From 4d4a8d8f9b68a1c6adc115e7e96de8102a7dbd18 Mon Sep 17 00:00:00 2001 From: Sharon Goliath Date: Fri, 29 Nov 2024 12:10:21 -0800 Subject: [PATCH 1/5] CADC_13844 - interim commit. --- gem2caom2/builder.py | 10 +- gem2caom2/composable.py | 35 +- gem2caom2/data_source.py | 26 +- gem2caom2/fits2caom2_augmentation.py | 10 +- gem2caom2/gem_name.py | 15 +- gem2caom2/gemini_metadata.py | 191 +- gem2caom2/main_app.py | 461 +- gem2caom2/obs_file_relationship.py | 1 - gem2caom2/pull_augmentation.py | 14 +- .../data/diskfiles_mock/query_limit.html | 8855 +++++++++++++++++ .../tests/data/programs/GS-2021A-Q-777.xml | 27 + gem2caom2/tests/gem_mocks.py | 186 +- gem2caom2/tests/test_builder.py | 3 +- gem2caom2/tests/test_caom_gen_visit.py | 94 +- gem2caom2/tests/test_composable.py | 85 +- gem2caom2/tests/test_data_source.py | 44 +- gem2caom2/tests/test_gemini_metadata.py | 14 +- gem2caom2/tests/test_meta_visit_edge_cases.py | 53 +- gem2caom2/tests/test_multi_plane.py | 94 +- gem2caom2/tests/test_visitors.py | 20 +- gem2caom2/util.py | 1 - 21 files changed, 9917 insertions(+), 322 deletions(-) create mode 100644 gem2caom2/tests/data/diskfiles_mock/query_limit.html create mode 100644 gem2caom2/tests/data/programs/GS-2021A-Q-777.xml diff --git a/gem2caom2/builder.py b/gem2caom2/builder.py index 0f69cbf..cc0166e 100644 --- a/gem2caom2/builder.py +++ b/gem2caom2/builder.py @@ -111,11 +111,11 @@ def build(self, entry): or self._config.use_local_files ): self._logger.debug(f'Using entry for source.') - result = gem_name.GemName(file_name=f_name) + result = gem_name.GemName(file_name=f_name, filter_cache=self._metadata_reader.filter_cache) result.source_names = [entry] elif '.fits' in entry or '.jpg' in entry: self._logger.debug('Using file_id for source.') - result = gem_name.GemName(file_name=f_name) + result = gem_name.GemName(file_name=f_name, filter_cache=self._metadata_reader.filter_cache) result.source_names = [result.file_id] elif '.fits' not in entry and '.jpg' not in entry: # this case exists so that retries.txt entries are @@ -129,7 +129,9 @@ def build(self, entry): 'entry might be file_id, try a made-up name.' ) made_up_file_name = f'{entry}.fits' - result = gem_name.GemName(file_name=made_up_file_name) + result = gem_name.GemName( + file_name=made_up_file_name, filter_cache=self._metadata_reader.filter_cache + ) result.source_names = [result.file_id] self._metadata_reader.set(result) # StorageName instance is only partially constructed at this @@ -139,5 +141,5 @@ def build(self, entry): return result except Exception as e: self._logger.error(e) - self._logger.debug(traceback.format_exc()) + self._logger.error(traceback.format_exc()) raise mc.CadcException(e) diff --git a/gem2caom2/composable.py b/gem2caom2/composable.py index 908159a..0f49203 100644 --- a/gem2caom2/composable.py +++ b/gem2caom2/composable.py @@ -79,6 +79,8 @@ from gem2caom2 import pull_augmentation, data_source, builder from gem2caom2 import cleanup_augmentation, fits2caom2_augmentation from gem2caom2 import gemini_metadata, svofps +from gem2caom2.gem_name import GemName + DATA_VISITORS = [ghost_preview_augmentation] META_VISITORS = [fits2caom2_augmentation, pull_augmentation, preview_augmentation, cleanup_augmentation] @@ -148,13 +150,11 @@ def _common_init(): clients = GemClientCollection(config) meta_visitors = META_VISITORS gemini_session = mc.get_endpoint_session() - provenance_finder = gemini_metadata.ProvenanceFinder( - config, clients.query_client, gemini_session - ) svofps_session = mc.get_endpoint_session() filter_cache = svofps.FilterMetadataCache(svofps_session) clients.gemini_session = gemini_session clients.svo_session = svofps_session + provenance_finder = gemini_metadata.ProvenanceFinder(clients, config) if config.use_local_files or mc.TaskType.SCRAPE in config.task_types: metadata_reader = gemini_metadata.GeminiFileMetadataReader( gemini_session, provenance_finder, filter_cache @@ -331,40 +331,21 @@ def _run_incremental_diskfiles(): clients = GemClientCollection(config) meta_visitors = META_VISITORS gemini_session = mc.get_endpoint_session() - provenance_finder = gemini_metadata.ProvenanceFinder(config, clients.query_client, gemini_session) svofps_session = mc.get_endpoint_session() filter_cache = svofps.FilterMetadataCache(svofps_session) clients.gemini_session = gemini_session clients.svo_session = svofps_session - metadata_reader = gemini_metadata.FileInfoBeforeJsonReader( - clients.data_client, gemini_session, provenance_finder, filter_cache - ) - reader_lookup = gemini_metadata.GeminiMetadataLookup(metadata_reader) - reader_lookup.reader = metadata_reader - name_builder = builder.GemObsIDBuilder(config, metadata_reader, reader_lookup) - incremental_source = data_source.IncrementalSourceDiskfiles(config, metadata_reader) - result = rc.run_by_state( + incremental_source = data_source.IncrementalSourceDiskfiles(config, gemini_session, GemName, filter_cache) + return rc.run_by_state_runner_meta( config=config, - name_builder=name_builder, meta_visitors=meta_visitors, data_visitors=DATA_VISITORS, sources=[incremental_source], clients=clients, - metadata_reader=metadata_reader, - organizer_module_name='gem2caom2.composable', - organizer_class_name='GemOrganizeExecutes', + organizer_module_name='gem2caom2.gemini_metadata', + organizer_class_name='GeminiOrganizeExecutesRunnerMeta', + storage_name_ctor=GemName, ) - if incremental_source.max_records_encountered: - # There's a currently 10k limit on the number of records returned from the archive.gemini.edu endpoints. - # As of this writing, if that limit is encountered, the ingestion requires manual intervention to recover. - # As opposed to stopping the incremental ingestion with a time-box where it will just continually fail - # with this same error, which is what raising the exception would do, the app notifies Ops via the log - # message, and then carries on, so as to more efficiently process large numbers of inputs. - logging.warning('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!') - logging.warning('Encountered maximum records!!') - logging.warning('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!') - result |= -1 - return result def run_incremental_diskfiles(): diff --git a/gem2caom2/data_source.py b/gem2caom2/data_source.py index e61270a..d572aae 100644 --- a/gem2caom2/data_source.py +++ b/gem2caom2/data_source.py @@ -230,13 +230,14 @@ class IncrementalSourceDiskfiles(dsc.IncrementalDataSource): entrytime is when the DB record behind the JSON being displayed was created. """ - def __init__(self, config, reader): + def __init__(self, config, gemini_session, storage_name_ctor, filter_cache): super().__init__(config, start_key=GEM_BOOKMARK) self._max_records_encountered = False self._encounter_start = None self._encounter_end = None - self._session = reader._session - self._metadata_reader = reader + self._session = gemini_session + self._storage_name_ctor = storage_name_ctor + self._filter_cache = filter_cache def _initialize_end_dt(self): self._end_dt = datetime.now() @@ -250,10 +251,14 @@ def get_time_box_work(self, prev_exec_dt, exec_dt): """ self._logger.debug(f'Begin get_time_box_work from {prev_exec_dt} to {exec_dt}.') + self._max_records_encountered = False # datetime format 2019-12-01T00:00:00 => no microseconds in the url prev_exec_dt_iso = prev_exec_dt.replace(microsecond=0) exec_dt_iso = exec_dt.replace(microsecond=0) - url = f'https://archive.gemini.edu/diskfiles/entrytimedaterange={prev_exec_dt_iso.isoformat()}--{exec_dt_iso.isoformat()}' + url = ( + f'https://archive.gemini.edu/diskfiles/entrytimedaterange=' + f'{prev_exec_dt_iso.isoformat()}--{exec_dt_iso.isoformat()}' + ) # needs to be ordered by timestamps when processed self._logger.info(f'Querying {url}') @@ -277,13 +282,14 @@ def get_time_box_work(self, prev_exec_dt, exec_dt): for entry_dt, values in metadata.items(): for value in values: file_name = value.get('filename') - entries.append(dsc.StateRunnerMeta(file_name, entry_dt)) - uri = build_uri(StorageName.collection, file_name, StorageName.scheme) - self._metadata_reader.add_file_info_html_record(uri, value) + storage_name = self._storage_name_ctor(file_name, self._filter_cache) + storage_name.file_info[storage_name.destination_uris[0]] = value + entries.append(dsc.RunnerMeta(storage_name, entry_dt)) finally: if response is not None: response.close() if len(entries) == MAX_ENTRIES: + self._logger.error(f'Max records window {self._encounter_start} to {self._encounter_end}.') self._max_records_encountered = True self._encounter_start = prev_exec_dt self._encounter_end = exec_dt @@ -310,11 +316,5 @@ def _parse_diskfiles_response(self, html_string): result = OrderedDict(sorted(temp.items())) return result - @property def max_records_encountered(self): - if self._max_records_encountered: - self._logger.error( - f'Max records window {self._encounter_start} to ' - f'{self._encounter_end}.' - ) return self._max_records_encountered diff --git a/gem2caom2/fits2caom2_augmentation.py b/gem2caom2/fits2caom2_augmentation.py index 1fad01b..a216a0a 100644 --- a/gem2caom2/fits2caom2_augmentation.py +++ b/gem2caom2/fits2caom2_augmentation.py @@ -71,17 +71,17 @@ from gem2caom2 import main_app -class GeminiFits2caom2Visitor(cc.Fits2caom2Visitor): +class GeminiFits2caom2Visitor(cc.Fits2caom2VisitorRunnerMeta): def __init__(self, observation, **kwargs): super().__init__(observation, **kwargs) - def _get_mapping(self, headers, _): + def _get_mapping(self, dest_uri): return main_app.mapping_factory( self._storage_name, - headers, - self._metadata_reader, + self._storage_name.metadata.get(dest_uri), + None, # metadata reader self._clients, - self._observable, + self._reporter._observable, self._observation, self._config, ) diff --git a/gem2caom2/gem_name.py b/gem2caom2/gem_name.py index e2a0cbf..edc14fc 100644 --- a/gem2caom2/gem_name.py +++ b/gem2caom2/gem_name.py @@ -66,6 +66,8 @@ # *********************************************************************** # +from os.path import basename + from caom2pipe import manage_composable as mc from gem2caom2.obs_file_relationship import remove_extensions @@ -145,10 +147,21 @@ class GemName(mc.StorageName): def __init__( self, file_name=None, + filter_cache=None, ): - super().__init__(file_name=file_name.replace('.header', '')) + super().__init__(file_name=basename(file_name.replace('.header', ''))) # use the file id because the extension doesn't help much in the archive.gemini.edu URL self._source_names = [self._file_id] + self._json_metadata = {} + self._filter_cache = filter_cache + + @property + def json_metadata(self): + return self._json_metadata + + @property + def name(self): + return self._file_id @property def prev(self): diff --git a/gem2caom2/gemini_metadata.py b/gem2caom2/gemini_metadata.py index 86b6ea7..24aa846 100644 --- a/gem2caom2/gemini_metadata.py +++ b/gem2caom2/gemini_metadata.py @@ -86,6 +86,7 @@ from caom2utils import data_util from caom2pipe.astro_composable import get_datetime_mjd from caom2pipe import client_composable as clc +from caom2pipe.execute_composable import MetaVisitRunnerMeta, OrganizeExecutesRunnerMeta from caom2pipe import manage_composable as mc from caom2pipe import reader_composable as rdc from gem2caom2.util import Inst @@ -201,7 +202,7 @@ def _retrieve_file_info(self, key, source_name): pass def _retrieve_headers(self, key, source_name): - self._headers[key] = retrieve_headers(source_name, self._logger, self._session) + self._headers[key] = retrieve_gemini_headers(source_name, self._logger, self._session) def set(self, storage_name): self._logger.debug(f'Begin set for {storage_name.file_name}') @@ -244,7 +245,7 @@ def set_headers(self, storage_name): self._logger.info(f'{storage_name.source_names[0]} not at CADC. Checking archive.gemini.edu.') for idx, entry in enumerate(storage_name.source_names): if '.jpg' not in entry: - self._headers[storage_name.destination_uris[idx]] = retrieve_headers( + self._headers[storage_name.destination_uris[idx]] = retrieve_gemini_headers( path.basename(entry), self._logger, self._session ) self._logger.debug(f'Found {entry} at archive.gemini.edu.') @@ -278,6 +279,7 @@ def add_file_info_html_record(self, uri, html_record): ) self._logger.debug(f'Adding FileInfo for {uri}') + class GeminiMetadataLookup: def __init__(self, metadata_reader): self._reader = metadata_reader @@ -411,13 +413,45 @@ def _search_fits(self, uri, lookup_key): temp = headers[1].get(lookup_key) return temp - @property - def reader(self): - return self._reader - @reader.setter - def reader(self, value): - self._reader = value +class GeminiMetadataLookupStorageName(GeminiMetadataLookup): + def __init__(self, storage_name): + super().