_standalone_manifest(sigpath: &Path) -> Result { debug!("multi from standalone manifest!"); let file = @@ -110,20 +112,9 @@ impl MultiCollection { let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); - // select out only the (name, md5) pairs that were present - // in the manifest - // @CTB par_iter? - let picklist: HashSet<_> = manifest - .clone() - .iter() - .map(|r| (r.name().clone(), r.md5().clone())) - .collect(); - - // @CTB transfer into MultiCollection too? - // @CTB par_iter? let colls = colls - .iter() - .map(|c| c.clone().select_picklist(&picklist)) + .par_iter() + .map(|c| c.clone().intersect_manifest(&manifest)) .collect(); Ok(MultiCollection::new(colls, false)) From bd256dd4fc153cf4d3a605fcf141b53c9444bf60 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 27 Aug 2024 07:13:27 -0700 Subject: [PATCH 45/91] update to latest sourmash code --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 8dbb18a4..d466ad9c 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#06754027ef00170f6aab1655e9fc14df434a6806" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#17f50efcf45f6b484d0c4e2f807a2bc2903538fd" dependencies = [ "az", "byteorder", From afa0faf21b93fc1b41a4f709ff341881ec747981 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 27 Aug 2024 07:23:48 -0700 Subject: [PATCH 46/91] remove unnecessary flag --- src/python/tests/test_multisearch.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index 5a2c5112..5db15da9 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -591,7 +591,6 @@ def test_empty_query(runtmp, capfd): captured = capfd.readouterr() print(captured.err) assert "No query signatures loaded, exiting." in captured.err - # @CTB def test_nomatch_query_warn(runtmp, capfd, zip_query): From d1205479c0c980d25c1499a3d5def4507361475d Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 8 Sep 2024 23:11:30 -0700 Subject: [PATCH 47/91] MRG: support & test loading of standalone manifests within pathlists (#450) * use recursion to load paths into a MultiCollection => mf support * MRG: clean up index to use `MultiCollection` (#451) * try making index work with standard code * kinda working * fmt * refactor * clear up the tests * refactor/clean up * cargo fmt * add tests for index warning & error * comment --- src/index.rs | 95 ++++++++++-------------- src/python/tests/test_fastgather.py | 4 + src/python/tests/test_fastmultigather.py | 11 ++- src/python/tests/test_index.py | 59 +++++++++++++-- src/python/tests/test_multisearch.py | 29 ++++++++ src/utils/multicollection.rs | 95 +++++++++++++++++++++--- 6 files changed, 220 insertions(+), 73 deletions(-) diff --git a/src/index.rs b/src/index.rs index 00202743..c303b09b 100644 --- a/src/index.rs +++ b/src/index.rs @@ -1,12 +1,9 @@ -use anyhow::Context; -use camino::Utf8PathBuf as PathBuf; use sourmash::index::revindex::RevIndex; use sourmash::index::revindex::RevIndexOps; use sourmash::prelude::*; -use std::fs::File; -use std::io::{BufRead, BufReader}; use std::path::Path; +use crate::utils::{load_collection, ReportType}; use sourmash::collection::{Collection, CollectionSet}; pub fn index>( @@ -14,68 +11,56 @@ pub fn index>( selection: &Selection, output: P, colors: bool, - _allow_failed_sigpaths: bool, + allow_failed_sigpaths: bool, use_internal_storage: bool, ) -> Result<(), Box> { - println!("Loading siglist"); + eprintln!("Loading sketches from {}", siglist); - let collection = match siglist { - x if x.ends_with(".zip") => Collection::from_zipfile(x)?, - x if x.ends_with(".sig") || x.ends_with(".sig.gz") => { - let signatures = Signature::from_path(&x) - .with_context(|| format!("Failed to load signatures from: '{}'", x))?; + let multi = match load_collection( + &siglist, + selection, + ReportType::General, + allow_failed_sigpaths, + ) { + Ok(multi) => multi, + Err(err) => return Err(err.into()), + }; + eprintln!("Found {} sketches total.", multi.len()); - Collection::from_sigs(signatures).with_context(|| { - format!( - "Loaded signatures but failed to load as collection: '{}'", - x - ) - })? + // Try to convert it into a Collection and then CollectionSet. + let collection = match Collection::try_from(multi.clone()) { + // conversion worked! + Ok(c) => { + let cs: CollectionSet = c.select(selection)?.try_into()?; + Ok(cs) } - _ => { - let file = File::open(siglist.clone()) - .with_context(|| format!("Failed to open pathlist file: '{}'", siglist))?; - - let reader = BufReader::new(file); - - // load list of paths - let lines: Vec<_> = reader - .lines() - .filter_map(|line| match line { - Ok(path) => { - let mut filename = PathBuf::new(); - filename.push(path); - Some(filename) - } - Err(_err) => None, - }) - .collect(); - - if lines.is_empty() { - return Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()); + // conversion failed; can we/should we load it into memory? + Err(_) => { + if use_internal_storage { + eprintln!("WARNING: loading all sketches into memory in order to index."); + eprintln!("See 'index' documentation for details."); + let c: Collection = multi.load_all_sigs(selection)?; + let cs: CollectionSet = c.try_into()?; + Ok(cs) } else { - match Collection::from_paths(&lines) { - Ok(collection) => collection, - Err(err) => { - eprintln!("Error in loading from '{}': {}", siglist, err); - return Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()); - } - } + Err( + anyhow::anyhow!("cannot index this type of collection with external storage") + .into(), + ) } } }; - let collection: CollectionSet = collection.select(selection)?.try_into()?; + match collection { + Ok(collection) => { + eprintln!("Indexing {} sketches.", collection.len()); + let mut index = RevIndex::create(output.as_ref(), collection, colors)?; - if collection.is_empty() { - Err(anyhow::anyhow!("Signatures failed to load. Exiting.").into()) - } else { - eprintln!("Indexing {} sketches.", collection.len()); - let mut index = RevIndex::create(output.as_ref(), collection, colors)?; - - if use_internal_storage { - index.internalize_storage()?; + if use_internal_storage { + index.internalize_storage()?; + } + Ok(()) } - Ok(()) + Err(e) => Err(e), } } diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index f444818f..ae26254f 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -16,6 +16,8 @@ def test_installed(runtmp): def test_simple(runtmp, capfd, indexed_query, indexed_against, zip_against, toggle_internal_storage): + if toggle_internal_storage == '--no-internal-storage': + raise pytest.xfail("not implemented") # test basic execution! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') @@ -60,6 +62,8 @@ def test_simple(runtmp, capfd, indexed_query, indexed_against, zip_against, togg def test_simple_with_prefetch(runtmp, zip_against, indexed, toggle_internal_storage): + if toggle_internal_storage == '--no-internal-storage': + raise pytest.xfail("not implemented") # test basic execution! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') diff --git a/src/python/tests/test_fastmultigather.py b/src/python/tests/test_fastmultigather.py index 6a5d99e3..f06f190c 100644 --- a/src/python/tests/test_fastmultigather.py +++ b/src/python/tests/test_fastmultigather.py @@ -203,6 +203,9 @@ def test_simple_read_manifests(runtmp): def test_simple_indexed(runtmp, zip_query, toggle_internal_storage): + if toggle_internal_storage == '--no-internal-storage': + raise pytest.xfail("not implemented") + # test basic execution! query = get_test_data('SRR606249.sig.gz') sig2 = get_test_data('2.fa.sig.gz') @@ -239,6 +242,8 @@ def test_simple_indexed(runtmp, zip_query, toggle_internal_storage): def test_simple_indexed_query_manifest(runtmp, toggle_internal_storage): + if toggle_internal_storage == '--no-internal-storage': + raise pytest.xfail("not implemented") # test basic execution! query = get_test_data('SRR606249.sig.gz') sig2 = get_test_data('2.fa.sig.gz') @@ -273,6 +278,8 @@ def test_simple_indexed_query_manifest(runtmp, toggle_internal_storage): def test_missing_querylist(runtmp, capfd, indexed, zip_query, toggle_internal_storage): + if toggle_internal_storage == '--no-internal-storage': + raise pytest.xfail("not implemented") # test missing querylist query_list = runtmp.output('query.txt') against_list = runtmp.output('against.txt') @@ -1174,7 +1181,9 @@ def test_rocksdb_no_internal_storage_gather_fails(runtmp, capfd): "47.fa.sig.gz", "63.fa.sig.gz"]) - # index! + # index! CTB, note this will fail currently. + raise pytest.xfail("not implemented") + runtmp.sourmash('scripts', 'index', against_list, '--no-internal-storage', '-o', 'subdir/against.rocksdb') diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py index 6f59425e..638913f4 100644 --- a/src/python/tests/test_index.py +++ b/src/python/tests/test_index.py @@ -16,6 +16,9 @@ def test_installed(runtmp): def test_index(runtmp, toggle_internal_storage): + if toggle_internal_storage == "--no-internal-storage": + raise pytest.xfail("not implemented currently") + # test basic index! siglist = runtmp.output('db-sigs.txt') @@ -35,6 +38,49 @@ def test_index(runtmp, toggle_internal_storage): assert 'index is done' in runtmp.last_result.err +def test_index_warning_message(runtmp, capfd): + # test basic index when it has to load things into memory - see #451. + siglist = runtmp.output('db-sigs.txt') + + sig2 = get_test_data('2.fa.sig.gz') + sig47 = get_test_data('47.fa.sig.gz') + sig63 = get_test_data('63.fa.sig.gz') + + make_file_list(siglist, [sig2, sig47, sig63]) + + output = runtmp.output('db.rocksdb') + + runtmp.sourmash('scripts', 'index', siglist, '-o', output) + assert os.path.exists(output) + print(runtmp.last_result.err) + + assert 'index is done' in runtmp.last_result.err + captured = capfd.readouterr() + print(captured.err) + assert "WARNING: loading all sketches into memory in order to index." in captured.err + + +def test_index_error_message(runtmp, capfd): + # test basic index when it errors out b/c can't load + siglist = runtmp.output('db-sigs.txt') + + sig2 = get_test_data('2.fa.sig.gz') + sig47 = get_test_data('47.fa.sig.gz') + sig63 = get_test_data('63.fa.sig.gz') + + make_file_list(siglist, [sig2, sig47, sig63]) + + output = runtmp.output('db.rocksdb') + + with pytest.raises(utils.SourmashCommandFailed): + runtmp.sourmash('scripts', 'index', siglist, '-o', output, + '--no-internal-storage') + + captured = capfd.readouterr() + print(captured.err) + assert "cannot index this type of collection with external storage" in captured.err + + def test_index_protein(runtmp, toggle_internal_storage): sigs = get_test_data('protein.zip') output = runtmp.output('db.rocksdb') @@ -82,10 +128,9 @@ def test_index_missing_siglist(runtmp, capfd, toggle_internal_storage): captured = capfd.readouterr() print(captured.err) - assert 'Failed to open pathlist file:' in captured.err + assert 'Error: No such file or directory: ' in captured.err -@pytest.mark.xfail(reason="not implemented yet") def test_index_sig(runtmp, capfd, toggle_internal_storage): # test index with a .sig.gz file instead of pathlist # (should work now) @@ -101,7 +146,6 @@ def test_index_sig(runtmp, capfd, toggle_internal_storage): assert 'index is done' in runtmp.last_result.err -@pytest.mark.xfail(reason="not implemented yet") def test_index_manifest(runtmp, capfd, toggle_internal_storage): # test index with a manifest file sig2 = get_test_data('2.fa.sig.gz') @@ -118,7 +162,6 @@ def test_index_manifest(runtmp, capfd, toggle_internal_storage): assert 'index is done' in runtmp.last_result.err -@pytest.mark.xfail(reason="needs more work") def test_index_bad_siglist_2(runtmp, capfd): # test with a bad siglist (containing a missing file) against_list = runtmp.output('against.txt') @@ -139,7 +182,6 @@ def test_index_bad_siglist_2(runtmp, capfd): assert "WARNING: could not load sketches from path 'no-exist'" in captured.err -@pytest.mark.xfail(reason="needs more work") def test_index_empty_siglist(runtmp, capfd): # test empty siglist file siglist = runtmp.output('db-sigs.txt') @@ -347,6 +389,8 @@ def test_index_zipfile_bad(runtmp, capfd): def test_index_check(runtmp, toggle_internal_storage): + if toggle_internal_storage == "--no-internal-storage": + raise pytest.xfail("not implemented currently") # test check index siglist = runtmp.output('db-sigs.txt') @@ -367,6 +411,8 @@ def test_index_check(runtmp, toggle_internal_storage): def test_index_check_quick(runtmp, toggle_internal_storage): + if toggle_internal_storage == "--no-internal-storage": + raise pytest.xfail("not implemented currently") # test check index siglist = runtmp.output('db-sigs.txt') @@ -387,6 +433,9 @@ def test_index_check_quick(runtmp, toggle_internal_storage): def test_index_subdir(runtmp, toggle_internal_storage): + if toggle_internal_storage == "--no-internal-storage": + raise pytest.xfail("not implemented currently") + # test basic index & output to subdir siglist = runtmp.output('db-sigs.txt') diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index 5db15da9..8371d6a2 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -256,6 +256,35 @@ def test_simple_ani_list_of_zips(runtmp): assert max_ani == 0.9772 +def test_simple_ani_list_of_csv(runtmp): + # test basic execution against a pathlist file of manifests + query_list = runtmp.output('query.txt') + against_list = runtmp.output('against.txt') + + sig2 = get_test_data('2.sig.zip') + sig47 = get_test_data('47.sig.zip') + sig63 = get_test_data('63.sig.zip') + + runtmp.sourmash('sig', 'collect', sig2, '-o', 'sig2.mf.csv', '-F', 'csv') + runtmp.sourmash('sig', 'collect', sig47, '-o', 'sig47.mf.csv', '-F', 'csv') + runtmp.sourmash('sig', 'collect', sig63, '-o', 'sig63.mf.csv', '-F', 'csv') + + make_file_list(query_list, ['sig2.mf.csv', 'sig47.mf.csv', 'sig63.mf.csv']) + make_file_list(against_list, ['sig2.mf.csv', 'sig47.mf.csv', 'sig63.mf.csv']) + + output = runtmp.output('out.csv') + + runtmp.sourmash('scripts', 'multisearch', query_list, against_list, + '-o', output, '--ani') + assert os.path.exists(output) + + df = pandas.read_csv(output) + assert len(df) == 5 + + dd = df.to_dict(orient='index') + print(dd) + + def test_simple_ani_standalone_manifest(runtmp): # test basic execution of a standalone manifest against_list = runtmp.output('against.sig.zip') diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index ae557cbc..a39f11c1 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -37,17 +37,26 @@ impl MultiCollection { } // Turn a set of paths into list of Collections. - fn load_set_of_paths(paths: HashSet) -> (Vec, usize) { + fn load_set_of_paths(paths: HashSet) -> (MultiCollection, usize) { let n_failed = AtomicUsize::new(0); // could just use a variant of load_collection here? - let colls: Vec<_> = paths + let colls: Vec = paths .par_iter() .filter_map(|iloc| match iloc { // load from zipfile x if x.ends_with(".zip") => { debug!("loading sigs from zipfile {}", x); - Some(Collection::from_zipfile(x).unwrap()) + let coll = Collection::from_zipfile(x).unwrap(); + Some(MultiCollection::from(coll)) + } + // load from CSV + x if x.ends_with(".csv") => { + debug!("vec from pathlist of standalone manifests!"); + + let x: String = x.into(); + let utf_path: &Path = x.as_str().into(); + MultiCollection::from_standalone_manifest(utf_path).ok() } // load from (by default) a sigfile _ => { @@ -77,7 +86,7 @@ impl MultiCollection { .build(), ), ); - Some(collection) + Some(MultiCollection::from(collection)) } None => { eprintln!("WARNING: could not load sketches from path '{}'", iloc); @@ -90,7 +99,7 @@ impl MultiCollection { .collect(); let n_failed = n_failed.load(atomic::Ordering::SeqCst); - (colls, n_failed) + (MultiCollection::from(colls), n_failed) } /// Build from a standalone manifest. Note: the tricky bit here @@ -112,12 +121,9 @@ impl MultiCollection { let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); - let colls = colls - .par_iter() - .map(|c| c.clone().intersect_manifest(&manifest)) - .collect(); + let multi = colls.intersect_manifest(&manifest); - Ok(MultiCollection::new(colls, false)) + Ok(multi) } } @@ -174,9 +180,9 @@ impl MultiCollection { }) .collect(); - let (colls, n_failed) = MultiCollection::load_set_of_paths(lines); + let (multi, n_failed) = MultiCollection::load_set_of_paths(lines); - Ok((MultiCollection::new(colls, false), n_failed)) + Ok((multi, n_failed)) } // Load from a sig file @@ -267,6 +273,36 @@ impl MultiCollection { Ok(sketchinfo) } + + fn intersect_manifest(self, manifest: &Manifest) -> MultiCollection { + let colls = self + .collections + .par_iter() + .map(|c| c.clone().intersect_manifest(&manifest)) + .collect(); + MultiCollection::new(colls, self.contains_revindex) + } + + // Load all sketches into memory, producing an in-memory Collection. + pub fn load_all_sigs(self, selection: &Selection) -> Result { + let all_sigs: Vec = self + .par_iter() + .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { + Ok(sig) => { + let sig = sig.clone().select(selection).ok()?; + Some(Signature::from(sig)) + } + Err(_) => { + eprintln!( + "FAILED to load sketch from '{}'", + record.internal_location() + ); + None + } + }) + .collect(); + Ok(Collection::from_sigs(all_sigs)?) + } } impl Select for MultiCollection { @@ -281,6 +317,41 @@ impl Select for MultiCollection { } } +// Convert a single Collection into a MultiCollection +impl From for MultiCollection { + fn from(coll: Collection) -> Self { + // @CTB check if revindex + MultiCollection::new(vec![coll], false) + } +} + +// Merge a bunch of MultiCollection structs into one +impl From> for MultiCollection { + fn from(multi: Vec) -> Self { + let mut x: Vec = vec![]; + for mc in multi.into_iter() { + for coll in mc.collections.into_iter() { + x.push(coll); + } + } + // @CTB check bool + MultiCollection::new(x, false) + } +} + +// Extract a single Collection from a MultiCollection, if possible +impl TryFrom for Collection { + type Error = &'static str; + + fn try_from(multi: MultiCollection) -> Result { + if multi.collections.len() == 1 { + Ok(multi.collections.into_iter().next().unwrap()) + } else { + Err("More than one Collection in this MultiCollection; cannot convert") + } + } +} + /// Track a name/minhash. pub struct SmallSignature { pub location: String, From 73c7f53c3578aa7808c2792699bd6258d7aa4d2b Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Mon, 9 Sep 2024 09:08:51 -0700 Subject: [PATCH 48/91] MRG: documentation updates based on new collection loading (#444) * update docs for #430 * upd documentation * upd --- doc/README.md | 211 +++++++++++++++++++++++++++++++++++--------------- 1 file changed, 150 insertions(+), 61 deletions(-) diff --git a/doc/README.md b/doc/README.md index 172237da..6863a245 100644 --- a/doc/README.md +++ b/doc/README.md @@ -34,7 +34,7 @@ polish and user experience. sourmash supports a variety of different storage formats for sketches (see [sourmash docs](https://sourmash.readthedocs.io/en/latest/command-line.html#choosing-signature-output-formats)), and the branchwater plugin works with some (but not all) of them. Branchwater _also_ supports an additional database type, a RocksDB-based inverted index, that is not (yet) supported natively by sourmash (through v4.8.11). - +**As of v0.9.8, we recommend using zip files or standalone manifest CSVs pointing to zip files whenever you need to provide multiple sketches.** | command | command input | database format | | -------- | -------- | -------- | @@ -53,62 +53,105 @@ When working with large collections of small sketches such as genomes, we sugges * sketches are compressed in zip files; * zip files can contain many sketches, including incompatible types (e.g. multiple k-mer sizes); -* zip files contain "manifests" listing their contents; -* subsets of zip files can be efficiently selected and loaded depending on what is needed; +* subsets of zip files can be efficiently selected and loaded; * in particular, _single_ sketches can be loaded on demand, supporting lower memory requirements for certain kinds of searches. -For all these reasons, zip files are the most efficient and effective basic storage type for sketches in sourmash, and as of the branchwater plugin v0.9.0, they are fully supported! +For all these reasons, zip files are the most efficient and effective +basic storage type for sketches in sourmash, and as of the branchwater +plugin v0.9.0, they are fully supported! You can create zipfiles with sourmash like so: ``` sourmash sig cat -o sigs.zip ``` - +will collect a list of all of the sketches under `/path/to/sig/files` +and make the list available through a combined manifest. + +Note here that manifests are _much_ smaller than the files containing all +of the sketches! + +Note also that manifests have many advantages over pathlists: in +particular, they contain metadata that enables fast loading of +specific sketches, and they support subsetting from large databases; +pathlists support neither. ### Using RocksDB inverted indexes -The branchwater plugin also supports a database type that is not yet supported by sourmash: inverted indexes stored in a RocksDB database. These indexes provide fast and low-memory lookups when searching very large datasets, and are used for the branchwater petabase scale search hosted at [branchwater.sourmash.bio](https://branchwater.sourmash.bio). +The branchwater plugin also supports a database type that is not yet +supported by sourmash: inverted indexes stored in a RocksDB +database. These indexes provide fast and low-memory lookups when +searching very large datasets, and are used for the branchwater +petabase scale search hosted at +[branchwater.sourmash.bio](https://branchwater.sourmash.bio). -Some commands - `fastmultigather` and `manysearch` - support using these RocksDB-based inverted indexes. They can be created by running `sourmash scripts index`. See [the `index` documentation, below](#Running-index). +Some commands - `fastmultigather` and `manysearch` - support using +these RocksDB-based inverted indexes for efficient search, and they +can be created by running `sourmash scripts index`. See +[the `index` documentation, below](#Running-index). ### Using "pathlists" - +**Note: We no longer recommend using "pathlists". Use zip files or + standalone manifests instead.** You can make a pathlist by listing a collection of .sig.gz files like so: ``` find /path/to/directory/ -name "*.sig.gz" -type f > directory.txt ``` -When using a pathlist for search, we load all signatures into memory at the start in order to generate a manifest. To avoid memory issues, the signatures are not kept in memory, but instead re-loaded as described below for each command (see: Notes on concurrency and efficiency). This makes using pathlists less efficient than `zip` files (as of v0.9.0). - - - +When using a pathlist for search, we load all signatures into memory +at the start in order to generate a manifest. To avoid memory issues, +the signatures are not kept in memory, but instead re-loaded as +described below for each command (see: Notes on concurrency and +efficiency). This makes using pathlists less efficient than `zip` +files (as of v0.9.0) or manifests (as of v0.9.8). ## Running the commands @@ -185,34 +228,37 @@ The `name` column will not be used. Instead, each sketch will be named from the ### Running `multisearch` and `pairwise` -The `multisearch` command compares one or more query genomes, and one or more subject genomes. It differs from `manysearch` by loading all genomes into memory. +The `multisearch` command compares one or more query genomes, and one or more subject genomes. It differs from `manysearch` because it loads everything into memory. `multisearch` takes two input collections and outputs a CSV: ``` sourmash scripts multisearch query.sig.gz database.zip -o results.csv ``` +The results file `results.csv`, will have 8 columns: `query` and +`query_md5`, `match` and `match_md5`, and `containment`, `jaccard`, +`max_containment`, and `intersect_hashes`. -The results file `results.csv`, will have 8 columns: `query` and `query_md5`, `match` and `match_md5`, and `containment`, `jaccard`, `max_containment`, and `intersect_hashes`. - -The `pairwise` command does the same comparisons as `multisearch` but takes -only a single collection of sketches, for which it calculates all the pairwise comparisons. Since the comparisons are symmetric, it is approximately -twice as fast as `multisearch`. +The `pairwise` command does the same comparisons as `multisearch` but +takes only a single collection of sketches, for which it calculates +all the pairwise comparisons. Since the comparisons are symmetric, it +is approximately twice as fast as `multisearch`. The `-t/--threshold` for `multisearch` and `pairwise` applies to the -containment of query-in-target and defaults to 0.01. To report -_any_ overlap between two sketches, set the threshold to 0. +containment of query-in-target and defaults to 0.01. To report _any_ +overlap between two sketches, set the threshold to 0. ### Running `fastgather` -The `fastgather` command is a much faster version of `sourmash gather`. +The `fastgather` command is parallelized (and typically much faster) +version of `sourmash gather`. `fastgather` takes a single query metagenome and a database, and outputs a CSV: ``` sourmash scripts fastgather query.sig.gz database.zip -o results.csv --cores 4 ``` -As of v0.9.5, `fastgather` outputs the same columns as `sourmash gather`, with only a few exceptions: +As of v0.9.5, `fastgather` outputs the same columns as `sourmash gather`, with only a few exception * `match_name` is output instead of `name`; * `match_md5` is output instead of `md5`; * `match_filename` is output instead of `filename`, and the value is different; @@ -224,33 +270,56 @@ As of v0.9.5, `fastgather` outputs the same columns as `sourmash gather`, with o ``` sourmash scripts fastmultigather queries.manifest.csv database.zip --cores 4 --save-matches ``` - -The main advantage that `fastmultigather` has over running `fastgather` on multiple queries is that `fastmultigather` only needs to load the database once for all queries, unlike with `fastgather`; this can be a significant time savings for large databases! +We suggest using standalone manifest CSVs wherever possible, especially if +the queries are large. + +The main advantage that `fastmultigather` has over running +`fastgather` on multiple queries is that `fastmultigather` only needs +to load the database once for all queries, unlike with `fastgather`; +this can be a significant time savings for large databases. #### Output files for `fastmultigather` -On a database of sketches (but not on RocksDB indexes) `fastmultigather` will output two CSV files for each query, a `prefetch` file containing all overlapping matches between that query and the database, and a `gather` file containing the minimum metagenome cover for that query in the database. +On a database of sketches (but not on RocksDB indexes) +`fastmultigather` will output two CSV files for each query, a +`prefetch` file containing all overlapping matches between that query +and the database, and a `gather` file containing the minimum +metagenome cover for that query in the database. -The prefetch CSV will be named `{signame}.prefetch.csv`, and the