__init__(None) + self._storage_name = storage_name + + def max_exputend(self, uri): + if self._max_exputend.get(uri) is None: + headers = self._storage_name.metadata.get(uri) + if headers is not None and len(headers) > 0: + exputend_values = deque() + for header in headers: + if header.get('EXPUTEND') is not None: + date_obs = header.get('DATE-OBS') + temp = header.get('EXPUTEND') + exputend_values.append(f'{date_obs} {temp}') + + if len(exputend_values) >= 2: + start = get_datetime_mjd(mc.make_datetime(exputend_values.popleft())) + end = get_datetime_mjd(mc.make_datetime(exputend_values.pop())) + if end < start: + # in case the observation crosses midnight + end = end + TimeDelta(1.0 * units.day) + self._max_exputend[uri] = end.value + return self._max_exputend.get(uri) + + def _search_json(self, uri, lookup_key): + return self._storage_name.json_metadata.get(uri).get(lookup_key) + + def _search_fits(self, uri, lookup_key): + temp = None + headers = self._storage_name.metadata.get(uri) + if headers is not None and len(headers) > 0: + # if headers are None, the file is proprietary at + # archive.gemini.edu, and cannot be retrieved + temp = headers[0].get(lookup_key) + if temp is None and len(headers) > 1: + temp = headers[1].get(lookup_key) + return temp class ProvenanceFinder: @@ -447,11 +481,12 @@ class ProvenanceFinder: for provenance T/F case. """ - def __init__(self, config, tap_client, gemini_session): + # def __init__(self, config, tap_client, gemini_session): + def __init__(self, clients, config): self._use_local_files = config.use_local_files self._connected = mc.TaskType.SCRAPE not in config.task_types - self._tap_client = tap_client - self._gemini_session = gemini_session + self._tap_client = clients.query_client + self._gemini_session = clients.gemini_session self._data_sources = config.data_sources self._logger = logging.getLogger(self.__class__.__name__) @@ -540,6 +575,126 @@ def get(self, uri): return repaired_data_label +class GeminiMetaVisitRunnerMeta(MetaVisitRunnerMeta): + """ + Defines the pipeline step for Collection creation or augmentation by a visitor of metadata into CAOM. + """ + + def __init__( + self, + clients, + config, + meta_visitors, + reporter, + ): + super().__init__( + clients=clients, + config=config, + meta_visitors=meta_visitors, + reporter=reporter, + ) + + def _set_preconditions(self): + """This is probably not the best approach, but I want to think about where the optimal location for the + retrieve_file_info and retrieve_headers methods will be long-term. So, for the moment, use them here.""" + self._logger.debug(f'Begin _set_preconditions for {self._storage_name.file_uri}') + # ask archive.gemini.edu for the information + for index, source_name in enumerate(self._storage_name.source_names): + uri = self._storage_name.destination_uris[index] + if uri not in self._storage_name.metadata: + self._storage_name.metadata[uri] = [] + if '.fits' in uri: + self._storage_name._metadata[uri] = retrieve_headers( + source_name, self._logger, self._clients, self._config + ) + # TODO - is there a time when not needing archive.gemini.edu is possible? + if uri not in self._storage_name.json_metadata: + json_record = retrieve_json(source_name, self._logger, self._clients.gemini_session) + # json is an array of dicts, one dict per file, find the right dict + for jj in json_record: + # choose this key, and the comparison, because the lhs can be + # a file id + f_name = uri.split('/')[-1] + if f_name in jj.get('filename'): + self._storage_name._json_metadata[uri] = jj + self._logger.debug(f'Adding JSON metadata for {uri}') + break + + if uri not in self._storage_name.file_info: + self._storage_name._file_info[uri] = FileInfo( + id=uri, + size=self._storage_name._json_metadata[uri].get('data_size'), + name=self._storage_name._json_metadata[uri].get('filename'), + md5sum=self._storage_name._json_metadata[uri].get('data_md5'), + lastmod=mc.make_datetime(self._storage_name._json_metadata[uri].get('lastmod')), + file_type=data_util.get_file_type(self._storage_name._json_metadata[uri].get('filename')), + encoding=data_util.get_file_encoding(self._storage_name._json_metadata[uri].get('filename')), + ) + if uri not in self._storage_name.file_info: + if self._config.use_local_files: + self._storage_name._file_info[uri] = data_util.get_local_file_info(source_name) + else: + self._storage_name._file_info[uri] = self._clients.data_client.info(uri) + + file_name = self._storage_name._json_metadata[uri].get('filename') + data_label = self._storage_name._json_metadata[uri].get('data_label') + repaired_data_label = obs_file_relationship.repair_data_label(file_name, data_label) + self._storage_name.obs_id = repaired_data_label + self._logger.debug('End _set_preconditions') + + +class GeminiOrganizeExecutesRunnerMeta(OrganizeExecutesRunnerMeta): + """A class that extends OrganizeExecutes to handle the choosing of the correct executors based on the config.yml. + Attributes: + _needs_delete (bool): if True, the CAOM repo action is delete/create instead of update. + _reporter: An instance responsible for reporting the execution status. + Methods: + _choose(): + Determines which descendants of CaomExecute to instantiate based on the content of the config.yml + file for an application. + """ + + def __init__( + self, + config, + meta_visitors, + data_visitors, + needs_delete=False, + store_transfer=None, + modify_transfer=None, + clients=None, + reporter=None, + ): + super().__init__( + config, + meta_visitors, + data_visitors, + store_transfer=store_transfer, + modify_transfer=modify_transfer, + clients=clients, + reporter=reporter, + needs_delete=needs_delete, + ) + + def _choose(self): + """The logic that decides which descendants of CaomExecute to instantiate. This is based on the content of + the config.yml file for an application. + """ + super()._choose() + for task_type in self.task_types: + if task_type == mc.TaskType.INGEST: + if self._needs_delete: + raise mc.CadcException('No need identified for this yet.') + else: + self._logger.debug(f'Choosing executor GeminiMetaVisit for {task_type}.') + self._executors = [] # over-ride the default choice. + self._executors.append( + GeminiMetaVisitRunnerMeta( + self._clients, self.config, self._meta_visitors, self._reporter + ) + ) + + def repair_instrument(in_name): if in_name == 'ALOPEKE': # because the value in JSON is a different case than the value in @@ -563,7 +718,19 @@ def repair_instrument(in_name): return Inst(in_name) -def retrieve_headers(source_name, logger, session): +def retrieve_headers(source_name, logger, clients, config): + result = None + if config.use_local_files: + result = data_util.get_local_file_headers(source_name) + else: + result = clients.data_client.get_head(f'{config.scheme}:{config.collection}/{path.basename(source_name)}') + if not result: + # if the header is not at CADC, retrieve it from archive.gemini.edu + result = retrieve_gemini_headers(source_name, logger, clients.gemini_session) + return result + + +def retrieve_gemini_headers(source_name, logger, session): logger.debug(f'Begin retrieve_headers for {source_name}') header_url = f'{HEADER_URL}{source_name}.fits' # Open the URL and fetch the JSON document for the observation diff --git a/gem2caom2/main_app.py b/gem2caom2/main_app.py index 7025216..fbd70f3 100644 --- a/gem2caom2/main_app.py +++ b/gem2caom2/main_app.py @@ -112,7 +112,7 @@ import gem2caom2.obs_file_relationship as ofr from gem2caom2.gem_name import GemName from gem2caom2 import program_metadata, svofps -from gem2caom2.gemini_metadata import GeminiMetadataLookup +from gem2caom2.gemini_metadata import GeminiMetadataLookup, GeminiMetadataLookupStorageName, ProvenanceFinder from gem2caom2.util import Inst @@ -206,12 +206,23 @@ class GeminiMapping(cc.TelescopeMapping): # value repair cache value_repair = GeminiValueRepair() - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): super().__init__(storage_name, headers, clients, observable, observation, config) - self._metadata_reader = lookup.reader self._instrument = instrument self._lookup = lookup - self._filter_cache = self._metadata_reader.filter_cache + self._filter_cache = self._storage_name._filter_cache + self._provenance_finder = provenance_finder self.fm = None def get_art_content_checksum(self, ext): @@ -326,11 +337,7 @@ def get_meta_release(self, ext): :return: The Observation/Plane release date, or None if not found. """ # TODO - this is a bit different ROTFL - if self._headers is None: - # GenericParser, so no headers retrieved from archive.gemini.edu, - # probably a 403 being returned by the site, assume proprietary - meta_release = self._lookup.release(self._storage_name.file_uri) - else: + if self._headers: # DB 21-08-19 # If PROP_MD is T, use JSON ‘release’ value for metadata release # date. If no PROP_MD present or value is F use the JSON @@ -342,6 +349,11 @@ def get_meta_release(self, ext): if meta_release is None or prop_md and prop_md == 'T' or prop_md: # a late value is better than None, since that makes the Observation unfindable meta_release = self._lookup.release(self._storage_name.file_uri) + else: + # GenericParser, so no headers retrieved from archive.gemini.edu, + # probably a 403 being returned by the site, assume proprietary + meta_release = self._lookup.release(self._storage_name.file_uri) + return mc.make_datetime(meta_release) def get_obs_intent(self, ext): @@ -635,7 +647,7 @@ def accumulate_blueprint(self, bp): self._accumulate_chunk_time_axis_blueprint(bp, 3) self._logger.debug('Done accumulate_blueprint.') - def update(self, file_info): + def update(self): if self._headers is None: # proprietary header metadata at archive.gemini.edu, so do nothing @@ -680,7 +692,7 @@ def update(self, file_info): continue if GemName.is_preview(artifact.uri): continue - update_artifact_meta(artifact, file_info) + update_artifact_meta(artifact, self._storage_name.file_info.get(artifact.uri)) self._update_artifact(artifact) processed = ofr.is_processed(self._storage_name.file_name) if self._instrument in [ @@ -934,7 +946,8 @@ def _repair_provenance_value(self, value, obs_id): # TODO - what to do about the data label search here? there's no # file metadata, it would be _most_ efficient to do this from CADC # so need to re-use this code somehow :( - prov_obs_id = self._metadata_reader.provenance_finder.get(uri) + prov_obs_id = self._provenance_finder.get(uri) + self._logger.error(f'{prov_obs_id} uri {uri} {self._provenance_finder.get}') except mc.CadcException as e: # the file id probably does not exist at on disk, at CADC, or at # Gemini, ignore, because it's provenance @@ -1224,8 +1237,21 @@ def _remove_processing_detritus(values, obs_id): class Bhros(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -1322,8 +1348,21 @@ def _update_position(self, part, chunk, ext): class Cirpass(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -1471,8 +1510,21 @@ def _update_position(self, part, chunk, ext): class F2(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -1661,8 +1713,21 @@ def _update_time(self, chunk): class Flamingos(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -1947,8 +2012,21 @@ def _update_position(self, part, chunk, ext): class Fox(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -2035,8 +2113,21 @@ def _update_time(self, chunk): class GHOSTSpectralTemporal(GeminiMapping): """Fibre-fed spectrograph""" - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model Observation level.""" @@ -2164,8 +2255,21 @@ def _update_time(self, chunk): class GHOSTSpatialSpectralTemporal(GHOSTSpectralTemporal): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model Observation level.""" @@ -2180,8 +2284,21 @@ def accumulate_blueprint(self, bp): class Gmos(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -2411,8 +2528,21 @@ def _update_energy(self, chunk, data_product_type, filter_name): class Gnirs(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -2916,8 +3046,21 @@ def _update_energy(self, chunk, data_product_type, filter_name): class Gpi(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -3063,8 +3206,21 @@ def _update_position(self, part, chunk, extension): class GracesSpectralTemporal(GeminiMapping): """Fibre-fed spectrograph""" - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model Observation level.""" @@ -3126,8 +3282,21 @@ def _update_time(self, chunk): class GracesSpatialSpectralTemporal(GracesSpectralTemporal): """Fibre-fed spectrograph""" - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model Observation level.""" @@ -3137,8 +3306,21 @@ def accumulate_blueprint(self, bp): class Gsaoi(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -3185,8 +3367,21 @@ def _update_energy(self, chunk, data_product_type, filter_name): class Hokupaa(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -3390,8 +3585,21 @@ def _update_position(self, part, chunk, ext): class Hrwfs(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -3453,8 +3661,21 @@ def _update_energy(self, chunk, data_product_type, filter_name): class Igrins(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -3535,8 +3756,21 @@ def _update_position(self, part, chunk, ext): class Michelle(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -3700,8 +3934,21 @@ def _update_energy(self, chunk, data_product_type, filter_name): class Nici(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -3799,8 +4046,21 @@ def _update_energy(self, chunk, data_product_type, filter_name): class Nifs(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -4075,8 +4335,21 @@ def _update_position(self, part, chunk, ext): class Niri(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -4363,8 +4636,21 @@ def _update_position(self, part, chunk, extension): class Oscir(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): super().accumulate_blueprint(bp) @@ -4532,8 +4818,21 @@ def _update_position(self, part, chunk, ext): class Phoenix(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -4804,8 +5103,21 @@ def _update_position(self, part, chunk, ext): class Texes(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -4927,8 +5239,21 @@ def _update_position(self, part, chunk, ext): class Trecs(GeminiMapping): - def __init__(self, storage_name, headers, lookup, instrument, clients, observable, observation, config): - super().__init__(storage_name, headers, lookup, instrument, clients, observable, observation, config) + def __init__( + self, + storage_name, + headers, + lookup, + instrument, + clients, + observable, + observation, + config, + provenance_finder, + ): + super().__init__( + storage_name, headers, lookup, instrument, clients, observable, observation, config, provenance_finder + ) def accumulate_blueprint(self, bp): """Configure the telescope-specific ObsBlueprint at the CAOM model @@ -5083,7 +5408,11 @@ def get_obs_type(lookup, storage_name): def mapping_factory(storage_name, headers, metadata_reader, clients, observable, observation, config): - metadata_lookup = GeminiMetadataLookup(metadata_reader) + if metadata_reader: + metadata_lookup = GeminiMetadataLookup(metadata_reader) + else: + metadata_lookup = GeminiMetadataLookupStorageName(storage_name) + provenance_finder = ProvenanceFinder(clients, config) inst = metadata_lookup.instrument(storage_name.file_uri) lookup = { Inst.BHROS: Bhros, @@ -5114,17 +5443,17 @@ def mapping_factory(storage_name, headers, metadata_reader, clients, observable, result = None if inst in lookup: result = lookup.get(inst)( - storage_name, headers, metadata_lookup, inst, clients, observable, observation, config + storage_name, headers, metadata_lookup, inst, clients, observable, observation, config, provenance_finder ) elif inst is Inst.GHOST: obs_type = get_obs_type(metadata_lookup, storage_name) if obs_type in ['ARC', 'BIAS', 'FLAT']: result = GHOSTSpectralTemporal( - storage_name, headers, metadata_lookup, inst, clients, observable, observation, config + storage_name, headers, metadata_lookup, inst, clients, observable, observation, config, provenance_finder ) else: result = GHOSTSpatialSpectralTemporal( - storage_name, headers, metadata_lookup, inst, clients, observable, observation, config + storage_name, headers, metadata_lookup, inst, clients, observable, observation, config, provenance_finder ) elif inst is Inst.GRACES: obs_type = get_obs_type(metadata_lookup, storage_name) @@ -5138,11 +5467,11 @@ def mapping_factory(storage_name, headers, metadata_reader, clients, observable, # Ignore spatial WCS for the GRACES dataset with EPOCH=0.0. Not important for a bias. For GMOS we skip # spatial WCS for biases (and maybe for some other instruments). result = GracesSpectralTemporal( - storage_name, headers, metadata_lookup, inst, clients, observable, observation, config + storage_name, headers, metadata_lookup, inst, clients, observable, observation, config, provenance_finder ) else: result = GracesSpatialSpectralTemporal( - storage_name, headers, metadata_lookup, inst, clients, observable, observation, config + storage_name, headers, metadata_lookup, inst, clients, observable, observation, config, provenance_finder ) else: observable.rejected.record(mc.Rejected.MYSTERY_VALUE, storage_name.file_name) diff --git a/gem2caom2/obs_file_relationship.py b/gem2caom2/obs_file_relationship.py index 514b165..696600f 100644 --- a/gem2caom2/obs_file_relationship.py +++ b/gem2caom2/obs_file_relationship.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # *********************************************************************** # ****************** CANADIAN ASTRONOMY DATA CENTRE ******************* # ************* CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES ************** diff --git a/gem2caom2/pull_augmentation.py b/gem2caom2/pull_augmentation.py index ef4344f..a38c321 100644 --- a/gem2caom2/pull_augmentation.py +++ b/gem2caom2/pull_augmentation.py @@ -88,12 +88,10 @@ def visit(observation, **kwargs): if clients is None: logging.warning('Need clients to update. Stopping pull visitor.') return - observable = kwargs.get('observable') - if observable is None: - raise mc.CadcException('Visitor needs a observable parameter.') - metadata_reader = kwargs.get('metadata_reader') - if metadata_reader is None: - raise mc.CadcException('Visitor needs a metadata_reader parameter.') + reporter = kwargs.get('reporter') + if reporter is None: + raise mc.CadcException('Visitor needs a reporter parameter.') + observable = reporter._observable storage_name = kwargs.get('storage_name') if storage_name is None: raise mc.CadcException('Visitor needs a storage_name parameter.') @@ -135,9 +133,7 @@ def visit(observation, **kwargs): # want to compare the checksum from the JSON, and the # checksum at CADC storage - if they are not the same, # retrieve the file from archive.gemini.edu again - json_md5sum = metadata_reader.file_info.get( - artifact.uri - ).md5sum + json_md5sum = storage_name.file_info.get(artifact.uri).md5sum look_pull_and_put( artifact.uri, fqn, file_url, clients, json_md5sum ) diff --git a/gem2caom2/tests/data/diskfiles_mock/query_limit.html b/gem2caom2/tests/data/diskfiles_mock/query_limit.html new file mode 100644 index 0000000..1a78db1 --- /dev/null +++ b/gem2caom2/tests/data/diskfiles_mock/query_limit.html @@ -0,0 +1,8855 @@ + + + + + + + + +FITS header diskfiles table + + + + + + + + + + +

WARNING: Your search does not constrain the number of results - ie you did not specify a date, + date range, program ID etc. Searches like this are limited to 500 results, and + this search hit that limit. Calibration association will not be available. You may want to + constrain your search. Constrained searches have a higher result limit. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + +

WARNING: Your search does not constrain the number of results - ie you did not specify a date, + date range, program ID etc. Searches like this are limited to 500 results, and this + search hit that limit. You may want to constrain your search. Constrained searches have a higher + result limit. + + + + + \ No newline at end of file diff --git a/gem2caom2/tests/data/programs/GS-2021A-Q-777.xml b/gem2caom2/tests/data/programs/GS-2021A-Q-777.xml new file mode 100644 index 0000000..d34280b --- /dev/null +++ b/gem2caom2/tests/data/programs/GS-2021A-Q-777.xml @@ -0,0 +1,27 @@ + + + + + + + +Detail for Program: GS-2021A-Q-777 + + + +

Program: GS-2021A-Q-777

+ + + + + +
Title:Hidden headers test
PI:Fredrik Rantakyro
Co-I(s):
+

Abstract

+
+No abstract +