gather CSV will be named `{signame}.gather.csv`. Here, `{signame}` is the name of your sourmash signature. +The prefetch CSV will be named `{signame}.prefetch.csv`, and the +gather CSV will be named `{signame}.gather.csv`. Here, `{signame}` is +the name of your sourmash signature. -`--save-matches` is an optional flag that will save the matched hashes for each query in a separate sourmash signature `{signame}.matches.sig`. This can be useful for debugging or for further analysis. +`--save-matches` is an optional flag that will save the matched hashes +for each query in a separate sourmash signature +`{signame}.matches.sig`. This can be useful for debugging or for +further analysis. -When searching against a RocksDB index, `fastmultigather` will output a single file containing all gather results, specified with `-o/--output`. No prefetch results will be output. +When searching against a RocksDB index, `fastmultigather` will output +a single file containing all gather results, specified with +`-o/--output`. No prefetch results will be output. `fastmultigather` gather CSVs provide the same columns as `fastgather`, above. -**Warning:** At the moment, if two different queries have the same `{signame}`, the CSVs for one of the queries will be overwritten by the other query. The behavior here is undefined in practice, because of multithreading: we don't know what queries will be executed when or files will be written first. +**Warning:** At the moment, if two different queries have the same + `{signame}`, the CSVs for one of the queries will be overwritten by + the other query. The behavior here is undefined in practice, because + of multithreading: we don't know what queries will be executed when + or files will be written first. ### Running `manysearch` -The `manysearch` command compares one or more collections of query sketches, and one or more collections of subject sketches. It is the core command we use for searching petabase-scale databases of metagenomes for contained genomes. +The `manysearch` command compares one or more collections of query +sketches, and one or more collections of subject sketches. It is the +core command we use for searching petabase-scale databases of +metagenomes for contained genomes. `manysearch` takes two collections as input, and outputs a CSV: ``` sourmash scripts manysearch queries.zip metagenomes.manifest.csv -o results.csv ``` - +We suggest using a manifest CSV for the metagenome collection. The results file here, `query.x.gtdb-reps.csv`, will have the following columns: `query`, `query_md5`, `match_name`, `match_md5`, @@ -264,7 +333,8 @@ following columns: , `match_containment_ani`, Finally, if using sketches that have abundance information, the results file will also contain the following columns: `average_abund`, -`median_abund`, `std_abund`, `n_weighted_found`, and `total_weighted_hashes`. +`median_abund`, `std_abund`, `n_weighted_found`, and +`total_weighted_hashes`. See [the prefetch CSV output column documentation](https://sourmash.readthedocs.io/en/latest/classifying-signatures.html#appendix-e-prefetch-csv-output-columns) @@ -282,11 +352,16 @@ when executing large searches. ### Running `cluster` -The `cluster` command conducts graph-based clustering via the sequence similarity measures in `pairwise` or `multisearch` outputs. It is a new command and we are exploring its utility. +The `cluster` command conducts graph-based clustering via the sequence +similarity measures in `pairwise` or `multisearch` outputs. It is a +new command and we are exploring its utility. -`cluster` takes the csv output of `pairwise` or `multisearch` input, and outputs two CSVs: +`cluster` takes the csv output of `pairwise` or `multisearch` input, +and outputs two CSVs: -1. `-o`, `--output` will contain the names of the clusters and the `ident` of each sequence included in the cluster (e.g. `Component_1, name1;name2`) +1. `-o`, `--output` will contain the names of the clusters and the + `ident` of each sequence included in the cluster + (e.g. `Component_1, name1;name2`) ``` cluster,nodes @@ -294,7 +369,9 @@ Component_1,name1;name2;name3 Component_2,name4 ``` -2. `--cluster-sizes` will contain information on cluster size, with a counts for the number of clusters of that size. For the two clusters above, the counts would look like this: +2. `--cluster-sizes` will contain information on cluster size, with a + counts for the number of clusters of that size. For the two + clusters above, the counts would look like this: ``` cluster_size,count @@ -302,13 +379,17 @@ cluster_size,count 1,1 ``` -`cluster` takes a `--similarity_column` argument to specify which of the similarity columns, with the following choices: `containment`, `max_containment`, `jaccard`, `average_containment_ani`, `maximum_containment_ani`. All values should be input as fractions (e.g. 0.9 for 90%) +`cluster` takes a `--similarity_column` argument to specify which of +the similarity columns, with the following choices: `containment`, +`max_containment`, `jaccard`, `average_containment_ani`, +`maximum_containment_ani`. All values should be input as fractions +(e.g. 0.9 for 90%) ### Running `index` The `index` subcommand creates a RocksDB inverted index that can be -used as a database for `manysearch` (containment queries into -mixtures) and `fastmultigather` (mixture decomposition against a +used as an efficient database for `manysearch` (containment queries +into mixtures) and `fastmultigather` (mixture decomposition against a database of genomes). RocksDB inverted indexes support fast, low-latency, and low-memory @@ -332,6 +413,13 @@ disk space required for large databases. You can provide an optional reduces the disk space needed for the index. Read below for technical details! +As of v0.9.8, `index` can take any of the supported input types, but +unless you are using a zip file, it may need to load all the sketches +into memory before indexing them. Moreover, you can only use external +storage with a zip file. We are working on improving this; see +[issue #415](https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/415) +for details. + #### Internal vs external storage of sketches in a RocksDB index (The below applies to v0.9.7 and later of the plugin; for v0.9.6 and @@ -380,9 +468,10 @@ if better support for relative paths is of interest! #### Links and more materials Note that RocksDB indexes are implemented in the core -[sourmash Rust library](https://crates.io/crates/sourmash), and -used in downstream software packages (this plugin, and -[the branchwater application code](https://github.com/sourmash-bio/branchwater)). The above documentation applies to sourmash core v0.15.0. +[sourmash Rust library](https://crates.io/crates/sourmash), and used +in downstream software packages (this plugin, and +[the branchwater application code](https://github.com/sourmash-bio/branchwater)). +The above documentation applies to sourmash core v0.15.0. ## Notes on concurrency and efficiency From 74d73679229e3455787d6c0740aca618e79cc933 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 10 Sep 2024 16:16:55 -0700 Subject: [PATCH 49/91] Update src/lib.rs Co-authored-by: Tessa Pierce Ward --- src/lib.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/lib.rs b/src/lib.rs index e9d5e298..711eec49 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,4 +1,4 @@ -//! Rust-to-Pyton interface code for sourmash_plugin_branchwater, using pyo3. +//! Rust-to-Python interface code for sourmash_plugin_branchwater, using pyo3. //! //! If you're using Rust, you're probably most interested in //! [utils](utils/index.html) From 4e28d644ea290b6d279956236a7034ca2dceac89 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 10 Sep 2024 16:20:03 -0700 Subject: [PATCH 50/91] switch unwrap to expect --- src/fastgather.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fastgather.rs b/src/fastgather.rs index e4271249..d5d8d598 100644 --- a/src/fastgather.rs +++ b/src/fastgather.rs @@ -33,7 +33,7 @@ pub fn fastgather( ) } // get single query sig and minhash - let query_sig = query_collection.get_first_sig().unwrap(); + let query_sig = query_collection.get_first_sig().expect("no queries!?"); let query_sig_ds = query_sig.clone().select(selection)?; // downsample let query_mh = match query_sig_ds.minhash() { Some(query_mh) => query_mh, From de35cd5e30ad7536400634a03a147ffa1afb0770 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 10 Sep 2024 16:27:36 -0700 Subject: [PATCH 51/91] move unwrap to expect --- src/utils/multicollection.rs | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index a39f11c1..0d79b99b 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -47,7 +47,7 @@ impl MultiCollection { // load from zipfile x if x.ends_with(".zip") => { debug!("loading sigs from zipfile {}", x); - let coll = Collection::from_zipfile(x).unwrap(); + let coll = Collection::from_zipfile(x).expect("nothing to load!?"); Some(MultiCollection::from(coll)) } // load from CSV @@ -345,6 +345,7 @@ impl TryFrom for Collection { fn try_from(multi: MultiCollection) -> Result { if multi.collections.len() == 1 { + // this must succeed b/c len > 0 Ok(multi.collections.into_iter().next().unwrap()) } else { Err("More than one Collection in this MultiCollection; cannot convert") From 1e5ac07cc5d07d18483fc03eab881e0bb889ce42 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 10 Sep 2024 16:46:02 -0700 Subject: [PATCH 52/91] minor cleanup --- src/fastmultigather.rs | 3 +-- src/utils/multicollection.rs | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index c09531ae..251fd04b 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -49,8 +49,7 @@ pub fn fastmultigather( 1 } } - .try_into() - .unwrap(); + .try_into()?; println!("threshold overlap: {} {}", threshold_hashes, threshold_bp); diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 0d79b99b..0e1fd2a3 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -224,7 +224,7 @@ impl MultiCollection { // first create a Vec of all triples (Collection, Idx, Record) let s: Vec<_> = self .collections - .iter() + .iter() // CTB: are we loading things into memory here? No... .flat_map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) .collect(); // then return a parallel iterator over the Vec. From 388a49a28b2e6fb1b306e93cfdd8fb44fb024d1a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 10 Sep 2024 17:25:42 -0700 Subject: [PATCH 53/91] cargo fmt --- src/utils/multicollection.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 0e1fd2a3..08b37199 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -224,7 +224,7 @@ impl MultiCollection { // first create a Vec of all triples (Collection, Idx, Record) let s: Vec<_> = self .collections - .iter() // CTB: are we loading things into memory here? No... + .iter() // CTB: are we loading things into memory here? No... .flat_map(|c| c.iter().map(move |(_idx, record)| (c, _idx, record))) .collect(); // then return a parallel iterator over the Vec. From 7be18834f09a3ee1b98a77c7d9c786d3730fde12 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 06:21:07 -0700 Subject: [PATCH 54/91] provide legacy method to avoid xfail on index loading --- src/python/tests/test_fastgather.py | 4 -- src/python/tests/test_fastmultigather.py | 10 ---- src/python/tests/test_index.py | 16 ++---- src/python/tests/test_multisearch.py | 2 +- src/utils/multicollection.rs | 64 +++++++++++++++++++++++- 5 files changed, 67 insertions(+), 29 deletions(-) diff --git a/src/python/tests/test_fastgather.py b/src/python/tests/test_fastgather.py index ae26254f..f444818f 100644 --- a/src/python/tests/test_fastgather.py +++ b/src/python/tests/test_fastgather.py @@ -16,8 +16,6 @@ def test_installed(runtmp): def test_simple(runtmp, capfd, indexed_query, indexed_against, zip_against, toggle_internal_storage): - if toggle_internal_storage == '--no-internal-storage': - raise pytest.xfail("not implemented") # test basic execution! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') @@ -62,8 +60,6 @@ def test_simple(runtmp, capfd, indexed_query, indexed_against, zip_against, togg def test_simple_with_prefetch(runtmp, zip_against, indexed, toggle_internal_storage): - if toggle_internal_storage == '--no-internal-storage': - raise pytest.xfail("not implemented") # test basic execution! query = get_test_data('SRR606249.sig.gz') against_list = runtmp.output('against.txt') diff --git a/src/python/tests/test_fastmultigather.py b/src/python/tests/test_fastmultigather.py index f06f190c..7bc54b3c 100644 --- a/src/python/tests/test_fastmultigather.py +++ b/src/python/tests/test_fastmultigather.py @@ -203,9 +203,6 @@ def test_simple_read_manifests(runtmp): def test_simple_indexed(runtmp, zip_query, toggle_internal_storage): - if toggle_internal_storage == '--no-internal-storage': - raise pytest.xfail("not implemented") - # test basic execution! query = get_test_data('SRR606249.sig.gz') sig2 = get_test_data('2.fa.sig.gz') @@ -242,8 +239,6 @@ def test_simple_indexed(runtmp, zip_query, toggle_internal_storage): def test_simple_indexed_query_manifest(runtmp, toggle_internal_storage): - if toggle_internal_storage == '--no-internal-storage': - raise pytest.xfail("not implemented") # test basic execution! query = get_test_data('SRR606249.sig.gz') sig2 = get_test_data('2.fa.sig.gz') @@ -278,8 +273,6 @@ def test_simple_indexed_query_manifest(runtmp, toggle_internal_storage): def test_missing_querylist(runtmp, capfd, indexed, zip_query, toggle_internal_storage): - if toggle_internal_storage == '--no-internal-storage': - raise pytest.xfail("not implemented") # test missing querylist query_list = runtmp.output('query.txt') against_list = runtmp.output('against.txt') @@ -1181,9 +1174,6 @@ def test_rocksdb_no_internal_storage_gather_fails(runtmp, capfd): "47.fa.sig.gz", "63.fa.sig.gz"]) - # index! CTB, note this will fail currently. - raise pytest.xfail("not implemented") - runtmp.sourmash('scripts', 'index', against_list, '--no-internal-storage', '-o', 'subdir/against.rocksdb') diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py index 638913f4..990fccb9 100644 --- a/src/python/tests/test_index.py +++ b/src/python/tests/test_index.py @@ -16,9 +16,6 @@ def test_installed(runtmp): def test_index(runtmp, toggle_internal_storage): - if toggle_internal_storage == "--no-internal-storage": - raise pytest.xfail("not implemented currently") - # test basic index! siglist = runtmp.output('db-sigs.txt') @@ -42,7 +39,8 @@ def test_index_warning_message(runtmp, capfd): # test basic index when it has to load things into memory - see #451. siglist = runtmp.output('db-sigs.txt') - sig2 = get_test_data('2.fa.sig.gz') + # note: can't use zip w/o breaking index. See sourmash-bio/sourmash#3321. + sig2 = get_test_data('2.sig.zip') sig47 = get_test_data('47.fa.sig.gz') sig63 = get_test_data('63.fa.sig.gz') @@ -64,7 +62,8 @@ def test_index_error_message(runtmp, capfd): # test basic index when it errors out b/c can't load siglist = runtmp.output('db-sigs.txt') - sig2 = get_test_data('2.fa.sig.gz') + # note: can't use zip w/o breaking index. See sourmash-bio/sourmash#3321. + sig2 = get_test_data('2.sig.zip') sig47 = get_test_data('47.fa.sig.gz') sig63 = get_test_data('63.fa.sig.gz') @@ -389,8 +388,6 @@ def test_index_zipfile_bad(runtmp, capfd): def test_index_check(runtmp, toggle_internal_storage): - if toggle_internal_storage == "--no-internal-storage": - raise pytest.xfail("not implemented currently") # test check index siglist = runtmp.output('db-sigs.txt') @@ -411,8 +408,6 @@ def test_index_check(runtmp, toggle_internal_storage): def test_index_check_quick(runtmp, toggle_internal_storage): - if toggle_internal_storage == "--no-internal-storage": - raise pytest.xfail("not implemented currently") # test check index siglist = runtmp.output('db-sigs.txt') @@ -433,9 +428,6 @@ def test_index_check_quick(runtmp, toggle_internal_storage): def test_index_subdir(runtmp, toggle_internal_storage): - if toggle_internal_storage == "--no-internal-storage": - raise pytest.xfail("not implemented currently") - # test basic index & output to subdir siglist = runtmp.output('db-sigs.txt') diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index 8371d6a2..ba01b3c6 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -387,7 +387,7 @@ def test_simple_manifest(runtmp): assert len(df) == 3 -@pytest.mark.xfail(reason="not implemented yet") +#@pytest.mark.xfail(reason="not implemented yet") def test_lists_of_standalone_manifests(runtmp): # test pathlists of manifests query_list = runtmp.output('query.txt') diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 08b37199..b57ece98 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -36,7 +36,55 @@ impl MultiCollection { } } - // Turn a set of paths into list of Collections. + // Try loading a set of paths as JSON files only - filters on sig/sig.gz + // extensions. This is a legacy method that supports pathlists for + // building RocksDB. See sourmash-bio/sourmash#3321 for background. + // + // NOTE: this could potentially have very poor performance if there are + // a lot of _good_ files, with one _bad_ one. Look into exiting first loop + // early. + fn load_set_of_json_files(paths: &HashSet) -> Result { + // load sketches from paths in parallel. + let n_failed = AtomicUsize::new(0); + let records: Vec = paths + .par_iter() + .filter_map(|path| match Signature::from_path(path) { + Ok(signatures) => { + let recs: Vec = signatures + .into_iter() + .flat_map(|v| Record::from_sig(&v, path)) + .collect(); + Some(recs) + } + Err(_) => { + let _ = n_failed.fetch_add(1, atomic::Ordering::SeqCst); + None + } + }) + .flatten() + .collect(); + + let n_failed = n_failed.load(atomic::Ordering::SeqCst); + + if records.is_empty() || n_failed > 0 { + return Err(anyhow!("cannot load everything as JSON files")); + } + + let manifest: Manifest = records.into(); + let collection = Collection::new( + manifest, + InnerStorage::new( + FSStorage::builder() + .fullpath("".into()) + .subdir("".into()) + .build(), + ), + ); + Ok(MultiCollection::from(collection)) + } + + // Turn a set of paths into list of Collections - works recursively + // if needed, and can handle paths of any supported type. fn load_set_of_paths(paths: HashSet) -> (MultiCollection, usize) { let n_failed = AtomicUsize::new(0); @@ -180,7 +228,19 @@ impl MultiCollection { }) .collect(); - let (multi, n_failed) = MultiCollection::load_set_of_paths(lines); + let val = MultiCollection::load_set_of_json_files(&lines); + + let (multi, n_failed) = match val { + Ok(collection) => { + eprintln!("SUCCEEDED in loading as JSON files, woot woot"); + // CTB note: if anything fails to load, this fn returns Err. + (collection, 0) + } + Err(_) => { + eprintln!("FAILED to load as JSON files; falling back to general recursive"); + MultiCollection::load_set_of_paths(lines) // @CTB borrow? + } + }; Ok((multi, n_failed)) } From 679b9722668d2214232163e94162f0551c516a42 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 06:23:42 -0700 Subject: [PATCH 55/91] switch to using reference --- src/utils/multicollection.rs | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index b57ece98..87b36fbe 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -36,13 +36,16 @@ impl MultiCollection { } } - // Try loading a set of paths as JSON files only - filters on sig/sig.gz - // extensions. This is a legacy method that supports pathlists for - // building RocksDB. See sourmash-bio/sourmash#3321 for background. + // Try loading a set of paths as JSON files only. Fails on any Err. // - // NOTE: this could potentially have very poor performance if there are - // a lot of _good_ files, with one _bad_ one. Look into exiting first loop - // early. + // This is a legacy method that supports pathlists for + // 'index'. See sourmash-bio/sourmash#3321 for background. + // + // Use load_set_of_paths for full generality! + // + // CTB NOTE: this could potentially have very poor performance if + // there are a lot of _good_ files, with one _bad_ one. Look into + // exiting first loop early. fn load_set_of_json_files(paths: &HashSet) -> Result { // load sketches from paths in parallel. let n_failed = AtomicUsize::new(0); @@ -85,7 +88,7 @@ impl MultiCollection { // Turn a set of paths into list of Collections - works recursively // if needed, and can handle paths of any supported type. - fn load_set_of_paths(paths: HashSet) -> (MultiCollection, usize) { + fn load_set_of_paths(paths: &HashSet) -> (MultiCollection, usize) { let n_failed = AtomicUsize::new(0); // could just use a variant of load_collection here? @@ -167,7 +170,7 @@ impl MultiCollection { Err(anyhow!("could not read as manifest: '{}'", sigpath)) } else { let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); - let (colls, _n_failed) = MultiCollection::load_set_of_paths(ilocs); + let (colls, _n_failed) = MultiCollection::load_set_of_paths(&ilocs); let multi = colls.intersect_manifest(&manifest); @@ -233,12 +236,13 @@ impl MultiCollection { let (multi, n_failed) = match val { Ok(collection) => { eprintln!("SUCCEEDED in loading as JSON files, woot woot"); - // CTB note: if anything fails to load, this fn returns Err. + // CTB note: if any path fails to load, + // load_set_of_json_files returns Err. (collection, 0) } Err(_) => { eprintln!("FAILED to load as JSON files; falling back to general recursive"); - MultiCollection::load_set_of_paths(lines) // @CTB borrow? + MultiCollection::load_set_of_paths(&lines) } }; From a9143d026f74eb190a09cae5ac881064a7babcf8 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 06:29:45 -0700 Subject: [PATCH 56/91] update docs to reflect pathlist behavior --- doc/README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/doc/README.md b/doc/README.md index 6863a245..931adea1 100644 --- a/doc/README.md +++ b/doc/README.md @@ -414,11 +414,13 @@ reduces the disk space needed for the index. Read below for technical details! As of v0.9.8, `index` can take any of the supported input types, but -unless you are using a zip file, it may need to load all the sketches -into memory before indexing them. Moreover, you can only use external -storage with a zip file. We are working on improving this; see +unless you are using a zip file or a pathlist of JSON files, it may +need to load all the sketches into memory before indexing +them. Moreover, you can only use external storage with a zip file. We +are working on improving this; see [issue #415](https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/415) -for details. +for details. A warning will be printed to stderr in situations where +the sketches are being loaded into memory. #### Internal vs external storage of sketches in a RocksDB index From 574cd28b54260795df18df8d3b95b4f4093045ef Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 06:41:55 -0700 Subject: [PATCH 57/91] test recursive nature of MultiCollection --- src/python/tests/test_index.py | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py index 990fccb9..105c1cb2 100644 --- a/src/python/tests/test_index.py +++ b/src/python/tests/test_index.py @@ -80,6 +80,36 @@ def test_index_error_message(runtmp, capfd): assert "cannot index this type of collection with external storage" in captured.err +def test_index_recursive(runtmp, capfd): + # test index of pathlist containing standalone manifest containing zip. + # a little ridiculous, but should hit the various branches in + # MultiCollection::load + siglist = runtmp.output('db-sigs.txt') + + # our basic list of sketches... + sig2_zip = get_test_data('2.sig.zip') + sig47 = get_test_data('47.fa.sig.gz') + sig63 = get_test_data('63.fa.sig.gz') + + # generate a standalone mf containing a sip + standalone_mf = runtmp.output('stand-mf.csv') + runtmp.sourmash('sig', 'collect', '-F', 'csv', '-o', standalone_mf, + sig2_zip) + + # now make a file list containing that mf + make_file_list(siglist, [standalone_mf, sig47, sig63]) + + output = runtmp.output('db.rocksdb') + + runtmp.sourmash('scripts', 'index', siglist, '-o', output) + + captured = capfd.readouterr() + print(captured.err) + assert "WARNING: loading all sketches into memory in order to index." in captured.err + assert 'index is done' in runtmp.last_result.err + assert 'Indexing 3 sketches.' in captured.err + + def test_index_protein(runtmp, toggle_internal_storage): sigs = get_test_data('protein.zip') output = runtmp.output('db.rocksdb') From a5b4299ec9a0cb010a9ad856071af2a9b8fa53d0 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 06:45:49 -0700 Subject: [PATCH 58/91] re-enable test that is now passing --- src/python/tests/test_multisearch.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py index ba01b3c6..8763c688 100644 --- a/src/python/tests/test_multisearch.py +++ b/src/python/tests/test_multisearch.py @@ -387,8 +387,7 @@ def test_simple_manifest(runtmp): assert len(df) == 3 -#@pytest.mark.xfail(reason="not implemented yet") -def test_lists_of_standalone_manifests(runtmp): +def test_lists_of_standalone_manifests(runtmp, capfd): # test pathlists of manifests query_list = runtmp.output('query.txt') against_list = runtmp.output('against.txt') @@ -422,6 +421,9 @@ def test_lists_of_standalone_manifests(runtmp): df = pandas.read_csv(output) assert len(df) == 3 + captured = capfd.readouterr() + print(captured.err) + def test_missing_query(runtmp, capfd, zip_query): # test with a missing query list From 74b9ae621645d2a2edda5d5ac1f2d4ebedc76382 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 17:20:36 -0700 Subject: [PATCH 59/91] update to latest sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index ff98cbb0..533adf1a 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#17f50efcf45f6b484d0c4e2f807a2bc2903538fd" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#2146f307f239705146a5f9e8860653e6f9d551a9" dependencies = [ "az", "byteorder", From 9df421dfc9595bb48c75064bb65479a26c1ab378 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 15 Sep 2024 18:12:17 -0700 Subject: [PATCH 60/91] upd sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 533adf1a..27eb715b 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1551,7 +1551,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#2146f307f239705146a5f9e8860653e6f9d551a9" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#32839ae5a5ee35442abc6002728b25454d965c70" dependencies = [ "az", "byteorder", From 847917f44817b36aa46316e491af497b181d1312 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 17 Sep 2024 08:36:47 -0700 Subject: [PATCH 61/91] update sourmash --- Cargo.lock | 75 ++++++++++++++++++++++-------------------------------- 1 file changed, 31 insertions(+), 44 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index bb282561..0ab9dfbf 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -198,7 +198,7 @@ dependencies = [ "regex", "rustc-hash", "shlex", - "syn 2.0.66", + "syn", ] [[package]] @@ -431,7 +431,7 @@ checksum = "67e77553c4162a157adbf834ebae5b415acbecbeafc7a74b0e886657506a7611" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -448,7 +448,7 @@ checksum = "97369cbbc041bc366949bc74d34658d6cda5621039731c6310521892a3a20ae0" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -472,7 +472,7 @@ dependencies = [ "once_cell", "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -560,14 +560,14 @@ dependencies = [ [[package]] name = "getset" -version = "0.1.2" +version = "0.1.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e45727250e75cc04ff2846a66397da8ef2b3db8e40e0cef4df67950a07621eb9" +checksum = "f636605b743120a8d32ed92fc27b6cde1a769f8f936c065151eb66f88ded513c" dependencies = [ - "proc-macro-error", + "proc-macro-error2", "proc-macro2", "quote", - "syn 1.0.109", + "syn", ] [[package]] @@ -838,9 +838,9 @@ checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3" [[package]] name = "memmap2" -version = "0.9.4" +version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322" +checksum = "fd3f7eed9d3848f8b98834af67102b720745c4ec028fcd0aa0239277e7de374f" dependencies = [ "libc", ] @@ -901,7 +901,7 @@ checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1046,7 +1046,7 @@ dependencies = [ "proc-macro2", "proc-macro2-diagnostics", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1142,7 +1142,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5f12335488a2f3b0a83b14edad48dca9879ce89b2edd10e80237e4e852dd645e" dependencies = [ "proc-macro2", - "syn 2.0.66", + "syn", ] [[package]] @@ -1166,27 +1166,25 @@ dependencies = [ ] [[package]] -name = "proc-macro-error" -version = "1.0.4" +name = "proc-macro-error-attr2" +version = "2.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c" +checksum = "96de42df36bb9bba5542fe9f1a054b8cc87e172759a1868aa05c1f3acc89dfc5" dependencies = [ - "proc-macro-error-attr", "proc-macro2", "quote", - "syn 1.0.109", - "version_check", ] [[package]] -name = "proc-macro-error-attr" -version = "1.0.4" +name = "proc-macro-error2" +version = "2.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869" +checksum = "11ec05c52be0a07b08061f7dd003e7d7092e0472bc731b4af7bb1ef876109802" dependencies = [ + "proc-macro-error-attr2", "proc-macro2", "quote", - "version_check", + "syn", ] [[package]] @@ -1206,7 +1204,7 @@ checksum = "af066a9c399a26e020ada66a034357a868728e72cd426f3adcd35f80d88d88c8" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", "version_check", "yansi", ] @@ -1259,7 +1257,7 @@ dependencies = [ "proc-macro2", "pyo3-macros-backend", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1272,7 +1270,7 @@ dependencies = [ "proc-macro2", "pyo3-build-config", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1496,7 +1494,7 @@ checksum = "243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1551,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#32839ae5a5ee35442abc6002728b25454d965c70" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#9c267528977fab0bb04dc1da86c47290bff68bf8" dependencies = [ "az", "byteorder", @@ -1649,17 +1647,6 @@ dependencies = [ "num-traits", ] -[[package]] -name = "syn" -version = "1.0.109" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237" -dependencies = [ - "proc-macro2", - "quote", - "unicode-ident", -] - [[package]] name = "syn" version = "2.0.66" @@ -1713,7 +1700,7 @@ checksum = "46c3384250002a6d5af4d114f2845d37b57521033f30d5c3f46c4d70e1197533" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1744,7 +1731,7 @@ checksum = "1f718dfaf347dcb5b983bfc87608144b0bad87970aebcbea5ce44d2a30c08e63" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] @@ -1835,7 +1822,7 @@ dependencies = [ "once_cell", "proc-macro2", "quote", - "syn 2.0.66", + "syn", "wasm-bindgen-shared", ] @@ -1857,7 +1844,7 @@ checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", "wasm-bindgen-backend", "wasm-bindgen-shared", ] @@ -2011,7 +1998,7 @@ checksum = "15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b" dependencies = [ "proc-macro2", "quote", - "syn 2.0.66", + "syn", ] [[package]] From 9733d474e21283a641e197272e831491e365440e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 18 Sep 2024 05:50:07 -0700 Subject: [PATCH 62/91] mut MultiCollection --- Cargo.lock | 2 +- src/utils/multicollection.rs | 17 +++++++---------- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 0ab9dfbf..57b5a590 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#9c267528977fab0bb04dc1da86c47290bff68bf8" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#9b9e17e791e3d0cd89a254b1701f821bdd460108" dependencies = [ "az", "byteorder", diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 87b36fbe..ddad2b15 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -170,11 +170,11 @@ impl MultiCollection { Err(anyhow!("could not read as manifest: '{}'", sigpath)) } else { let ilocs: HashSet<_> = manifest.internal_locations().map(String::from).collect(); - let (colls, _n_failed) = MultiCollection::load_set_of_paths(&ilocs); + let (mut colls, _n_failed) = MultiCollection::load_set_of_paths(&ilocs); - let multi = colls.intersect_manifest(&manifest); + colls.intersect_manifest(&manifest); - Ok(multi) + Ok(colls) } } @@ -338,13 +338,10 @@ impl MultiCollection { Ok(sketchinfo) } - fn intersect_manifest(self, manifest: &Manifest) -> MultiCollection { - let colls = self - .collections - .par_iter() - .map(|c| c.clone().intersect_manifest(&manifest)) - .collect(); - MultiCollection::new(colls, self.contains_revindex) + fn intersect_manifest(&mut self, manifest: &Manifest) -> () { + for coll in self.collections.iter_mut() { + coll.intersect_manifest(&manifest); + } } // Load all sketches into memory, producing an in-memory Collection. From 019fd1b0bb5b0183e562ce246dfabba072b00b1a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 18 Sep 2024 05:53:50 -0700 Subject: [PATCH 63/91] cleanup --- Cargo.lock | 2 +- src/utils/multicollection.rs | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 57b5a590..66be049c 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#9b9e17e791e3d0cd89a254b1701f821bdd460108" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#aa109f804e62672c5e7bc20d4267334eb4bca0e8" dependencies = [ "az", "byteorder", diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index ddad2b15..3460a45d 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -338,9 +338,9 @@ impl MultiCollection { Ok(sketchinfo) } - fn intersect_manifest(&mut self, manifest: &Manifest) -> () { + fn intersect_manifest(&mut self, manifest: &Manifest) { for coll in self.collections.iter_mut() { - coll.intersect_manifest(&manifest); + coll.intersect_manifest(manifest); } } From 780fbda5edea0487c5966df01beb1294799eac1e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 21 Sep 2024 10:25:23 -0700 Subject: [PATCH 64/91] update after merge of sourmash-bio/sourmash#3305 --- Cargo.lock | 2 +- Cargo.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 66be049c..62e68c3b 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=remove_unwrap#aa109f804e62672c5e7bc20d4267334eb4bca0e8" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=latest#ada039a691092c620b16a032f1160c2621105d92" dependencies = [ "az", "byteorder", diff --git a/Cargo.toml b/Cargo.toml index 3a90db91..ee57507f 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -11,7 +11,7 @@ crate-type = ["cdylib"] [dependencies] pyo3 = { version = "0.22.3", features = ["extension-module", "anyhow"] } rayon = "1.10.0" -sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "remove_unwrap", features = ["branchwater"] } +sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "latest", features = ["branchwater"] } serde = { version = "1.0.210", features = ["derive"] } serde_json = "1.0.128" niffler = "2.4.0" From 84934a7ca58a0b8f45f2c4a7c242a9b15f58d28b Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 22 Sep 2024 06:56:10 -0700 Subject: [PATCH 65/91] fix contains_revindex --- src/utils/multicollection.rs | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 3460a45d..1bc4a230 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -25,7 +25,7 @@ use sourmash::storage::{FSStorage, InnerStorage, SigStore}; #[derive(Clone)] pub struct MultiCollection { collections: Vec, - pub contains_revindex: bool, + pub contains_revindex: bool, // track whether one or more Collection is a RevIndex } impl MultiCollection { @@ -381,7 +381,7 @@ impl Select for MultiCollection { // Convert a single Collection into a MultiCollection impl From for MultiCollection { fn from(coll: Collection) -> Self { - // @CTB check if revindex + // CTB: how can we check if revindex? MultiCollection::new(vec![coll], false) } } @@ -390,13 +390,14 @@ impl From for MultiCollection { impl From> for MultiCollection { fn from(multi: Vec) -> Self { let mut x: Vec = vec![]; + let mut contains_revindex = false; for mc in multi.into_iter() { for coll in mc.collections.into_iter() { x.push(coll); } + contains_revindex = contains_revindex || mc.contains_revindex; } - // @CTB check bool - MultiCollection::new(x, false) + MultiCollection::new(x, contains_revindex) } } From 56fb948d915a1f098963b63796443e790b13c9cc Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 22 Sep 2024 07:23:04 -0700 Subject: [PATCH 66/91] add trace commands for tracing loading --- src/fastmultigather.rs | 12 +++++++++++- src/utils/multicollection.rs | 9 ++++++++- 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index 251fd04b..cf70326f 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -2,7 +2,7 @@ use anyhow::Result; use rayon::prelude::*; -use sourmash::prelude::ToWriter; +use sourmash::prelude::{Storage, ToWriter}; use sourmash::{selection::Selection, signature::SigsTrait}; use std::sync::atomic; @@ -15,6 +15,8 @@ use camino::Utf8Path as PathBuf; use std::collections::HashSet; use std::fs::File; +use log::trace; + use sourmash::signature::Signature; use sourmash::sketch::minhash::KmerMinHash; use sourmash::sketch::Sketch; @@ -33,6 +35,8 @@ pub fn fastmultigather( save_matches: bool, create_empty_results: bool, ) -> Result<()> { + let _ = env_logger::try_init(); + // load query collection let query_collection = load_collection( &query_filepath, @@ -72,6 +76,12 @@ pub fn fastmultigather( // increment counter of # of queries. q: could we instead use the _idx from par_iter(), or will it vary based on thread? let _i = processed_queries.fetch_add(1, atomic::Ordering::SeqCst); // Load query sig (downsampling happens here) + trace!( + "fastmultigather query load: from:{} idx:{} loc:{}", + c.storage().spec(), + _idx, + record.internal_location() + ); match c.sig_from_record(record) { Ok(query_sig) => { let name = query_sig.name(); diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index 1bc4a230..b9fa53ce 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -1,11 +1,12 @@ //! MultiCollection implementation to handle sketches coming from multiple files. use rayon::prelude::*; +use sourmash::prelude::*; use anyhow::{anyhow, Context, Result}; use camino::Utf8Path as Path; use camino::Utf8PathBuf; -use log::debug; +use log::{debug, trace}; use std::collections::HashSet; use std::fs::File; use std::io::{BufRead, BufReader}; @@ -315,6 +316,12 @@ impl MultiCollection { .par_iter() .filter_map(|(coll, _idx, record)| match coll.sig_from_record(record) { Ok(sig) => { + trace!( + "MultiCollection load sketch: from:{} idx:{} loc:{}", + coll.storage().spec(), + _idx, + record.internal_location() + ); let selected_sig = sig.clone().select(selection).ok()?; let minhash = selected_sig.minhash()?.clone(); From 6550683741c6c9f897ba114486edce8b3bee4086 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 25 Sep 2024 15:09:29 -0700 Subject: [PATCH 67/91] use released version of sourmash --- Cargo.lock | 5 +++-- Cargo.toml | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 62e68c3b..cdae4f21 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1548,8 +1548,9 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" -version = "0.15.1" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=latest#ada039a691092c620b16a032f1160c2621105d92" +version = "0.15.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9a73bae93170d8d0f816e18b6a630d76e134b90958850985ee2f0fb2f641d4de" dependencies = [ "az", "byteorder", diff --git a/Cargo.toml b/Cargo.toml index ee57507f..77b32793 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -11,7 +11,7 @@ crate-type = ["cdylib"] [dependencies] pyo3 = { version = "0.22.3", features = ["extension-module", "anyhow"] } rayon = "1.10.0" -sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "latest", features = ["branchwater"] } +sourmash = { version = "0.15.2", features = ["branchwater"] } serde = { version = "1.0.210", features = ["derive"] } serde_json = "1.0.128" niffler = "2.4.0" From b510e8e1620e4dc273513cf1632cbaa6f020cdac Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 2 Oct 2024 06:05:27 -0700 Subject: [PATCH 68/91] add support for ignoring abundance --- src/lib.rs | 7 ++++++- src/manysearch.rs | 3 ++- src/python/sourmash_plugin_branchwater/__init__.py | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/src/lib.rs b/src/lib.rs index 40789191..26c62f09 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -24,7 +24,7 @@ mod singlesketch; use camino::Utf8PathBuf as PathBuf; #[pyfunction] -#[pyo3(signature = (querylist_path, siglist_path, threshold, ksize, scaled, moltype, output_path=None))] +#[pyo3(signature = (querylist_path, siglist_path, threshold, ksize, scaled, moltype, output_path=None, ignore_abundance=false))] fn do_manysearch( querylist_path: String, siglist_path: String, @@ -33,14 +33,18 @@ fn do_manysearch( scaled: usize, moltype: String, output_path: Option, + ignore_abundance: Option ) -> anyhow::Result { let againstfile_path: PathBuf = siglist_path.clone().into(); let selection = build_selection(ksize, scaled, &moltype); eprintln!("selection scaled: {:?