+ + + + + \ No newline at end of file diff --git a/gem2caom2/tests/gem_mocks.py b/gem2caom2/tests/gem_mocks.py index f6c4ecd..8cc4147 100644 --- a/gem2caom2/tests/gem_mocks.py +++ b/gem2caom2/tests/gem_mocks.py @@ -86,8 +86,9 @@ from caom2pipe import astro_composable as ac from caom2pipe import manage_composable as mc from caom2pipe.run_composable import set_logging +from caom2utils.data_util import get_local_file_headers -from gem2caom2 import data_source, obs_file_relationship, builder, svofps +from gem2caom2 import data_source, obs_file_relationship, svofps from gem2caom2 import gemini_metadata, fits2caom2_augmentation from gem2caom2.gem_name import GemName from gem2caom2.util import Inst @@ -622,10 +623,10 @@ def mock_get_file_info(file_id): def mock_retrieve_json(source_name, ign1, ign2): - return mock_get_obs_metadata(source_name) + return mock_get_obs_metadata(source_name, ign1, ign2) -def mock_get_obs_metadata(file_id): +def mock_get_obs_metadata(file_id, ignore1, ignore2): file_id = obs_file_relationship.remove_extensions(file_id.split('/')[-1]) try: fname = f'{TEST_DATA_DIR}/json/{file_id}.json' @@ -652,10 +653,14 @@ def mock_get_obs_metadata(file_id): logging.error(tb) +def mock_get_obs_metadata_37(file_id): + return mock_get_obs_metadata(file_id, None, None) + + def mock_get_data_label(uri): ignore_scheme, ignore_collection, f_name = mc.decompose_uri(uri) file_id = GemName.remove_extensions(f_name) - temp = mock_get_obs_metadata(file_id) + temp = mock_get_obs_metadata(file_id, None, None) result = None for ii in temp: y = obs_file_relationship.remove_extensions(ii.get('filename')) @@ -788,6 +793,17 @@ def mock_query_endpoint_4(url, timeout=-1): return result +def mock_query_endpoint_5(url, timeout=-1): + # returns response.text + result = Object() + result.text = 'x' + + if url.startswith('https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-08-28T17:05:00'): + with open(f'{TEST_DATA_DIR}/diskfiles_mock/query_limit.html') as f: + result.text = f.read() + return result + + def mock_session_get_not_found(url): # returns json via response.text, depending on url result = Object() @@ -856,18 +872,24 @@ def mock_repo_update(ignore1): def compare(expected_fqn, actual_fqn, observation): - try: - expected = mc.read_obs_from_file(expected_fqn) - compare_result = get_differences(expected, observation) - except Exception as e: - mc.write_obs_to_file(observation, actual_fqn) - assert False, f'{e}' - if compare_result is not None: - mc.write_obs_to_file(observation, actual_fqn) - compare_text = '\n'.join([r for r in compare_result]) - raise AssertionError( - f'Differences found in observation {expected.observation_id}\n{compare_text}.\nCheck {actual_fqn}' - ) + if observation: + if os.path.exists(expected_fqn): + expected = mc.read_obs_from_file(expected_fqn) + try: + compare_result = get_differences(expected, observation) + except Exception as e: + mc.write_obs_to_file(observation, actual_fqn) + assert False, f'{e}' + if compare_result is not None: + mc.write_obs_to_file(observation, actual_fqn) + compare_text = '\n'.join([r for r in compare_result]) + raise AssertionError( + f'Differences found in observation {expected.observation_id}\n{compare_text}.\nCheck {actual_fqn}' + ) + else: + raise AssertionError(f'No expected observation here {expected_fqn}. See actual here {actual_fqn}') + else: + raise AssertionError(f'No observation created for comparison with {expected_fqn}') def _query_mock_none(ignore1, ignore2): @@ -948,10 +970,21 @@ def _mock_retrieve_headers(mock_name, ign1, ign2): return _mock_headers(mock_name, mock_name) +def _mock_retrieve_headers_37(mock_name, ign1, ign2, ignore3): + return _mock_headers(mock_name, mock_name) + + def _mock_get_head(file_id): return _mock_headers(file_id, file_id) +from caom2 import Algorithm, SimpleObservation + + +def read_mock_37(collection, obs_id): + return SimpleObservation(collection='OMM', observation_id='test_obs_id', algorithm=Algorithm(name='exposure')) + + class MockFileReader(gemini_metadata.GeminiFileMetadataReader): def __init__(self, pf_mock, filter_mock): @@ -967,6 +1000,7 @@ def _run_test_common( get_pi_mock, svofps_mock, pf_mock, + header_mock, json_mock, file_type_mock, test_set, @@ -977,66 +1011,66 @@ def _run_test_common( warnings.simplefilter('ignore', AstropyWarning) get_pi_mock.side_effect = mock_get_pi_metadata svofps_mock.side_effect = mock_get_votable - pf_mock.get.side_effect = mock_get_data_label + pf_mock.return_value.get.side_effect = mock_get_data_label json_mock.side_effect = mock_get_obs_metadata file_type_mock.return_value = 'application/fits' - orig_cwd = os.getcwd() - try: - os.chdir(tmp_path) - test_config.task_types = [mc.TaskType.SCRAPE] - test_config.use_local_files = True - test_config.data_sources = data_sources - test_config.change_working_directory(tmp_path.as_posix()) - test_config.proxy_file_name = 'test_proxy.pem' - test_config.logging_level = 'ERROR' - test_config.write_to_file(test_config) - set_logging(test_config) - - with open(test_config.proxy_fqn, 'w') as f: - f.write('test content') - - observation = None - in_fqn = expected_fqn.replace('.expected.', '.in.') - if os.path.exists(in_fqn): - observation = mc.read_obs_from_file(in_fqn) - actual_fqn = expected_fqn.replace('expected', 'actual') - if os.path.exists(actual_fqn): - os.unlink(actual_fqn) - - test_observable = mc.Observable(test_config) - for entry in test_set: - filter_cache = svofps.FilterMetadataCache(svofps_mock) - metadata_reader = MockFileReader(pf_mock, filter_cache) - test_metadata = gemini_metadata.GeminiMetadataLookup( - metadata_reader - ) - test_builder = builder.GemObsIDBuilder( - test_config, metadata_reader, test_metadata - ) - storage_name = test_builder.build(entry) - client_mock = Mock() - kwargs = { - 'storage_name': storage_name, - 'metadata_reader': metadata_reader, - 'clients': client_mock, - 'observable': test_observable, - 'config': test_config, - } - try: - observation = fits2caom2_augmentation.visit(observation, **kwargs) - except mc.CadcException as e: - if storage_name.file_name in ['N20220915S0113.fits', 'S20230301S0170.fits']: - assert ( - test_observable.rejected.is_mystery_value(storage_name.file_name) - ), 'expect rejected mystery value record' - raise e - - compare(expected_fqn, actual_fqn, observation) - - if observation.observation_id in ['GS-2022B-Q-235-137-045', 'GS-2023A-LP-103-23-017']: - assert test_observable.rejected.is_bad_metadata(storage_name.file_name), 'expect rejected record' - else: - assert not test_observable.rejected.is_bad_metadata(storage_name.file_name), 'expect no rejected record' - finally: - os.chdir(orig_cwd) + test_config.task_types = [mc.TaskType.SCRAPE] + test_config.use_local_files = True + test_config.log_to_file = True # set the xml creation location + test_config.data_sources = data_sources + test_config.change_working_directory(tmp_path.as_posix()) + test_config.proxy_file_name = 'test_proxy.pem' + test_config.logging_level = 'ERROR' + test_config.write_to_file(test_config) + set_logging(test_config) + + with open(test_config.proxy_fqn, 'w') as f: + f.write('test content') + + observation = None + in_fqn = expected_fqn.replace('.expected.', '.in.') + if os.path.exists(in_fqn): + observation = mc.read_obs_from_file(in_fqn) + actual_fqn = expected_fqn.replace('expected', 'actual') + if os.path.exists(actual_fqn): + os.unlink(actual_fqn) + + test_reporter = mc.ExecutionReporter2(test_config) + filter_cache = svofps.FilterMetadataCache(svofps_mock) + clients_mock = Mock() + for entry in test_set: + storage_name = GemName(entry, filter_cache) + test_subject = gemini_metadata.GeminiMetaVisitRunnerMeta( + clients_mock, test_config, [fits2caom2_augmentation], test_reporter + ) + + def _read_header_mock(ignore1, ignore2, ignore3, ignore4): + if 'S20210518S0022' in entry: + return [] + else: + return get_local_file_headers(entry) + header_mock.side_effect = _read_header_mock + + clients_mock.metadata_client.read.return_value = observation + + context = {'storage_name': storage_name} + try: + test_subject.execute(context) + except mc.CadcException as e: + if storage_name.file_name in ['N20220915S0113.fits', 'S20230301S0170.fits']: + assert ( + test_reporter._observable.rejected.is_mystery_value(storage_name.file_name) + ), 'expect rejected mystery value record' + raise e + + compare(expected_fqn, actual_fqn, test_subject._observation) + + if test_subject._observation.observation_id in ['GS-2022B-Q-235-137-045', 'GS-2023A-LP-103-23-017']: + assert ( + test_reporter._observable.rejected.is_bad_metadata(storage_name.file_name) + ), 'expect rejected record' + else: + assert ( + not test_reporter._observable.rejected.is_bad_metadata(storage_name.file_name) + ), 'expect no rejected record' diff --git a/gem2caom2/tests/test_builder.py b/gem2caom2/tests/test_builder.py index a3646f4..5e2ea58 100644 --- a/gem2caom2/tests/test_builder.py +++ b/gem2caom2/tests/test_builder.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # *********************************************************************** # ****************** CANADIAN ASTRONOMY DATA CENTRE ******************* # ************* CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES ************** @@ -80,7 +79,7 @@ @patch('gem2caom2.gemini_metadata.GeminiMetadataReader._retrieve_headers') @patch('gem2caom2.gemini_metadata.GeminiMetadataReader._retrieve_json') def test_builder(file_info_mock, header_mock, test_config): - file_info_mock.side_effect = gem_mocks.mock_get_obs_metadata + file_info_mock.side_effect = gem_mocks.mock_get_obs_metadata_37 test_config.working_directory = '/test_files' test_config.proxy_fqn = os.path.join( diff --git a/gem2caom2/tests/test_caom_gen_visit.py b/gem2caom2/tests/test_caom_gen_visit.py index ad9cbeb..b17c72d 100644 --- a/gem2caom2/tests/test_caom_gen_visit.py +++ b/gem2caom2/tests/test_caom_gen_visit.py @@ -71,11 +71,15 @@ import pytest +from astropy.utils.exceptions import AstropyWarning from astropy.wcs import FITSFixedWarning +from caom2utils import data_util +from caom2pipe.manage_composable import CadcException, ExecutionReporter2, read_obs_from_file, TaskType from gem2caom2.util import Inst -from gem2caom2 import obs_file_relationship +from gem2caom2 import fits2caom2_augmentation, gemini_metadata, obs_file_relationship, svofps +from gem2caom2.gem_name import GemName -from unittest.mock import patch +from unittest.mock import Mock, patch import gem_mocks @@ -124,37 +128,91 @@ def pytest_generate_tests(metafunc): @patch('caom2utils.data_util.get_file_type') -@patch('gem2caom2.gemini_metadata.AbstractGeminiMetadataReader._retrieve_json') +@patch('gem2caom2.gemini_metadata.retrieve_headers') +@patch('gem2caom2.gemini_metadata.retrieve_json') @patch('caom2pipe.astro_composable.get_vo_table_session') @patch('gem2caom2.program_metadata.get_pi_metadata') -@patch('gem2caom2.gemini_metadata.ProvenanceFinder') +@patch('gem2caom2.main_app.ProvenanceFinder') def test_visitor( pf_mock, get_pi_mock, svofps_mock, json_mock, + header_mock, file_type_mock, test_name, test_config, tmp_path, + change_test_dir, ): warnings.simplefilter('ignore', category=FITSFixedWarning) - test_file_id = obs_file_relationship.remove_extensions( - os.path.basename(test_name) - ) + warnings.simplefilter('ignore', AstropyWarning) + test_file_id = obs_file_relationship.remove_extensions(os.path.basename(test_name)) + get_pi_mock.side_effect = gem_mocks.mock_get_pi_metadata + svofps_mock.side_effect = gem_mocks.mock_get_votable + pf_mock.return_value.get.side_effect = gem_mocks.mock_get_data_label + json_mock.side_effect = gem_mocks.mock_get_obs_metadata + file_type_mock.return_value = 'application/fits' + + test_config.task_types = [TaskType.SCRAPE] + test_config.use_local_files = True + test_config.log_to_file = True + test_config.data_sources = [tmp_path.as_posix()] + test_config.change_working_directory(tmp_path.as_posix()) + test_config.proxy_file_name = 'test_proxy.pem' + test_config.logging_level = 'ERROR' + test_config.write_to_file(test_config) + gem_mocks.set_logging(test_config) + + with open(test_config.proxy_fqn, 'w') as f: + f.write('test content') + expected_fqn = f'{os.path.dirname(test_name)}/{test_file_id}.expected.xml' - gem_mocks._run_test_common( - data_sources=[os.path.dirname(test_name)], - get_pi_mock=get_pi_mock, - svofps_mock=svofps_mock, - pf_mock=pf_mock, - json_mock=json_mock, - file_type_mock=file_type_mock, - test_set=[test_name], - expected_fqn=expected_fqn, - test_config=test_config, - tmp_path=tmp_path, + in_fqn = expected_fqn.replace('.expected.', '.in.') + + clients_mock = Mock() + def _mock_repo_read(collection, obs_id): + input_observation = None + if os.path.exists(in_fqn): + input_observation = read_obs_from_file(in_fqn) + return input_observation + clients_mock.metadata_client.read.side_effect = _mock_repo_read + + def _read_header_mock(ignore1, ignore2, ignore3, ignore4): + return