}", selection.scaled()); let allow_failed_sigpaths = true; + let ignore_abundance = ignore_abundance.unwrap_or(false); + // if siglist_path is revindex, run mastiff_manysearch; otherwise run manysearch if is_revindex_database(&againstfile_path) { + // note: mastiff_manysearch ignores abundance automatically. match mastiff_manysearch::mastiff_manysearch( querylist_path, againstfile_path, @@ -63,6 +67,7 @@ fn do_manysearch( threshold, output_path, allow_failed_sigpaths, + ignore_abundance, ) { Ok(_) => Ok(0), Err(e) => { diff --git a/src/manysearch.rs b/src/manysearch.rs index a200b52d..e7703fdd 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -21,6 +21,7 @@ pub fn manysearch( threshold: f64, output: Option, allow_failed_sigpaths: bool, + ignore_abundance: bool, ) -> Result<()> { // Load query collection let query_collection = load_collection( @@ -72,7 +73,7 @@ pub fn manysearch( if let Some(against_mh) = against_sig.minhash() { for query in query_sketchlist.iter() { // to do - let user choose? - let calc_abund_stats = against_mh.track_abundance(); + let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).unwrap(); let overlap = diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py index 4280a257..2efc0bc6 100755 --- a/src/python/sourmash_plugin_branchwater/__init__.py +++ b/src/python/sourmash_plugin_branchwater/__init__.py @@ -65,6 +65,8 @@ def __init__(self, p): p.add_argument('-N', '--no-pretty-print', action='store_false', dest='pretty_print', help="do not display results (e.g. for large output)") + p.add_argument('--ignore-abundance', action='store_true', + help="do not do expensive abundance calculations") def main(self, args): print_version() @@ -80,7 +82,8 @@ def main(self, args): args.ksize, args.scaled, args.moltype, - args.output) + args.output, + args.ignore_abundance) if status == 0: notify(f"...manysearch is done! results in '{args.output}'") From 0993b39c6377f289c0ec199a3aecc53cc326928d Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Wed, 2 Oct 2024 06:14:22 -0700 Subject: [PATCH 69/91] cargo fmt --- src/lib.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/lib.rs b/src/lib.rs index 26c62f09..1c7379d8 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -33,7 +33,7 @@ fn do_manysearch( scaled: usize, moltype: String, output_path: Option, - ignore_abundance: Option + ignore_abundance: Option, ) -> anyhow::Result { let againstfile_path: PathBuf = siglist_path.clone().into(); let selection = build_selection(ksize, scaled, &moltype); From ac82fb355a9aab5315da66c9b573a482fd6d6de7 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 4 Oct 2024 06:22:54 -0700 Subject: [PATCH 70/91] avoid downsampling until we know there is overlap --- src/lib.rs | 1 - src/manysearch.rs | 11 +++++------ 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/lib.rs b/src/lib.rs index 1c7379d8..0f653337 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,6 +1,5 @@ /// Python interface Rust code for sourmash_plugin_branchwater. use pyo3::prelude::*; -use singlesketch::singlesketch; #[macro_use] extern crate simple_error; diff --git a/src/manysearch.rs b/src/manysearch.rs index e7703fdd..725124a8 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -72,15 +72,14 @@ pub fn manysearch( Ok(against_sig) => { if let Some(against_mh) = against_sig.minhash() { for query in query_sketchlist.iter() { - // to do - let user choose? - let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; - - let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).unwrap(); - let overlap = - query.minhash.count_common(&against_mh_ds, false).unwrap() as f64; + // avoid calculating details unless there is overlap + let overlap = query.minhash.count_common(against_mh, false).expect("incompatible sketches") as f64; // only calculate results if we have shared hashes if overlap > 0.0 { + let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; + + let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); let query_size = query.minhash.size() as f64; let containment_query_in_target = overlap / query_size; if containment_query_in_target > threshold { From 7ea9a402674d0d5ee68c1be58f9a5757dc30b5df Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 11:44:46 -0700 Subject: [PATCH 71/91] change downsample to true; add panic assertion --- src/manysearch.rs | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index 725124a8..d73bd998 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -73,7 +73,7 @@ pub fn manysearch( if let Some(against_mh) = against_sig.minhash() { for query in query_sketchlist.iter() { // avoid calculating details unless there is overlap - let overlap = query.minhash.count_common(against_mh, false).expect("incompatible sketches") as f64; + let overlap = query.minhash.count_common(against_mh, true).expect("incompatible sketches") as f64; // only calculate results if we have shared hashes if overlap > 0.0 { @@ -104,6 +104,7 @@ pub fn manysearch( let max_containment_ani = Some(f64::max(qani, mani)); let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { + panic!("should not be reached."); match query.minhash.inflated_abundances(&against_mh_ds) { Ok((abunds, sum_weighted_overlap)) => { let sum_all_abunds = against_mh_ds.sum_abunds() as usize; From 03b9da0f84a3298760ce984ec5f3b9638f2c8d04 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 12:42:11 -0700 Subject: [PATCH 72/91] move downsampling side guard --- src/manysearch.rs | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index d73bd998..dd43ee65 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -79,7 +79,6 @@ pub fn manysearch( if overlap > 0.0 { let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; - let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); let query_size = query.minhash.size() as f64; let containment_query_in_target = overlap / query_size; if containment_query_in_target > threshold { @@ -105,6 +104,8 @@ pub fn manysearch( let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { panic!("should not be reached."); + let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); + match query.minhash.inflated_abundances(&against_mh_ds) { Ok((abunds, sum_weighted_overlap)) => { let sum_all_abunds = against_mh_ds.sum_abunds() as usize; From b954daabea0d0d9879a2d9764ff56f0cc1fd48cd Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 13:39:03 -0700 Subject: [PATCH 73/91] eliminate redundant overlap check --- src/manysearch.rs | 128 ++++++++++++++++++++++------------------------ 1 file changed, 62 insertions(+), 66 deletions(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index dd43ee65..324f91eb 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -75,74 +75,70 @@ pub fn manysearch( // avoid calculating details unless there is overlap let overlap = query.minhash.count_common(against_mh, true).expect("incompatible sketches") as f64; + let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; + let query_size = query.minhash.size() as f64; + let containment_query_in_target = overlap / query_size; // only calculate results if we have shared hashes - if overlap > 0.0 { - let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; - - let query_size = query.minhash.size() as f64; - let containment_query_in_target = overlap / query_size; - if containment_query_in_target > threshold { - let target_size = against_mh.size() as f64; - let containment_target_in_query = overlap / target_size; - - let max_containment = - containment_query_in_target.max(containment_target_in_query); - let jaccard = overlap / (target_size + query_size - overlap); - - let qani = ani_from_containment( - containment_query_in_target, - against_mh.ksize() as f64, - ); - let mani = ani_from_containment( - containment_target_in_query, - against_mh.ksize() as f64, - ); - let query_containment_ani = Some(qani); - let match_containment_ani = Some(mani); - let average_containment_ani = Some((qani + mani) / 2.); - let max_containment_ani = Some(f64::max(qani, mani)); - - let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { - panic!("should not be reached."); - let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); - - match query.minhash.inflated_abundances(&against_mh_ds) { - Ok((abunds, sum_weighted_overlap)) => { - let sum_all_abunds = against_mh_ds.sum_abunds() as usize; - let average_abund = sum_weighted_overlap as f64 / abunds.len() as f64; - let median_abund = median(abunds.iter().cloned()).unwrap(); - let std_abund = stddev(abunds.iter().cloned()); - (Some(sum_all_abunds), Some(sum_weighted_overlap as usize), Some(average_abund), Some(median_abund), Some(std_abund)) - } - Err(e) => { - eprintln!("Error calculating abundances for query: {}, against: {}; Error: {}", query.name, against_sig.name(), e); - continue; - } + if containment_query_in_target > threshold { + let target_size = against_mh.size() as f64; + let containment_target_in_query = overlap / target_size; + + let max_containment = + containment_query_in_target.max(containment_target_in_query); + let jaccard = overlap / (target_size + query_size - overlap); + + let qani = ani_from_containment( + containment_query_in_target, + against_mh.ksize() as f64, + ); + let mani = ani_from_containment( + containment_target_in_query, + against_mh.ksize() as f64, + ); + let query_containment_ani = Some(qani); + let match_containment_ani = Some(mani); + let average_containment_ani = Some((qani + mani) / 2.); + let max_containment_ani = Some(f64::max(qani, mani)); + + let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { + let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); + + match query.minhash.inflated_abundances(&against_mh_ds) { + Ok((abunds, sum_weighted_overlap)) => { + let sum_all_abunds = against_mh_ds.sum_abunds() as usize; + let average_abund = sum_weighted_overlap as f64 / abunds.len() as f64; + let median_abund = median(abunds.iter().cloned()).unwrap(); + let std_abund = stddev(abunds.iter().cloned()); + (Some(sum_all_abunds), Some(sum_weighted_overlap as usize), Some(average_abund), Some(median_abund), Some(std_abund)) } - } else { - (None, None, None, None, None) - }; - - results.push(SearchResult { - query_name: query.name.clone(), - query_md5: query.md5sum.clone(), - match_name: against_sig.name(), - containment: containment_query_in_target, - intersect_hashes: overlap as usize, - match_md5: Some(against_sig.md5sum()), - jaccard: Some(jaccard), - max_containment: Some(max_containment), - average_abund, - median_abund, - std_abund, - query_containment_ani, - match_containment_ani, - average_containment_ani, - max_containment_ani, - n_weighted_found, - total_weighted_hashes, - }); - } + Err(e) => { + eprintln!("Error calculating abundances for query: {}, against: {}; Error: {}", query.name, against_sig.name(), e); + continue; + } + } + } else { + (None, None, None, None, None) + }; + + results.push(SearchResult { + query_name: query.name.clone(), + query_md5: query.md5sum.clone(), + match_name: against_sig.name(), + containment: containment_query_in_target, + intersect_hashes: overlap as usize, + match_md5: Some(against_sig.md5sum()), + jaccard: Some(jaccard), + max_containment: Some(max_containment), + average_abund, + median_abund, + std_abund, + query_containment_ani, + match_containment_ani, + average_containment_ani, + max_containment_ani, + n_weighted_found, + total_weighted_hashes, + }); } } } else { From b0bcc660b2b191ad820e5ba0ee63de376f37ff71 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 13:39:43 -0700 Subject: [PATCH 74/91] move calc_abund_stats --- src/manysearch.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index 324f91eb..82b7f5a3 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -75,7 +75,6 @@ pub fn manysearch( // avoid calculating details unless there is overlap let overlap = query.minhash.count_common(against_mh, true).expect("incompatible sketches") as f64; - let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; let query_size = query.minhash.size() as f64; let containment_query_in_target = overlap / query_size; // only calculate results if we have shared hashes @@ -100,6 +99,7 @@ pub fn manysearch( let average_containment_ani = Some((qani + mani) / 2.); let max_containment_ani = Some(f64::max(qani, mani)); + let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); From a2871c0d58d4d3bddde224479d0e49376d100ad2 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 14:34:46 -0700 Subject: [PATCH 75/91] extract abundance code into own function; avoid downsampling if poss --- src/manysearch.rs | 49 ++++++++++++++++++++++++++++++++--------------- 1 file changed, 34 insertions(+), 15 deletions(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index 82b7f5a3..d93b3eb6 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -13,6 +13,9 @@ use crate::utils::{csvwriter_thread, load_collection, load_sketches, ReportType, use sourmash::ani_utils::ani_from_containment; use sourmash::selection::Selection; use sourmash::signature::SigsTrait; +use sourmash::sketch::minhash::KmerMinHash; +use sourmash::errors::SourmashError; + pub fn manysearch( query_filepath: String, @@ -101,21 +104,11 @@ pub fn manysearch( let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { - let against_mh_ds = against_mh.downsample_scaled(query.minhash.scaled()).expect("cannot downsample sketch"); - - match query.minhash.inflated_abundances(&against_mh_ds) { - Ok((abunds, sum_weighted_overlap)) => { - let sum_all_abunds = against_mh_ds.sum_abunds() as usize; - let average_abund = sum_weighted_overlap as f64 / abunds.len() as f64; - let median_abund = median(abunds.iter().cloned()).unwrap(); - let std_abund = stddev(abunds.iter().cloned()); - (Some(sum_all_abunds), Some(sum_weighted_overlap as usize), Some(average_abund), Some(median_abund), Some(std_abund)) - } - Err(e) => { - eprintln!("Error calculating abundances for query: {}, against: {}; Error: {}", query.name, against_sig.name(), e); - continue; - } - } + downsample_and_inflate_abundances(&query.minhash, against_mh).ok()? +// Err(e) => { +// eprintln!("Error calculating abundances for query: {}, against: {}; Error: {}", query.name, against_sig.name(), e); +// continue; +// } } else { (None, None, None, None, None) }; @@ -195,3 +188,29 @@ pub fn manysearch( Ok(()) } + + +fn downsample_and_inflate_abundances(query: &KmerMinHash, against: &KmerMinHash) -> Result<(Option, Option, Option, Option, Option), SourmashError> { + let query_scaled = query.scaled(); + let against_scaled = against.scaled(); + + let abunds: Vec; + let sum_weighted: u64; + let sum_all_abunds : usize; + + // avoid downsampling if we can + if against_scaled != query_scaled { + let against_ds = against.downsample_scaled(query.scaled()).expect("cannot downsample sketch"); + (abunds, sum_weighted) = query.inflated_abundances(&against_ds)?; + sum_all_abunds = against_ds.sum_abunds() as usize; + } else { + (abunds, sum_weighted) = query.inflated_abundances(against)?; + sum_all_abunds = against.sum_abunds() as usize; + } + + let average_abund = sum_weighted as f64 / abunds.len() as f64; + let median_abund = median(abunds.iter().cloned()).expect("error"); + let std_abund = stddev(abunds.iter().cloned()); + + Ok((Some(sum_all_abunds), Some(sum_weighted as usize), Some(average_abund), Some(median_abund), Some(std_abund))) +} From d853ef38a4367b475608592bed972d10f44d0c1c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 14:35:34 -0700 Subject: [PATCH 76/91] cleanup --- src/manysearch.rs | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index d93b3eb6..d453c857 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -105,10 +105,6 @@ pub fn manysearch( let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { downsample_and_inflate_abundances(&query.minhash, against_mh).ok()? -// Err(e) => { -// eprintln!("Error calculating abundances for query: {}, against: {}; Error: {}", query.name, against_sig.name(), e); -// continue; -// } } else { (None, None, None, None, None) }; From 453f943351c6c702235e1b085cd04d3616b1a09a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 5 Oct 2024 19:06:43 -0400 Subject: [PATCH 77/91] fmt --- src/manysearch.rs | 52 +++++++++++++++++++++++++++++++++++++---------- 1 file changed, 41 insertions(+), 11 deletions(-) diff --git a/src/manysearch.rs b/src/manysearch.rs index d453c857..d343493d 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -11,11 +11,10 @@ use std::sync::atomic::AtomicUsize; use crate::utils::{csvwriter_thread, load_collection, load_sketches, ReportType, SearchResult}; use sourmash::ani_utils::ani_from_containment; +use sourmash::errors::SourmashError; use sourmash::selection::Selection; use sourmash::signature::SigsTrait; use sourmash::sketch::minhash::KmerMinHash; -use sourmash::errors::SourmashError; - pub fn manysearch( query_filepath: String, @@ -76,7 +75,11 @@ pub fn manysearch( if let Some(against_mh) = against_sig.minhash() { for query in query_sketchlist.iter() { // avoid calculating details unless there is overlap - let overlap = query.minhash.count_common(against_mh, true).expect("incompatible sketches") as f64; + let overlap = query + .minhash + .count_common(against_mh, true) + .expect("incompatible sketches") + as f64; let query_size = query.minhash.size() as f64; let containment_query_in_target = overlap / query_size; @@ -102,9 +105,17 @@ pub fn manysearch( let average_containment_ani = Some((qani + mani) / 2.); let max_containment_ani = Some(f64::max(qani, mani)); - let calc_abund_stats = against_mh.track_abundance() && !ignore_abundance; - let (total_weighted_hashes, n_weighted_found, average_abund, median_abund, std_abund) = if calc_abund_stats { - downsample_and_inflate_abundances(&query.minhash, against_mh).ok()? + let calc_abund_stats = + against_mh.track_abundance() && !ignore_abundance; + let ( + total_weighted_hashes, + n_weighted_found, + average_abund, + median_abund, + std_abund, + ) = if calc_abund_stats { + downsample_and_inflate_abundances(&query.minhash, against_mh) + .ok()? } else { (None, None, None, None, None) }; @@ -185,18 +196,31 @@ pub fn manysearch( Ok(()) } - -fn downsample_and_inflate_abundances(query: &KmerMinHash, against: &KmerMinHash) -> Result<(Option, Option, Option, Option, Option), SourmashError> { +fn downsample_and_inflate_abundances( + query: &KmerMinHash, + against: &KmerMinHash, +) -> Result< + ( + Option, + Option, + Option, + Option, + Option, + ), + SourmashError, +> { let query_scaled = query.scaled(); let against_scaled = against.scaled(); let abunds: Vec; let sum_weighted: u64; - let sum_all_abunds : usize; + let sum_all_abunds: usize; // avoid downsampling if we can if against_scaled != query_scaled { - let against_ds = against.downsample_scaled(query.scaled()).expect("cannot downsample sketch"); + let against_ds = against + .downsample_scaled(query.scaled()) + .expect("cannot downsample sketch"); (abunds, sum_weighted) = query.inflated_abundances(&against_ds)?; sum_all_abunds = against_ds.sum_abunds() as usize; } else { @@ -208,5 +232,11 @@ fn downsample_and_inflate_abundances(query: &KmerMinHash, against: &KmerMinHash) let median_abund = median(abunds.iter().cloned()).expect("error"); let std_abund = stddev(abunds.iter().cloned()); - Ok((Some(sum_all_abunds), Some(sum_weighted as usize), Some(average_abund), Some(median_abund), Some(std_abund))) + Ok(( + Some(sum_all_abunds), + Some(sum_weighted as usize), + Some(average_abund), + Some(median_abund), + Some(std_abund), + )) } From 69fd38bed0db859786a4f55c6b16f14a46f8746c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 11 Oct 2024 09:57:03 -0400 Subject: [PATCH 78/91] update to next sourmash release --- Cargo.lock | 5 ++--- Cargo.toml | 3 ++- src/manysearch.rs | 1 + src/utils.rs | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index f4acf157..968f5cea 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1548,9 +1548,8 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" -version = "0.15.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9a73bae93170d8d0f816e18b6a630d76e134b90958850985ee2f0fb2f641d4de" +version = "0.16.0" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#9b9fc5a4d40521e14390766fb6ffde4c6921062c" dependencies = [ "az", "byteorder", diff --git a/Cargo.toml b/Cargo.toml index 7935aa38..7dbc99cf 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,8 @@ crate-type = ["cdylib"] pyo3 = { version = "0.22.3", features = ["extension-module", "anyhow"] } rayon = "1.10.0" serde = { version = "1.0.210", features = ["derive"] } -sourmash = { version = "0.15.2", features = ["branchwater"] } +#sourmash = { version = "0.15.2", features = ["branchwater"] } +sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "refactor_rs_downsample", features = ["branchwater"] } serde_json = "1.0.128" niffler = "2.4.0" log = "0.4.22" diff --git a/src/manysearch.rs b/src/manysearch.rs index d343493d..199af8b5 100644 --- a/src/manysearch.rs +++ b/src/manysearch.rs @@ -219,6 +219,7 @@ fn downsample_and_inflate_abundances( // avoid downsampling if we can if against_scaled != query_scaled { let against_ds = against + .clone() .downsample_scaled(query.scaled()) .expect("cannot downsample sketch"); (abunds, sum_weighted) = query.inflated_abundances(&against_ds)?; diff --git a/src/utils.rs b/src/utils.rs index 33f78316..f0a81d5f 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -478,7 +478,7 @@ pub fn load_sketches_above_threshold( if let Ok(against_sig) = against_collection.sig_from_record(against_record) { if let Some(against_mh) = against_sig.minhash() { // downsample against_mh, but keep original md5sum - let against_mh_ds = against_mh.downsample_scaled(query.scaled()).unwrap(); + let against_mh_ds = against_mh.clone().downsample_scaled(query.scaled()).unwrap(); if let Ok(overlap) = against_mh_ds.count_common(query, false) { if overlap >= threshold_hashes { let result = PrefetchResult { From ee580b683ae9f5564b5c48c8e70cda4586c8fbe9 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 11 Oct 2024 10:04:16 -0400 Subject: [PATCH 79/91] cargo fmt --- src/utils.rs | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/utils.rs b/src/utils.rs index f0a81d5f..a702378f 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -478,7 +478,10 @@ pub fn load_sketches_above_threshold( if let Ok(against_sig) = against_collection.sig_from_record(against_record) { if let Some(against_mh) = against_sig.minhash() { // downsample against_mh, but keep original md5sum - let against_mh_ds = against_mh.clone().downsample_scaled(query.scaled()).unwrap(); + let against_mh_ds = against_mh + .clone() + .downsample_scaled(query.scaled()) + .unwrap(); if let Ok(overlap) = against_mh_ds.count_common(query, false) { if overlap >= threshold_hashes { let result = PrefetchResult { From 981405166f6e4c341242357db28c1b58beddbe5e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 11 Oct 2024 15:53:16 -0400 Subject: [PATCH 80/91] upd sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 968f5cea..7e2264f7 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.16.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#9b9fc5a4d40521e14390766fb6ffde4c6921062c" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#79afb857967d5f48393341a77e43ea27ab3caf22" dependencies = [ "az", "byteorder", From d27b03e8e677a6b96d866ea2c89208dcc7135aa4 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 11 Oct 2024 16:38:32 -0400 Subject: [PATCH 81/91] correct numbers --- Cargo.lock | 2 +- src/python/tests/test_fastmultigather.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 7e2264f7..7b1eb621 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.16.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#79afb857967d5f48393341a77e43ea27ab3caf22" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ddcb049e99749f1d16c414e0fdb2d06d55a38db7" dependencies = [ "az", "byteorder", diff --git a/src/python/tests/test_fastmultigather.py b/src/python/tests/test_fastmultigather.py index f485b7f0..653b0ba5 100644 --- a/src/python/tests/test_fastmultigather.py +++ b/src/python/tests/test_fastmultigather.py @@ -959,7 +959,7 @@ def test_indexed_full_output(runtmp): # check a few columns average_ani = set(df['average_containment_ani']) avg_ani = set([round(x, 4) for x in average_ani]) - assert avg_ani == {0.8502, 0.8584, 0.8602} + assert avg_ani == {0.9221, 0.9306, 0.9316} # @CTB check against py gather f_unique_weighted = set(df['f_unique_weighted']) f_unique_weighted = set([round(x, 4) for x in f_unique_weighted]) @@ -967,7 +967,7 @@ def test_indexed_full_output(runtmp): unique_intersect_bp = set(df['unique_intersect_bp']) unique_intersect_bp = set([round(x,4) for x in unique_intersect_bp]) - assert unique_intersect_bp == {44000, 18000, 22000} + assert unique_intersect_bp == {4400000, 1800000, 2200000} def test_nonindexed_full_vs_sourmash_gather(runtmp): From e35111a7d2a6a5c510a23b04f8bb091a4ca30e76 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 12 Oct 2024 06:08:38 -0400 Subject: [PATCH 82/91] upd sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 7b1eb621..da608df5 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.16.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ddcb049e99749f1d16c414e0fdb2d06d55a38db7" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#6eb86a390c53fc243bf65dd38fab3d1712c9f579" dependencies = [ "az", "byteorder", From 4778862e9def28528a7e9cc65d8d75c6ec2dc9f0 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 12 Oct 2024 06:24:42 -0400 Subject: [PATCH 83/91] upd sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index da608df5..f1218059 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.16.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#6eb86a390c53fc243bf65dd38fab3d1712c9f579" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#62f03eb3de8f4b05307efad74f321ced04de40f1" dependencies = [ "az", "byteorder", From 2563b0b605af33ddb7f453b4b594c6c9807c2fdf Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 12 Oct 2024 07:05:42 -0400 Subject: [PATCH 84/91] upd sourmash --- Cargo.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/Cargo.toml b/Cargo.toml index 5e28367b..ace206e3 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -15,7 +15,6 @@ serde = { version = "1.0.210", features = ["derive"] } #sourmash = { version = "0.15.2", features = ["branchwater"] } sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "refactor_rs_downsample", features = ["branchwater"] } serde_json = "1.0.128" -sourmash = { version = "0.15.2", features = ["branchwater"] } niffler = "2.4.0" log = "0.4.22" env_logger = { version = "0.11.5" } From a0e02efb86ad084e1fcd18585a5f71253ca105ad Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 07:19:58 -0400 Subject: [PATCH 85/91] upd sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index f1218059..a56788cf 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.16.