data_util.get_local_file_headers(test_name) + header_mock.side_effect = _read_header_mock + + actual_fqn = expected_fqn.replace('expected', 'actual') + if os.path.exists(actual_fqn): + os.unlink(actual_fqn) + + test_reporter = ExecutionReporter2(test_config) + filter_cache = svofps.FilterMetadataCache(svofps_mock) + test_subject = gemini_metadata.GeminiMetaVisitRunnerMeta( + clients_mock, test_config, [fits2caom2_augmentation], test_reporter ) + storage_name = GemName(test_name, filter_cache) + context = {'storage_name': storage_name} + try: + test_subject.execute(context) + except CadcException as e: + if storage_name.file_name in ['N20220915S0113.fits', 'S20230301S0170.fits']: + assert ( + test_reporter._observable.rejected.is_mystery_value(storage_name.file_name) + ), 'expect rejected mystery value record' + else: + raise e + + gem_mocks.compare(expected_fqn, actual_fqn, test_subject._observation) + + if test_subject._observation.observation_id in ['GS-2022B-Q-235-137-045', 'GS-2023A-LP-103-23-017']: + assert ( + test_reporter._observable.rejected.is_bad_metadata(storage_name.file_name) + ), 'expect rejected record' + else: + assert ( + not test_reporter._observable.rejected.is_bad_metadata(storage_name.file_name) + ), 'expect no rejected record' def _get_inst_name(inst): diff --git a/gem2caom2/tests/test_composable.py b/gem2caom2/tests/test_composable.py index 295edc8..911e4fb 100644 --- a/gem2caom2/tests/test_composable.py +++ b/gem2caom2/tests/test_composable.py @@ -76,7 +76,7 @@ from collections import deque from datetime import datetime, timedelta, timezone from traceback import format_exc -from unittest.mock import call, patch, Mock, PropertyMock +from unittest.mock import ANY, call, patch, Mock, PropertyMock import gem_mocks from cadcdata import FileInfo @@ -532,7 +532,7 @@ def _mock_dir_list(arg1, output_file='', data_only=True, response_format='arg4') ), 'put call count, no previews because it is just a STORE task' put_calls = [ call( - f'{tmp_path.as_posix()}/GS-2005B-SV-301-16-005', + f'{tmp_path.as_posix()}/S20050825S0143', f'{test_config.scheme}:{test_config.collection}/S20050825S0143.fits', ), ] @@ -590,13 +590,11 @@ def test_run_is_valid_fails(cap_mock, summary_mock, test_config, tmp_path): @patch('gem2caom2.composable.GemClientCollection') @patch('gem2caom2.gemini_metadata.retrieve_headers') @patch('gem2caom2.gemini_metadata.retrieve_json') -@patch('caom2pipe.execute_composable.OrganizeExecutes.do_one') @patch('gem2caom2.data_source.query_endpoint_session') @patch('caom2pipe.client_composable.query_tap_client') def test_run_incremental_diskfiles( tap_mock, query_mock, - run_mock, json_mock, header_mock, clients_mock, @@ -607,7 +605,8 @@ def test_run_incremental_diskfiles( query_mock.side_effect = gem_mocks.mock_query_endpoint_4 tap_mock.side_effect = gem_mocks.mock_query_tap json_mock.side_effect = gem_mocks.mock_retrieve_json - header_mock.side_effect = gem_mocks._mock_retrieve_headers + header_mock.side_effect = gem_mocks._mock_retrieve_headers_37 + clients_mock.return_value.metadata_client.read.side_effect = gem_mocks.read_mock_37 test_config.change_working_directory(tmp_path) test_config.proxy_file_name = 'testproxy.pem' @@ -623,17 +622,73 @@ def test_run_incremental_diskfiles( fqn=test_config.state_fqn, ) - run_mock.return_value = (0, None) + test_result = composable._run_incremental_diskfiles() + assert test_result is not None, 'expect result' + assert test_result == -1, 'expect failure, no metadata mocking results set up' + assert not clients_mock.return_value.data_client.put.called, 'data put called' + # 16 is the number of records processed + assert clients_mock.return_value.metadata_client.read.called, 'meta read called' + assert clients_mock.return_value.metadata_client.read.call_count == 16, 'meta read count' + assert not clients_mock.return_value.metadata_client.update.called, 'meta update called' + assert not tap_mock.called, 'tap called' + assert query_mock.called, 'query endpoint session called' + # https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-10-20T20:03:00--2024-11-01T23:03:00 + assert query_mock.call_count == 1, 'query endpoint session count' + assert json_mock.called, 'json mock called' + assert json_mock.call_count == 16, 'json mock count' + assert header_mock.called, 'header mock called' + assert header_mock.call_count == 16, 'header mock count' - composable._run_incremental_diskfiles() - assert run_mock.called, 'run_mock should have been called' - args, kwargs = run_mock.call_args - test_storage = args[0] - assert isinstance(test_storage, gem_name.GemName), type(test_storage) - assert test_storage.obs_id == 'test_data_label', 'wrong obs id' - test_fid = 'S20241030S0203' - assert test_storage.file_name == f'{test_fid}.fits', 'wrong file_name' - assert test_storage.file_id == f'{test_fid}', 'wrong file_id' + + + +@patch('gem2caom2.gemini_metadata.GeminiOrganizeExecutesRunnerMeta.do_one') +@patch('gem2caom2.composable.GemClientCollection') +@patch('gem2caom2.data_source.query_endpoint_session') +@patch('caom2pipe.client_composable.query_tap_client') +def test_run_incremental_diskfiles_limit( + tap_mock, + query_mock, + clients_mock, + do_one_mock, + test_config, + tmp_path, + change_test_dir, +): + query_mock.side_effect = gem_mocks.mock_query_endpoint_5 + tap_mock.side_effect = gem_mocks.mock_query_tap + clients_mock.return_value.metadata_client.read.side_effect = gem_mocks.read_mock_37 + do_one_mock.return_value = (0, None) + + test_config.change_working_directory(tmp_path) + test_config.proxy_file_name = 'testproxy.pem' + test_config.task_types = [TaskType.INGEST] + test_config.interval = 60 + test_config.logging_level = 'WARNING' + Config.write_to_file(test_config) + with open(test_config.proxy_fqn, 'w') as f: + f.write('test content') + + _write_state( + prior_timestamp='2024-08-28 17:05:00.000000', + end_timestamp=datetime(year=2024, month=8, day=28, hour=18, minute=5, second=0), + fqn=test_config.state_fqn, + ) + + test_result = composable._run_incremental_diskfiles() + assert test_result is not None, 'expect result' + assert test_result == 0, 'expect success' + assert query_mock.called, 'query endpoint session called' + # https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-10-20T20:03:00--2024-11-01T23:03:00 + assert query_mock.call_count == 2, 'query endpoint session count' + query_mock.assert_has_calls([ + call('https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-08-28T17:05:00--2024-08-28T18:05:00', ANY), + call('https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-08-28T17:07:32--2024-08-28T18:05:00', ANY), + ]) + assert not clients_mock.return_value.data_client.put.called, 'data put called' + assert not clients_mock.return_value.metadata_client.read.called, 'meta read called' + assert not clients_mock.return_value.metadata_client.update.called, 'meta update called' + assert not tap_mock.called, 'tap called' def _write_state(prior_timestamp=None, end_timestamp=None, fqn=STATE_FILE): diff --git a/gem2caom2/tests/test_data_source.py b/gem2caom2/tests/test_data_source.py index 75131ca..ba78a52 100644 --- a/gem2caom2/tests/test_data_source.py +++ b/gem2caom2/tests/test_data_source.py @@ -68,7 +68,8 @@ from datetime import datetime from mock import call, Mock, patch -from gem2caom2 import data_source, gemini_metadata +from gem2caom2 import data_source +from gem2caom2.gem_name import GemName import gem_mocks @@ -139,14 +140,8 @@ def test_diskfiles_incremental_source(query_mock, test_config): # get results query_mock.side_effect = gem_mocks.mock_query_endpoint_4 - test_data_client = Mock() test_http_session = Mock() - test_provenance_finder = Mock() - test_filter_cache = Mock() - test_reader = gemini_metadata.FileInfoBeforeJsonReader( - test_data_client, test_http_session, test_provenance_finder, test_filter_cache - ) - test_subject = data_source.IncrementalSourceDiskfiles(test_config, reader=test_reader) + test_subject = data_source.IncrementalSourceDiskfiles(test_config, test_http_session, GemName, Mock()) assert test_subject is not None, 'expect construction success' test_reporter = Mock() test_subject.reporter = test_reporter @@ -158,10 +153,39 @@ def test_diskfiles_incremental_source(query_mock, test_config): assert test_result is not None, 'expect a result' assert len(test_result) == 16, 'wrong number of results' test_first_entry = test_result.popleft() - assert test_first_entry.entry_name == 'S20241030S0188.fits', 'wrong first file' + assert test_first_entry.storage_entry.file_name == 'S20241030S0188.fits', 'wrong first file' assert test_first_entry.entry_dt == datetime(2024, 10, 30, 10, 51, 37, 360130), 'wrong fits datetime' test_last_entry = test_result.pop() - assert test_last_entry.entry_name == 'S20241030S0203.fits', 'wrong 2nd file' + assert test_last_entry.storage_entry.file_name == 'S20241030S0203.fits', 'wrong 2nd file' + assert test_last_entry.entry_dt == datetime(2024, 10, 30, 10, 54, 45, 941860), 'wrong last datetime' + assert test_reporter.capture_todo.called, 'capture_todo' + assert test_reporter.capture_todo.call_count == 1, 'wrong number of capture_todo calls' + test_reporter.capture_todo.assert_called_with(16, 0, 0) + + +@patch('gem2caom2.data_source.query_endpoint_session') +def test_diskfiles_incremental_source_limit(query_mock, test_config): + # https://archive.gemini.edu/diskfiles/entrytimedaterange=-- + # get results + query_mock.side_effect = gem_mocks.mock_query_endpoint_5 + + test_http_session = Mock() + test_subject = data_source.IncrementalSourceDiskfiles(test_config, test_http_session, GemName, Mock()) + assert test_subject is not None, 'expect construction success' + test_reporter = Mock() + test_subject.reporter = test_reporter + + prev_exec_time = datetime(year=2021, month=1, day=1, hour=20, minute=3, second=0) + exec_time = datetime(year=2021, month=1, day=1, hour=22, minute=13, second=0) + + test_result = test_subject.get_time_box_work(prev_exec_time, exec_time) + assert test_result is not None, 'expect a result' + assert len(test_result) == 16, 'wrong number of results' + test_first_entry = test_result.popleft() + assert test_first_entry.storage_entry.file_name == 'S20241030S0188.fits', 'wrong first file' + assert test_first_entry.entry_dt == datetime(2024, 10, 30, 10, 51, 37, 360130), 'wrong fits datetime' + test_last_entry = test_result.pop() + assert test_last_entry.storage_entry.file_name == 'S20241030S0203.fits', 'wrong 2nd file' assert test_last_entry.entry_dt == datetime(2024, 10, 30, 10, 54, 45, 941860), 'wrong last datetime' assert test_reporter.capture_todo.called, 'capture_todo' assert test_reporter.capture_todo.call_count == 1, 'wrong number of capture_todo calls' diff --git a/gem2caom2/tests/test_gemini_metadata.py b/gem2caom2/tests/test_gemini_metadata.py index 85a758e..fcfcb14 100644 --- a/gem2caom2/tests/test_gemini_metadata.py +++ b/gem2caom2/tests/test_gemini_metadata.py @@ -80,10 +80,10 @@ import gem_mocks -@patch('gem2caom2.gemini_metadata.retrieve_headers') +@patch('gem2caom2.gemini_metadata.retrieve_gemini_headers') @patch('gem2caom2.gemini_metadata.GeminiMetadataReader._retrieve_json') def test_set(retrieve_json_mock, retrieve_headers_mock): - retrieve_json_mock.side_effect = gem_mocks.mock_get_obs_metadata + retrieve_json_mock.side_effect = gem_mocks.mock_get_obs_metadata_37 test_f_name = 'N20030104S0065.fits' test_obs_id = 'GN-CAL20030104-14-001' retrieve_headers_mock.side_effect = gem_mocks._mock_retrieve_headers @@ -140,9 +140,7 @@ def _local_mock(ignore): else: test_config.task_types = [mc.TaskType.SCRAPE] - test_subject = gemini_metadata.ProvenanceFinder( - test_config, Mock(), Mock() - ) + test_subject = gemini_metadata.ProvenanceFinder(Mock(), test_config) assert test_subject is not None, ( f'ctor does not work:: ' f'local {test_use_local}, ' @@ -169,10 +167,8 @@ def test_header_not_at_cadc(retrieve_json_mock, clients_mock, test_config): # the file is private, re-ingestion fails to find headers at CADC, needs to go back to archive.gemini.edu test_f_name = 'N20220314S0229.fits.bz2' test_obs_id = 'GN-CAL20220314-18-083' - retrieve_json_mock.side_effect = gem_mocks.mock_get_obs_metadata - test_provenance_finder = gemini_metadata.ProvenanceFinder( - test_config, clients_mock.return_value.query_client, Mock() - ) + retrieve_json_mock.side_effect = gem_mocks.mock_get_obs_metadata_37 + test_provenance_finder = gemini_metadata.ProvenanceFinder(clients_mock, test_config) clients_mock.return_value.data_client.get_head.side_effect = exceptions.UnexpectedException test_session_mock = Mock() test_session_mock.get.side_effect = gem_mocks.mock_fullheader_endpoint diff --git a/gem2caom2/tests/test_meta_visit_edge_cases.py b/gem2caom2/tests/test_meta_visit_edge_cases.py index 04e634e..8561c2f 100644 --- a/gem2caom2/tests/test_meta_visit_edge_cases.py +++ b/gem2caom2/tests/test_meta_visit_edge_cases.py @@ -72,7 +72,7 @@ from cadcutils import exceptions from caom2pipe import astro_composable as ac from caom2pipe import manage_composable as mc -from gem2caom2 import svofps, gemini_metadata, builder +from gem2caom2 import svofps, gemini_metadata, gem_name from gem2caom2 import fits2caom2_augmentation from mock import ANY, patch, Mock @@ -80,18 +80,21 @@ @patch('caom2utils.data_util.get_file_type') -@patch('gem2caom2.gemini_metadata.AbstractGeminiMetadataReader._retrieve_json') +@patch('gem2caom2.gemini_metadata.retrieve_headers') +@patch('gem2caom2.gemini_metadata.retrieve_json') @patch('caom2pipe.astro_composable.get_vo_table_session') @patch('gem2caom2.program_metadata.get_pi_metadata') -@patch('gem2caom2.gemini_metadata.ProvenanceFinder') +@patch('gem2caom2.main_app.ProvenanceFinder') def test_broken_obs( pf_mock, get_pi_mock, svofps_mock, json_mock, + header_mock, file_type_mock, test_config, tmp_path, + change_test_dir, ): # the observation is broken, test that retrieval will handle that test_f_name = 'gS20171114S0185_bias.fits.header' @@ -106,6 +109,7 @@ def test_broken_obs( get_pi_mock=get_pi_mock, svofps_mock=svofps_mock, pf_mock=pf_mock, + header_mock=header_mock, json_mock=json_mock, file_type_mock=file_type_mock, test_set=[test_fqn], @@ -119,15 +123,17 @@ def test_broken_obs( 'gem2caom2.gemini_metadata.GeminiFileMetadataReader._retrieve_file_info' ) @patch('caom2utils.data_util.get_file_type') -@patch('gem2caom2.gemini_metadata.AbstractGeminiMetadataReader._retrieve_json') +@patch('gem2caom2.gemini_metadata.retrieve_headers') +@patch('gem2caom2.gemini_metadata.retrieve_json') @patch('caom2pipe.astro_composable.get_vo_table_session') @patch('gem2caom2.program_metadata.get_pi_metadata') -@patch('gem2caom2.gemini_metadata.ProvenanceFinder') +@patch('gem2caom2.main_app.ProvenanceFinder') def test_unauthorized_at_gemini( pf_mock, get_pi_mock, svofps_mock, json_mock, + header_mock, file_type_mock, file_info_mock, test_config, @@ -149,6 +155,7 @@ def test_unauthorized_at_gemini( svofps_mock=svofps_mock, pf_mock=pf_mock, json_mock=json_mock, + header_mock=header_mock, file_type_mock=file_type_mock, test_set=[test_fqn], expected_fqn=expected_fqn, @@ -159,8 +166,7 @@ def test_unauthorized_at_gemini( @patch('gem2caom2.gemini_metadata.retrieve_headers') @patch('caom2utils.data_util.get_file_type') -@patch('gem2caom2.gemini_metadata.AbstractGeminiMetadataReader._retrieve_json') -@patch('caom2pipe.reader_composable.StorageClientReader.set_headers') +@patch('gem2caom2.gemini_metadata.retrieve_json') @patch('caom2pipe.astro_composable.get_vo_table_session') @patch('gem2caom2.program_metadata.get_pi_metadata') @patch('gem2caom2.gemini_metadata.ProvenanceFinder') @@ -168,7 +174,6 @@ def test_going_public( pf_mock, get_pi_mock, svofps_mock, - headers_mock, json_mock, file_type_mock, remote_headers_mock, @@ -189,7 +194,6 @@ def test_going_public( get_pi_mock.side_effect = gem_mocks.mock_get_pi_metadata svofps_mock.side_effect = gem_mocks.mock_get_votable - headers_mock.side_effect = exceptions.UnexpectedException pf_mock.get.side_effect = gem_mocks.mock_get_data_label json_mock.side_effect = gem_mocks.mock_get_obs_metadata file_type_mock.return_value = 'application/fits' @@ -199,6 +203,7 @@ def test_going_public( test_config.data_sources = [f'{gem_mocks.TEST_DATA_DIR}/broken_files'] test_config.change_working_directory(tmp_path.as_posix()) test_config.proxy_file_name = 'test_proxy.pem' + test_config.log_to_file = True with open(test_config.proxy_fqn, 'w') as f: f.write('test content') @@ -210,25 +215,15 @@ def test_going_public( unlink(actual_fqn) filter_cache = svofps.FilterMetadataCache(svofps_mock) - metadata_reader = gemini_metadata.GeminiStorageClientReader( - Mock(), Mock(), pf_mock, filter_cache - ) - test_metadata = gemini_metadata.GeminiMetadataLookup(metadata_reader) - test_builder = builder.GemObsIDBuilder( - test_config, metadata_reader, test_metadata - ) - storage_name = test_builder.build(mock_return_fqn) + storage_name = gem_name.GemName(mock_return_fqn, filter_cache) client_mock = Mock() - client_mock.metadata_client = headers_mock - kwargs = { - 'storage_name': storage_name, - 'metadata_reader': metadata_reader, - 'clients': client_mock, - 'config': test_config, - } - ignore = fits2caom2_augmentation.visit(observation, **kwargs) - + client_mock.data_client.get_head.side_effect = exceptions.UnexpectedException + client_mock.metadata_client.read.return_value = observation + test_reporter = mc.ExecutionReporter2(test_config) + test_subject = gemini_metadata.GeminiMetaVisitRunnerMeta( + client_mock, test_config, [fits2caom2_augmentation], test_reporter + ) + context = {'storage_name': storage_name} + test_subject.execute(context) assert remote_headers_mock.called, 'expect remote header retrieval' - remote_headers_mock.assert_called_with( - 'N20150929S0013.fits.header', ANY, ANY - ), 'wrong remote header args' + remote_headers_mock.assert_called_with('N20150929S0013', ANY, ANY, ANY), 'wrong remote header args' diff --git a/gem2caom2/tests/test_multi_plane.py b/gem2caom2/tests/test_multi_plane.py index dd2758d..2063cb3 100644 --- a/gem2caom2/tests/test_multi_plane.py +++ b/gem2caom2/tests/test_multi_plane.py @@ -68,8 +68,16 @@ import os import pytest +import warnings -from unittest.mock import patch +from astropy.utils.exceptions import AstropyWarning +from astropy.wcs import FITSFixedWarning +from caom2utils import data_util +from caom2pipe.manage_composable import CadcException, ExecutionReporter2, read_obs_from_file, TaskType +from gem2caom2 import fits2caom2_augmentation, gemini_metadata, obs_file_relationship, svofps +from gem2caom2.gem_name import GemName + +from unittest.mock import Mock, patch import gem_mocks @@ -122,7 +130,8 @@ def pytest_generate_tests(metafunc): @patch('caom2utils.data_util.get_file_type') -@patch('gem2caom2.gemini_metadata.AbstractGeminiMetadataReader._retrieve_json') +@patch('gem2caom2.gemini_metadata.retrieve_headers') +@patch('gem2caom2.gemini_metadata.retrieve_json') @patch('caom2pipe.astro_composable.get_vo_table_session') @patch('gem2caom2.gemini_metadata.ProvenanceFinder') @patch('gem2caom2.program_metadata.get_pi_metadata') @@ -131,10 +140,12 @@ def test_visitor( pf_mock, svofps_mock, json_mock, + header_mock, file_type_mock, test_name, test_config, tmp_path, + change_test_dir, ): expected_fqn = ( f'{gem_mocks.TEST_DATA_DIR}/multi_plane/' f'{test_name}.expected.xml' @@ -144,15 +155,72 @@ def test_visitor( test_set.append( f'{gem_mocks.TEST_DATA_DIR}/multi_plane/{f_name}.fits.header' ) - gem_mocks._run_test_common( - data_sources=[os.path.dirname(test_name)], - get_pi_mock=get_pi_mock, - svofps_mock=svofps_mock, - pf_mock=pf_mock, - json_mock=json_mock, - file_type_mock=file_type_mock, - test_set=test_set, - expected_fqn=expected_fqn, - test_config=test_config, - tmp_path=tmp_path, + warnings.simplefilter('ignore', category=FITSFixedWarning) + warnings.simplefilter('ignore', AstropyWarning) + get_pi_mock.side_effect = gem_mocks.mock_get_pi_metadata + svofps_mock.side_effect = gem_mocks.mock_get_votable + pf_mock.return_value.get.side_effect = gem_mocks.mock_get_data_label + json_mock.side_effect = gem_mocks.mock_get_obs_metadata + file_type_mock.return_value = 'application/fits' + + test_config.task_types = [TaskType.SCRAPE] + test_config.use_local_files = True + test_config.log_to_file = True + test_config.data_sources = [tmp_path.as_posix()] + test_config.change_working_directory(tmp_path.as_posix()) + test_config.proxy_file_name = 'test_proxy.pem' + test_config.logging_level = 'ERROR' + test_config.write_to_file(test_config) + gem_mocks.set_logging(test_config) + + with open(test_config.proxy_fqn, 'w') as f: + f.write('test content') + + in_fqn = expected_fqn.replace('.expected.', '.in.') + input_observation = None + if os.path.exists(in_fqn): + input_observation = read_obs_from_file(in_fqn) + + clients_mock = Mock() + + actual_fqn = expected_fqn.replace('expected', 'actual') + if os.path.exists(actual_fqn): + os.unlink(actual_fqn) + + test_reporter = ExecutionReporter2(test_config) + filter_cache = svofps.FilterMetadataCache(svofps_mock) + test_subject = gemini_metadata.GeminiMetaVisitRunnerMeta( + clients_mock, test_config, [fits2caom2_augmentation], test_reporter ) + test_subject._observation = input_observation + for entry in test_set: + + def _mock_repo_read(collection, obs_id): + return test_subject._observation + clients_mock.metadata_client.read.side_effect = _mock_repo_read + + def _read_header_mock(ignore1, ignore2, ignore3, ignore4): + return data_util.get_local_file_headers(entry) + header_mock.side_effect = _read_header_mock + + storage_name = GemName(entry, filter_cache) + context = {'storage_name': storage_name} + try: + test_subject.execute(context) + except CadcException as e: + if storage_name.file_name in ['N20220915S0113.fits', 'S20230301S0170.fits']: + assert ( + test_reporter._observable.rejected.is_mystery_value(storage_name.file_name) + ), 'expect rejected mystery value record' + raise e + + gem_mocks.compare(expected_fqn, actual_fqn, test_subject._observation) + + if test_subject._observation.observation_id in ['GS-2022B-Q-235-137-045', 'GS-2023A-LP-103-23-017']: + assert ( + test_reporter._observable.rejected.is_bad_metadata(storage_name.file_name) + ), 'expect rejected record' + else: + assert ( + not test_reporter._observable.rejected.is_bad_metadata(storage_name.file_name) + ), 'expect no rejected record' diff --git a/gem2caom2/tests/test_visitors.py b/gem2caom2/tests/test_visitors.py index 93390fb..f42fb72 100644 --- a/gem2caom2/tests/test_visitors.py +++ b/gem2caom2/tests/test_visitors.py @@ -193,10 +193,10 @@ def test_preview_augment_unknown_no_preview(test_data_dir, test_config): @patch('caom2utils.data_util.get_file_type') -@patch('gem2caom2.gemini_metadata.GeminiFileMetadataReader._retrieve_headers') @patch('gem2caom2.gemini_metadata.retrieve_json') @patch('caom2pipe.manage_composable.http_get') -def test_pull_augmentation(http_mock, json_mock, header_mock, file_type_mock, test_config, test_data_dir): +def test_pull_augmentation(http_mock, json_mock, file_type_mock, test_config, test_data_dir, tmp_path): + test_config.change_working_directory(tmp_path) obs = mc.read_obs_from_file(f'{test_data_dir}/visit_original_uri_start.xml') obs.planes[TEST_PRODUCT_ID].data_release = datetime.now(tz=timezone.utc).replace(tzinfo=None) original_uri = 'gemini:GEMINI/GN2001BQ013-04.fits' @@ -206,28 +206,26 @@ def test_pull_augmentation(http_mock, json_mock, header_mock, file_type_mock, te ), 'initial condition' test_uri = f'{test_config.scheme}:{test_config.collection}/{TEST_PRODUCT_ID}.fits' - test_observable = mc.Observable(test_config) + test_reporter = mc.ExecutionReporter2(test_config) cadc_client_mock = Mock() cadc_client_mock.return_value.info.return_value = None clients_mock = Mock() clients_mock.data_client = cadc_client_mock json_mock.side_effect = gem_mocks.mock_retrieve_json filter_cache = svofps.FilterMetadataCache(Mock()) - test_reader = gemini_metadata.GeminiFileMetadataReader( - Mock(), Mock(), filter_cache - ) - test_storage_name = gem_name.GemName(file_name='GN2001BQ013-04.fits') - header_mock.side_effect = gem_mocks._mock_headers + test_storage_name = gem_name.GemName(file_name='GN2001BQ013-04.fits', filter_cache=filter_cache) file_type_mock.return_values = 'application/fits' - test_reader.set(test_storage_name) kwargs = { 'working_directory': test_data_dir, 'clients': clients_mock, - 'observable': test_observable, - 'metadata_reader': test_reader, + 'reporter': test_reporter, 'storage_name': test_storage_name, } + test_precondition = gemini_metadata.GeminiMetaVisitRunnerMeta(clients_mock, test_config, [], test_reporter) + test_precondition._storage_name = test_storage_name + test_precondition._set_preconditions() + obs = pull_augmentation.visit(obs, **kwargs) test_url = f'{pull_augmentation.FILE_URL}/{TEST_PRODUCT_ID}.fits' test_prev = f'{test_data_dir}/{TEST_PRODUCT_ID}.fits' diff --git a/gem2caom2/util.py b/gem2caom2/util.py index 5b40226..72385a7 100644 --- a/gem2caom2/util.py +++ b/gem2caom2/util.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # *********************************************************************** # ****************** CANADIAN ASTRONOMY DATA CENTRE ******************* # ************* CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES ************** From b1beda5f559fc9a3898cad0c9d26a0ba09f947c6 Mon Sep 17 00:00:00 2001 From: Sharon Goliath Date: Mon, 9 Dec 2024 15:56:42 -0800 Subject: [PATCH 2/5] fix(data_source.py): handle incremental time-boxes that exceed the source query limits --- gem2caom2/tests/test_composable.py | 9 ++++++++- gem2caom2/tests/test_data_source.py | 16 ++++++++-------- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/gem2caom2/tests/test_composable.py b/gem2caom2/tests/test_composable.py index 911e4fb..4655979 100644 --- a/gem2caom2/tests/test_composable.py +++ b/gem2caom2/tests/test_composable.py @@ -82,7 +82,7 @@ from cadcdata import FileInfo from caom2 import SimpleObservation, Algorithm from caom2pipe.data_source_composable import StateRunnerMeta -from caom2pipe.manage_composable import Config, make_datetime, TaskType, write_as_yaml +from caom2pipe.manage_composable import Config, make_datetime, State, TaskType, write_as_yaml from gem2caom2 import composable, gem_name from gem2caom2.data_source import GEM_BOOKMARK @@ -655,6 +655,10 @@ def test_run_incremental_diskfiles_limit( tmp_path, change_test_dir, ): + + # test that, when the limit of files is hit, the datetime for the increment is that from the time of the record + # at the limit, not the upper end of the timebox + query_mock.side_effect = gem_mocks.mock_query_endpoint_5 tap_mock.side_effect = gem_mocks.mock_query_tap clients_mock.return_value.metadata_client.read.side_effect = gem_mocks.read_mock_37 @@ -690,6 +694,9 @@ def test_run_incremental_diskfiles_limit( assert not clients_mock.return_value.metadata_client.update.called, 'meta update called' assert not tap_mock.called, 'tap called' + test_state_post = State(test_config.state_fqn, zone=timezone.utc) + assert test_state_post.get_bookmark(test_config.bookmark) == datetime(2024, 8, 28, 18, 5, 0, 0), 'saved state' + def _write_state(prior_timestamp=None, end_timestamp=None, fqn=STATE_FILE): # to ensure at least one spin through the execution loop, test case diff --git a/gem2caom2/tests/test_data_source.py b/gem2caom2/tests/test_data_source.py index ba78a52..3e39da0 100644 --- a/gem2caom2/tests/test_data_source.py +++ b/gem2caom2/tests/test_data_source.py @@ -175,18 +175,18 @@ def test_diskfiles_incremental_source_limit(query_mock, test_config): test_reporter = Mock() test_subject.reporter = test_reporter - prev_exec_time = datetime(year=2021, month=1, day=1, hour=20, minute=3, second=0) - exec_time = datetime(year=2021, month=1, day=1, hour=22, minute=13, second=0) + prev_exec_time = datetime(year=2024, month=8, day=28, hour=17, minute=5, second=0) + exec_time = datetime(year=2024, month=8, day=28, hour=18, minute=0, second=0) test_result = test_subject.get_time_box_work(prev_exec_time, exec_time) assert test_result is not None, 'expect a result' - assert len(test_result) == 16, 'wrong number of results' + assert len(test_result) == 500, 'wrong number of results' test_first_entry = test_result.popleft() - assert test_first_entry.storage_entry.file_name == 'S20241030S0188.fits', 'wrong first file' - assert test_first_entry.entry_dt == datetime(2024, 10, 30, 10, 51, 37, 360130), 'wrong fits datetime' + assert test_first_entry.storage_entry.file_name == 'S20190619Z0121b.fits', 'wrong first file' + assert test_first_entry.entry_dt == datetime(2024, 8, 28, 17, 5, 0, 127507), 'wrong fits datetime' test_last_entry = test_result.pop() - assert test_last_entry.storage_entry.file_name == 'S20241030S0203.fits', 'wrong 2nd file' - assert test_last_entry.entry_dt == datetime(2024, 10, 30, 10, 54, 45, 941860), 'wrong last datetime' + assert test_last_entry.storage_entry.file_name == 'N20190618S1656.fits', 'wrong 2nd file' + assert test_last_entry.entry_dt == datetime(2024, 8, 28, 17, 7, 32, 267675), 'wrong last datetime' assert test_reporter.capture_todo.called, 'capture_todo' assert test_reporter.capture_todo.call_count == 1, 'wrong number of capture_todo calls' - test_reporter.capture_todo.assert_called_with(16, 0, 0) + assert test_subject.max_records_encountered(), 'limit warning' From f716be0681ebf6a3d13ccfc9918d1915341522ba Mon Sep 17 00:00:00 2001 From: Sharon Goliath Date: Tue, 10 Dec 2024 10:43:08 -0800 Subject: [PATCH 3/5] fix(data_source.py): skip the -fits!-md! records, set the obs_id from the data label earlier --- gem2caom2/data_source.py | 10 ++++-- gem2caom2/gemini_metadata.py | 12 +++---- gem2caom2/tests/gem_mocks.py | 31 ++++++++++++++++--- gem2caom2/tests/test_caom_gen_visit.py | 4 +++ gem2caom2/tests/test_data_source.py | 31 +++++++++++++++++++ gem2caom2/tests/test_gemini_metadata.py | 18 ++++++++++- gem2caom2/tests/test_meta_visit_edge_cases.py | 7 +++-- 7 files changed, 97 insertions(+), 16 deletions(-) diff --git a/gem2caom2/data_source.py b/gem2caom2/data_source.py index d572aae..a92f5a6 100644 --- a/gem2caom2/data_source.py +++ b/gem2caom2/data_source.py @@ -74,6 +74,7 @@ from caom2pipe import data_source_composable as dsc from caom2pipe.manage_composable import build_uri, CaomName, ISO_8601_FORMAT, make_datetime, query_endpoint_session from caom2pipe.manage_composable import StorageName +from gem2caom2.obs_file_relationship import repair_data_label __all__ = ['GEM_BOOKMARK', 'IncrementalSource', 'PublicIncremental'] @@ -284,6 +285,8 @@ def get_time_box_work(self, prev_exec_dt, exec_dt): file_name = value.get('filename') storage_name = self._storage_name_ctor(file_name, self._filter_cache) storage_name.file_info[storage_name.destination_uris[0]] = value + repaired_data_label = repair_data_label(file_name, value.get('datalabel')) + storage_name.obs_id = repaired_data_label entries.append(dsc.RunnerMeta(storage_name, entry_dt)) finally: if response is not None: @@ -304,9 +307,12 @@ def _parse_diskfiles_response(self, html_string): for row in rows: cells = row.find_all('td') entry_time = make_datetime(cells[5].text.strip()) # what the https query is keyed on + file_name = cells[0].text.strip() + if file_name.endswith('-fits!-md!'): + continue value = { - 'filename': cells[0].text.strip(), - 'datalabel': cells[1].text.strip(), + 'filename': file_name, + 'datalabel': cells[1].text.strip().split('\n')[-1], 'instrument': cells[2].text.strip(), 'lastmod': make_datetime(cells[6].text.strip()), 'data_size': cells[10].text.strip(), diff --git a/gem2caom2/gemini_metadata.py b/gem2caom2/gemini_metadata.py index 24aa846..d4f5abe 100644 --- a/gem2caom2/gemini_metadata.py +++ b/gem2caom2/gemini_metadata.py @@ -636,10 +636,6 @@ def _set_preconditions(self): else: self._storage_name._file_info[uri] = self._clients.data_client.info(uri) - file_name = self._storage_name._json_metadata[uri].get('filename') - data_label = self._storage_name._json_metadata[uri].get('data_label') - repaired_data_label = obs_file_relationship.repair_data_label(file_name, data_label) - self._storage_name.obs_id = repaired_data_label self._logger.debug('End _set_preconditions') @@ -723,9 +719,11 @@ def retrieve_headers(source_name, logger, clients, config): if config.use_local_files: result = data_util.get_local_file_headers(source_name) else: - result = clients.data_client.get_head(f'{config.scheme}:{config.collection}/{path.basename(source_name)}') - if not result: - # if the header is not at CADC, retrieve it from archive.gemini.edu + try: + result = clients.data_client.get_head(f'{config.scheme}:{config.collection}/{path.basename(source_name)}') + except exceptions.UnexpectedException as e: + # the exceptions.NotFoundException is turned into exceptions.UnexpectedException in data_util + # the header is not at CADC, retrieve it from archive.gemini.edu result = retrieve_gemini_headers(source_name, logger, clients.gemini_session) return result diff --git a/gem2caom2/tests/gem_mocks.py b/gem2caom2/tests/gem_mocks.py index 8cc4147..7f932d9 100644 --- a/gem2caom2/tests/gem_mocks.py +++ b/gem2caom2/tests/gem_mocks.py @@ -305,6 +305,14 @@ 'S20170905S0318': ['GS-2017A-Q-58-66-027', Inst.F2, 'GS-2017A-Q-58'], 'S20191214S0301': ['GS-CAL20191214-1-029', Inst.F2, 'GS-CAL20191214'], 'S20141130S0001': ['GS-CAL20141129-3-001', Inst.F2, 'GS-CAL20141129'], + 'S20210522S0033': ['GS-2021A-Q-322-12-033', Inst.F2, 'GS-2021A-Q-322'], + 'S20230301S0170': ['GS-2023A-LP-103-23-017', Inst.F2, '>GS-2023A-LP-103'], + 'S20210530S0047': ['GS-2021A-Q-416-20-001', Inst.F2, 'GS-2021A-Q-416'], + 'S20220220S0198': ['GS-CAL20220220-3-012', Inst.F2, 'GS-CAL20220220'], + 'S20220912S0299': ['GS-2022B-Q-306-70-014', Inst.F2, 'GS-2022B-Q-306'], + 'S20221020S0034': ['GS-2022B-DD-101-31-004', Inst.F2, 'GS-2022B-DD-101'], + 'S20220203S0019': ['GS-CAL20220203-1-005', Inst.F2, 'GS-CAL20220203'], + 'S20221115S0124': ['GS-2022B-Q-235-137-045', Inst.F2, 'GS-2022B-Q-235'], # Flamingos '02jul07.0186': ['GS-2002A-Q-13-2-0186', Inst.FLAMINGOS, 'GS-2002A-Q-13'], '02jun25.0071': ['GS-2002A-Q-7-1-0071', Inst.FLAMINGOS, 'GS-2002A-Q-7'], @@ -329,6 +337,12 @@ # GHOST 'S20240601S0038_blue001_dragons': ['GS-2024A-LP-106-12-013-BLUE-001-SQ-BLUE001-DRAGONS', Inst.GHOST, 'GS-2024A-LP-106-12-013'], 'S20240607S0038': ['GS-2024A-Q-144-3-004', Inst.GHOST, 'GS-2024A-Q-144'], + 'S20230517S0047': ['GS-CAL20230517-12-001', Inst.GHOST, 'GS-CAL20230517'], + 'S20240215S0050': ['GS-CAL20240215-15-001', Inst.GHOST, 'GS-CAL20240215'], + 'S20231224S0444': ['GS-CAL20231224-19-001', Inst.GHOST, 'GS-CAL20231224'], + 'S20230518S0121': ['GS-2023A-SV-101-13-009', Inst.GHOST, 'GS-2023A-SV-101'], + 