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#62f03eb3de8f4b05307efad74f321ced04de40f1" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#e4e5555fd81a9a8677bbe065cf7f528270b01fed" dependencies = [ "az", "byteorder", From 9b448c8a873e9fde1bc4cb84f441863078677eb9 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 07:29:52 -0400 Subject: [PATCH 86/91] use new try_into() and eliminate several clone()s --- src/utils.rs | 38 ++++++++++++++++++++------------------ 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/src/utils.rs b/src/utils.rs index a702378f..0b7df6c9 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -476,28 +476,30 @@ pub fn load_sketches_above_threshold( let mut results = Vec::new(); // Load against into memory if let Ok(against_sig) = against_collection.sig_from_record(against_record) { - if let Some(against_mh) = against_sig.minhash() { - // downsample against_mh, but keep original md5sum - let against_mh_ds = against_mh - .clone() - .downsample_scaled(query.scaled()) - .unwrap(); - if let Ok(overlap) = against_mh_ds.count_common(query, false) { - if overlap >= threshold_hashes { - let result = PrefetchResult { - name: against_record.name().to_string(), - md5sum: against_mh.md5sum(), - minhash: against_mh_ds.clone(), - location: against_record.internal_location().to_string(), - overlap, - }; - results.push(result); - } + let against_filename = against_sig.filename(); + let against_mh: KmerMinHash = against_sig.try_into().expect("cannot get sketch"); + let against_md5 = against_mh.md5sum(); // keep original md5sum + + let against_mh_ds = against_mh + .downsample_scaled(query.scaled()) + .expect("cannot downsample sketch"); + + // good? ok, store as candidate from prefetch. + if let Ok(overlap) = against_mh_ds.count_common(query, false) { + if overlap >= threshold_hashes { + let result = PrefetchResult { + name: against_record.name().to_string(), + md5sum: against_md5, + minhash: against_mh_ds, + location: against_record.internal_location().to_string(), + overlap, + }; + results.push(result); } } else { eprintln!( "WARNING: no compatible sketches in path '{}'", - against_sig.filename() + against_filename ); let _i = skipped_paths.fetch_add(1, atomic::Ordering::SeqCst); } From 4a780f4dadea8bcbfbc17d174d2dd59ea1475337 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 07:56:58 -0400 Subject: [PATCH 87/91] refactor a bit more --- src/fastgather.rs | 7 +- src/fastmultigather.rs | 141 +++++++++++++++++++++-------------------- src/utils/mod.rs | 10 +-- 3 files changed, 85 insertions(+), 73 deletions(-) diff --git a/src/fastgather.rs b/src/fastgather.rs index d5d8d598..67a2f341 100644 --- a/src/fastgather.rs +++ b/src/fastgather.rs @@ -34,6 +34,8 @@ pub fn fastgather( } // get single query sig and minhash let query_sig = query_collection.get_first_sig().expect("no queries!?"); + + // @CTB avoid clone? let query_sig_ds = query_sig.clone().select(selection)?; // downsample let query_mh = match query_sig_ds.minhash() { Some(query_mh) => query_mh, @@ -89,7 +91,10 @@ pub fn fastgather( } if prefetch_output.is_some() { - write_prefetch(&query_sig, prefetch_output, &matchlist).ok(); + let query_filename = query_sig.filename(); + let query_name = query_sig.name(); + let query_md5 = query_sig.md5sum(); + write_prefetch(query_filename, query_name, query_md5, prefetch_output, &matchlist).ok(); } // run the gather! diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index cf70326f..a4e37905 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -87,80 +87,85 @@ pub fn fastmultigather( let name = query_sig.name(); let prefix = name.split(' ').next().unwrap_or_default().to_string(); let location = PathBuf::new(&prefix).file_name().unwrap(); - if let Some(query_mh) = query_sig.minhash() { - let mut matching_hashes = if save_matches { Some(Vec::new()) } else { None }; - let matchlist: BinaryHeap = against - .iter() - .filter_map(|against| { - let mut mm: Option = None; - if let Ok(overlap) = against.minhash.count_common(query_mh, false) { - if overlap >= threshold_hashes { - if save_matches { - if let Ok(intersection) = - against.minhash.intersection(query_mh) - { - matching_hashes - .as_mut() - .unwrap() - .extend(intersection.0); - } + + let query_filename = query_sig.filename(); + let query_name = query_sig.name(); + let query_md5 = query_sig.md5sum(); + + let query_mh = query_sig.minhash().expect("cannot get sketch"); + let mut matching_hashes = if save_matches { Some(Vec::new()) } else { None }; + let matchlist: BinaryHeap = against + .iter() + .filter_map(|against| { + let mut mm: Option = None; + if let Ok(overlap) = against.minhash.count_common(query_mh, false) { + if overlap >= threshold_hashes { + if save_matches { + if let Ok(intersection) = + against.minhash.intersection(query_mh) + { + matching_hashes + .as_mut() + .unwrap() + .extend(intersection.0); } - let result = PrefetchResult { - name: against.name.clone(), - md5sum: against.md5sum.clone(), - minhash: against.minhash.clone(), - location: against.location.clone(), - overlap, - }; - mm = Some(result); } + let result = PrefetchResult { + name: against.name.clone(), + md5sum: against.md5sum.clone(), + minhash: against.minhash.clone(), + location: against.location.clone(), + overlap, + }; + mm = Some(result); } - mm - }) - .collect(); - if !matchlist.is_empty() { - let prefetch_output = format!("{}.prefetch.csv", location); - let gather_output = format!("{}.gather.csv", location); - - // Save initial list of matches to prefetch output - write_prefetch(&query_sig, Some(prefetch_output), &matchlist).ok(); - - // Now, do the gather! - consume_query_by_gather( - query_sig.clone(), - scaled as u64, - matchlist, - threshold_hashes, - Some(gather_output), - ) + } + mm + }) + .collect(); + + if !matchlist.is_empty() { + let prefetch_output = format!("{}.prefetch.csv", location); + let gather_output = format!("{}.gather.csv", location); + + // Save initial list of matches to prefetch output + write_prefetch(query_filename, query_name, query_md5, Some(prefetch_output), &matchlist).ok(); + + // Now, do the gather! + consume_query_by_gather( + query_sig.clone(), + scaled as u64, + matchlist, + threshold_hashes, + Some(gather_output), + ) .ok(); - // Save matching hashes to .sig file if save_matches is true - if save_matches { - if let Some(hashes) = matching_hashes { - let sig_filename = format!("{}.matches.sig", name); - if let Ok(mut file) = File::create(&sig_filename) { - let unique_hashes: HashSet = hashes.into_iter().collect(); - let mut new_mh = KmerMinHash::new( - query_mh.scaled(), - query_mh.ksize().try_into().unwrap(), - query_mh.hash_function().clone(), - query_mh.seed(), - false, - query_mh.num(), - ); - new_mh - .add_many(&unique_hashes.into_iter().collect::>()) - .ok(); - let mut signature = Signature::default(); - signature.push(Sketch::MinHash(new_mh)); - signature.set_filename(&name); - if let Err(e) = signature.to_writer(&mut file) { - eprintln!("Error writing signature file: {}", e); - } - } else { - eprintln!("Error creating signature file: {}", sig_filename); + // Save matching hashes to .sig file if save_matches is true + if save_matches { + if let Some(hashes) = matching_hashes { + let sig_filename = format!("{}.matches.sig", name); + if let Ok(mut file) = File::create(&sig_filename) { + let unique_hashes: HashSet = hashes.into_iter().collect(); + let mut new_mh = KmerMinHash::new( + query_mh.scaled(), + query_mh.ksize().try_into().unwrap(), + query_mh.hash_function().clone(), + query_mh.seed(), + false, + query_mh.num(), + ); + new_mh + .add_many(&unique_hashes.into_iter().collect::>()) + .ok(); + let mut signature = Signature::default(); + signature.push(Sketch::MinHash(new_mh)); + signature.set_filename(&name); + if let Err(e) = signature.to_writer(&mut file) { + eprintln!("Error writing signature file: {}", e); } + } else { + eprintln!("Error creating signature file: {}", sig_filename); } } } else { diff --git a/src/utils/mod.rs b/src/utils/mod.rs index b9de4bd0..b39ade63 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -90,7 +90,9 @@ pub fn prefetch( /// Write list of prefetch matches. pub fn write_prefetch( - query: &SigStore, + query_filename: String, + query_name: String, + query_md5: String, prefetch_output: Option, matchlist: &BinaryHeap, ) -> Result<(), Box> { @@ -120,9 +122,9 @@ pub fn write_prefetch( writeln!( &mut writer, "{},\"{}\",{},\"{}\",{},{}", - query.filename(), - query.name(), - query.md5sum(), + query_filename, + query_name, + query_md5, m.name, m.md5sum, m.overlap From c43f0d97598c643d8a58afff3b1503f6d7c515bf Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 10:23:09 -0400 Subject: [PATCH 88/91] deallocate collection? --- src/utils/multicollection.rs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs index b9fa53ce..b2ffe093 100644 --- a/src/utils/multicollection.rs +++ b/src/utils/multicollection.rs @@ -308,7 +308,7 @@ impl MultiCollection { // Load all sketches into memory, using SmallSignature to track original // signature metadata. - pub fn load_sketches(&self, selection: &Selection) -> Result> { + pub fn load_sketches(self, selection: &Selection) -> Result> { if self.contains_revindex { eprintln!("WARNING: loading all sketches from a RocksDB into memory!"); } From 87118def94436483c2ef8f945c14b47c48a0b905 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 10:44:31 -0400 Subject: [PATCH 89/91] upd sourmash --- Cargo.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index a56788cf..14c16762 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7" [[package]] name = "sourmash" version = "0.16.0" -source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#e4e5555fd81a9a8677bbe065cf7f528270b01fed" +source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ceaea393d95b3b85575b51c20784d3b9442da149" dependencies = [ "az", "byteorder", From ee296e709ea54c1660a781fe18032aaa39f8302e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 11:01:16 -0400 Subject: [PATCH 90/91] cargo fmt --- src/fastgather.rs | 9 ++++++++- src/fastmultigather.rs | 19 +++++++++++-------- src/utils/mod.rs | 7 +------ 3 files changed, 20 insertions(+), 15 deletions(-) diff --git a/src/fastgather.rs b/src/fastgather.rs index 67a2f341..686e702e 100644 --- a/src/fastgather.rs +++ b/src/fastgather.rs @@ -94,7 +94,14 @@ pub fn fastgather( let query_filename = query_sig.filename(); let query_name = query_sig.name(); let query_md5 = query_sig.md5sum(); - write_prefetch(query_filename, query_name, query_md5, prefetch_output, &matchlist).ok(); + write_prefetch( + query_filename, + query_name, + query_md5, + prefetch_output, + &matchlist, + ) + .ok(); } // run the gather! diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index a4e37905..bc9d6f5b 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -101,13 +101,9 @@ pub fn fastmultigather( if let Ok(overlap) = against.minhash.count_common(query_mh, false) { if overlap >= threshold_hashes { if save_matches { - if let Ok(intersection) = - against.minhash.intersection(query_mh) + if let Ok(intersection) = against.minhash.intersection(query_mh) { - matching_hashes - .as_mut() - .unwrap() - .extend(intersection.0); + matching_hashes.as_mut().unwrap().extend(intersection.0); } } let result = PrefetchResult { @@ -129,7 +125,14 @@ pub fn fastmultigather( let gather_output = format!("{}.gather.csv", location); // Save initial list of matches to prefetch output - write_prefetch(query_filename, query_name, query_md5, Some(prefetch_output), &matchlist).ok(); + write_prefetch( + query_filename, + query_name, + query_md5, + Some(prefetch_output), + &matchlist, + ) + .ok(); // Now, do the gather! consume_query_by_gather( @@ -139,7 +142,7 @@ pub fn fastmultigather( threshold_hashes, Some(gather_output), ) - .ok(); + .ok(); // Save matching hashes to .sig file if save_matches is true if save_matches { diff --git a/src/utils/mod.rs b/src/utils/mod.rs index b39ade63..b2e36db6 100644 --- a/src/utils/mod.rs +++ b/src/utils/mod.rs @@ -122,12 +122,7 @@ pub fn write_prefetch( writeln!( &mut writer, "{},\"{}\",{},\"{}\",{},{}", - query_filename, - query_name, - query_md5, - m.name, - m.md5sum, - m.overlap + query_filename, query_name, query_md5, m.name, m.md5sum, m.overlap ) .ok(); } From a5bf5fa9696f8de88bd135a306982b38b378fd71 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 13 Oct 2024 11:14:21 -0400 Subject: [PATCH 91/91] fix merge foo --- src/fastmultigather.rs | 37 +++++++++++++++---------------------- 1 file changed, 15 insertions(+), 22 deletions(-) diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs index bc9d6f5b..379b9cfe 100644 --- a/src/fastmultigather.rs +++ b/src/fastmultigather.rs @@ -171,31 +171,24 @@ pub fn fastmultigather( eprintln!("Error creating signature file: {}", sig_filename); } } - } else { - println!("No matches to '{}'", location); - if create_empty_results { - let prefetch_output = format!("{}.prefetch.csv", location); - let gather_output = format!("{}.gather.csv", location); - // touch output files - match std::fs::File::create(&prefetch_output) { - Ok(_) => {} - Err(e) => { - eprintln!("Failed to create empty prefetch output: {}", e) - } - } - match std::fs::File::create(&gather_output) { - Ok(_) => {} - Err(e) => eprintln!("Failed to create empty gather output: {}", e), + } + } else { + println!("No matches to '{}'", location); + if create_empty_results { + let prefetch_output = format!("{}.prefetch.csv", location); + let gather_output = format!("{}.gather.csv", location); + // touch output files + match std::fs::File::create(&prefetch_output) { + Ok(_) => {} + Err(e) => { + eprintln!("Failed to create empty prefetch output: {}", e) } } + match std::fs::File::create(&gather_output) { + Ok(_) => {} + Err(e) => eprintln!("Failed to create empty gather output: {}", e), + } } - } else { - // different warning here? Could not load sig from record?? - eprintln!( - "WARNING: no compatible sketches in path '{}'", - record.internal_location() - ); - let _ = skipped_paths.fetch_add(1, atomic::Ordering::SeqCst); } } Err(_) => {