'S20230516S0039': ['GS-2023A-SV-104-12-003', Inst.GHOST, 'GS-2023A-SV-104'], + 'S20231208S0060': ['GS-2023B-FT-104-11-001', Inst.GHOST, 'GS-2023B-FT-104'], # GMOS 'N20030107S0163': ['GN-2003A-Q-22-3-004', Inst.GMOS, 'GN-2003A-Q-22'], 'N20071219S0193': ['GN-2007B-Q-112-14-018', Inst.GMOS, 'GN-2007B-Q-112'], @@ -367,6 +381,7 @@ 'N20120117S0009_stack_fringe': ['GN-CAL20120117-900-009-STACK-FRINGE', Inst.GMOS, 'GS-CAL20131007-1'], 'rS20040502S0077': ['GS-CAL20040502-3-002', Inst.GMOS, 'GS-CAL20040502-3'], 'S20131007S0001_flat': ['GS-CAL20131007-1-001-FLAT', Inst.GMOS, 'GS-CAL20131007-1'], + 'N20220915S0113': ['GN-CAL20220915-20-001', Inst.GMOSN, 'GN-CAL20220915'], # GNIRS 'N20100915S0167': ['GN-2010B-Q-2-44-003', Inst.GNIRS, 'GN-2010B-Q-2'], 'N20100722S0185': ['GN-2010B-SV-142-10-007', Inst.GNIRS, 'GN-2010B-SV-142'], @@ -388,6 +403,8 @@ 'N20180224S0063': ['GN-CAL20180224-3-001', Inst.GNIRS, 'GN-CAL20180224-3'], 'N20171106S0187': ['GN-2017B-LP-16-470-002', Inst.GNIRS, 'GN-2017B-LP-16'], 'N20170210S0013': ['GN-CAL20170209-5-003', Inst.GNIRS, 'GN-CAL20170209-5'], + 'S20040212S0191': ['GS-2004A-SV-1-1-002', Inst.GNIRS, 'GS-2004A-SV-1'], + 'S20040212S0281': ['GS-2004A-SV-1-4-024', Inst.GNIRS, 'GS-2004A-SV-1'], # GPI 'S20140422S0167': ['GS-2014A-SV-408-6-003', Inst.GPI, 'GS-2014A-SV-408'], 'S20180313S0108': ['GS-2018A-FT-101-5-043', Inst.GPI, 'GS-2018A-FT-101'], @@ -433,6 +450,7 @@ 'N20050826S0137': ['GN-2005B-Q-16-85-001', Inst.MICHELLE, 'GN-2005B-Q-16'], 'N20060413S0129': ['GN-CAL20060413-7-001', Inst.MICHELLE, 'GN-CAL20060413'], 'N20080308S0086': ['GN-CAL20080308-8-016', Inst.MICHELLE, 'GN-CAL20080308'], + 'N20100116S0154': ['GN-2009B-Q-3-64-002', Inst.MICHELLE, 'GN-2009B-Q-3'], # NICI 'S20100102S0035': ['GS-2009B-Q-14-129-029', Inst.NICI, 'GS-2009B-Q-14'], 'S20100218S0028': ['GS-2009B-Q-21-19-001', Inst.NICI, 'GS-2009B-Q-21'], @@ -472,6 +490,7 @@ 'N20141203S0891': ['GN-2014B-C-1-157-100', Inst.NIRI, 'GN-2014B-C-1'], 'N20030325S0098': ['GN-2003A-Q-51-2-004', Inst.NIRI, 'GN-2003A-Q-51'], 'N20211017S0139': ['GN-2021B-Q-110-28-126', Inst.NIRI, 'GN-2021B-Q-110'], + 'N20030325S0353': ['GN-CAL20030325-21-003', Inst.NIRI, 'GN-CAL20030325'], # OSCIR 'r01dec05_007': ['GS-2001B-Q-31-9-007', Inst.OSCIR, 'GS-2001B-Q-31'], '01MAY08_023': ['GN-2001A-C-4-11-9023', Inst.OSCIR, 'GN-2001A-C-4'], @@ -801,6 +820,9 @@ def mock_query_endpoint_5(url, timeout=-1): if url.startswith('https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-08-28T17:05:00'): with open(f'{TEST_DATA_DIR}/diskfiles_mock/query_limit.html') as f: result.text = f.read() + elif url.startswith('https://archive.gemini.edu/diskfiles/entrytimedaterange=2024-08-27T03:50:00'): + with open(f'{TEST_DATA_DIR}/diskfiles_mock/md.html') as f: + result.text = f.read() return result @@ -1039,17 +1061,18 @@ def _run_test_common( test_reporter = mc.ExecutionReporter2(test_config) filter_cache = svofps.FilterMetadataCache(svofps_mock) clients_mock = Mock() - for entry in test_set: - storage_name = GemName(entry, filter_cache) + for test_f_name, test_obs_id in test_set.items(): + storage_name = GemName(test_f_name, filter_cache) + storage_name.obs_id = test_obs_id test_subject = gemini_metadata.GeminiMetaVisitRunnerMeta( clients_mock, test_config, [fits2caom2_augmentation], test_reporter ) def _read_header_mock(ignore1, ignore2, ignore3, ignore4): - if 'S20210518S0022' in entry: + if 'S20210518S0022' in test_f_name: return [] else: - return get_local_file_headers(entry) + return get_local_file_headers(test_f_name) header_mock.side_effect = _read_header_mock clients_mock.metadata_client.read.return_value = observation diff --git a/gem2caom2/tests/test_caom_gen_visit.py b/gem2caom2/tests/test_caom_gen_visit.py index b17c72d..a0ad4a1 100644 --- a/gem2caom2/tests/test_caom_gen_visit.py +++ b/gem2caom2/tests/test_caom_gen_visit.py @@ -192,6 +192,10 @@ def _read_header_mock(ignore1, ignore2, ignore3, ignore4): clients_mock, test_config, [fits2caom2_augmentation], test_reporter ) storage_name = GemName(test_name, filter_cache) + if gem_mocks.LOOKUP[test_file_id][1] == Inst.ZORRO: + storage_name.obs_id = test_file_id[:-1] + else: + storage_name.obs_id = gem_mocks.LOOKUP[test_file_id][0] context = {'storage_name': storage_name} try: test_subject.execute(context) diff --git a/gem2caom2/tests/test_data_source.py b/gem2caom2/tests/test_data_source.py index 3e39da0..217bdaf 100644 --- a/gem2caom2/tests/test_data_source.py +++ b/gem2caom2/tests/test_data_source.py @@ -190,3 +190,34 @@ def test_diskfiles_incremental_source_limit(query_mock, test_config): assert test_reporter.capture_todo.called, 'capture_todo' assert test_reporter.capture_todo.call_count == 1, 'wrong number of capture_todo calls' assert test_subject.max_records_encountered(), 'limit warning' + + +@patch('gem2caom2.data_source.query_endpoint_session') +def test_diskfiles_incremental_source_md(query_mock, test_config): + # https://archive.gemini.edu/diskfiles/entrytimedaterange=-- + # get results + query_mock.side_effect = gem_mocks.mock_query_endpoint_5 + + test_http_session = Mock() + test_subject = data_source.IncrementalSourceDiskfiles(test_config, test_http_session, GemName, Mock()) + assert test_subject is not None, 'expect construction success' + test_reporter = Mock() + test_subject.reporter = test_reporter + + prev_exec_time = datetime(year=2024, month=8, day=27, hour=3, minute=50, second=0) + exec_time = datetime(year=2024, month=8, day=27, hour=4, minute=0, second=0) + + test_result = test_subject.get_time_box_work(prev_exec_time, exec_time) + assert test_result is not None, 'expect a result' + assert len(test_result) == 3, 'wrong number of results' + test_first_entry = test_result.popleft() + assert test_first_entry.storage_entry.file_name == 'S20240827S0034.fits', 'wrong first file' + assert test_first_entry.entry_dt == datetime(2024, 8, 27, 3, 54, 50, 692569), 'wrong fits datetime' + assert test_first_entry.storage_entry.obs_id == 'GS-2024B-DD-103-8-001', 'wrong first obs id' + test_last_entry = test_result.pop() + assert test_last_entry.storage_entry.file_name == 'S20240827S0035.fits', 'wrong 2nd file' + assert test_last_entry.entry_dt == datetime(2024, 8, 27, 3, 56, 43, 418974), 'wrong last datetime' + assert test_last_entry.storage_entry.obs_id == 'GS-2024B-DD-103-8-002', 'wrong last obs id' + assert test_reporter.capture_todo.called, 'capture_todo' + assert test_reporter.capture_todo.call_count == 1, 'wrong number of capture_todo calls' + assert not test_subject.max_records_encountered(), 'limit warning' diff --git a/gem2caom2/tests/test_gemini_metadata.py b/gem2caom2/tests/test_gemini_metadata.py index fcfcb14..6c8147f 100644 --- a/gem2caom2/tests/test_gemini_metadata.py +++ b/gem2caom2/tests/test_gemini_metadata.py @@ -71,7 +71,7 @@ from astropy.io import fits from astropy.table import Table -from mock import patch, Mock +from mock import ANY, patch, Mock from cadcutils import exceptions from caom2pipe import manage_composable as mc @@ -187,3 +187,19 @@ def test_header_not_at_cadc(retrieve_json_mock, clients_mock, test_config): test_session_mock.get.assert_called_with( 'https://archive.gemini.edu/fullheader/N20220314S0229.fits', timeout=20 ), 'wrong mock args' + + +@patch('caom2pipe.client_composable.ClientCollection') +@patch('gem2caom2.gemini_metadata.retrieve_gemini_headers') +def test_header_not_at_cadc_no_reader(retrieve_gemini_mock, clients_mock, test_config): + # the file is private, re-ingestion fails to find headers at CADC, needs to go back to archive.gemini.edu + test_f_name = 'N20220314S0229.fits.bz2' + test_obs_id = 'GN-CAL20220314-18-083' + retrieve_gemini_mock.side_effect = gem_mocks._mock_retrieve_headers + clients_mock.data_client.get_head.side_effect = exceptions.UnexpectedException + test_storage_name = gem_name.GemName(file_name=test_f_name) + test_storage_name.obs_id = test_obs_id + test_result = gemini_metadata.retrieve_headers(test_f_name, Mock(), clients_mock, test_config) + assert test_result is not None, 'expect a result' + assert retrieve_gemini_mock.called, 'retrieve mock not called' + retrieve_gemini_mock.assert_called_with(test_f_name, ANY, ANY ), 'wrong mock args' diff --git a/gem2caom2/tests/test_meta_visit_edge_cases.py b/gem2caom2/tests/test_meta_visit_edge_cases.py index 8561c2f..c3744f0 100644 --- a/gem2caom2/tests/test_meta_visit_edge_cases.py +++ b/gem2caom2/tests/test_meta_visit_edge_cases.py @@ -104,6 +104,8 @@ def test_broken_obs( f'{gem_mocks.TEST_DATA_DIR}/broken_files/{test_obs_id}.expected.xml' ) + test_set = {test_fqn: test_obs_id} + gem_mocks._run_test_common( data_sources=[f'{gem_mocks.TEST_DATA_DIR}/broken_files'], get_pi_mock=get_pi_mock, @@ -112,7 +114,7 @@ def test_broken_obs( header_mock=header_mock, json_mock=json_mock, file_type_mock=file_type_mock, - test_set=[test_fqn], + test_set=test_set, expected_fqn=expected_fqn, test_config=test_config, tmp_path=tmp_path, @@ -149,6 +151,7 @@ def test_unauthorized_at_gemini( # non-zero length list test_fqn = f'{gem_mocks.TEST_DATA_DIR}/broken_files/{test_f_name}' expected_fqn = f'{gem_mocks.TEST_DATA_DIR}/GMOS/{test_fid}.expected.xml' + test_set = {test_fqn: 'GS-2021A-Q-777-1-001'} gem_mocks._run_test_common( data_sources=[f'{gem_mocks.TEST_DATA_DIR}/broken_files'], get_pi_mock=get_pi_mock, @@ -157,7 +160,7 @@ def test_unauthorized_at_gemini( json_mock=json_mock, header_mock=header_mock, file_type_mock=file_type_mock, - test_set=[test_fqn], + test_set=test_set, expected_fqn=expected_fqn, test_config=test_config, tmp_path=tmp_path, From 46febab740648a4437dbcb30178d43f727d021a9 Mon Sep 17 00:00:00 2001 From: Sharon Goliath Date: Tue, 10 Dec 2024 13:43:37 -0800 Subject: [PATCH 4/5] CADC-13844 - integrating the existing working code back in. --- gem2caom2/fits2caom2_augmentation.py | 22 ++- gem2caom2/main_app.py | 8 +- gem2caom2/preview_augmentation.py | 11 +- gem2caom2/pull_augmentation.py | 10 +- gem2caom2/tests/data/diskfiles_mock/md.html | 131 ++++++++++++++++++ .../tests/data/programs/GN-CAL20220915.xml | 27 ++++ 6 files changed, 199 insertions(+), 10 deletions(-) create mode 100644 gem2caom2/tests/data/diskfiles_mock/md.html create mode 100644 gem2caom2/tests/data/programs/GN-CAL20220915.xml diff --git a/gem2caom2/fits2caom2_augmentation.py b/gem2caom2/fits2caom2_augmentation.py index a216a0a..9d5fdaa 100644 --- a/gem2caom2/fits2caom2_augmentation.py +++ b/gem2caom2/fits2caom2_augmentation.py @@ -70,8 +70,23 @@ from caom2pipe import caom_composable as cc from gem2caom2 import main_app +class GeminiFits2caom2Visitor(cc.Fits2caom2Visitor): + def __init__(self, observation, **kwargs): + super().__init__(observation, **kwargs) + + def _get_mapping(self, headers, _): + return main_app.mapping_factory( + self._storage_name, + headers, + self._metadata_reader, + self._clients, + self._observable, + self._observation, + self._config, + ) + -class GeminiFits2caom2Visitor(cc.Fits2caom2VisitorRunnerMeta): +class GeminiFits2caom2VisitorRunnerMeta(cc.Fits2caom2VisitorRunnerMeta): def __init__(self, observation, **kwargs): super().__init__(observation, **kwargs) @@ -88,4 +103,7 @@ def _get_mapping(self, dest_uri): def visit(observation, **kwargs): - return GeminiFits2caom2Visitor(observation, **kwargs).visit() + if 'reporter' in kwargs: + return GeminiFits2caom2VisitorRunnerMeta(observation, **kwargs).visit() + else: + return GeminiFits2caom2Visitor(observation, **kwargs).visit() diff --git a/gem2caom2/main_app.py b/gem2caom2/main_app.py index fbd70f3..02b32bd 100644 --- a/gem2caom2/main_app.py +++ b/gem2caom2/main_app.py @@ -692,7 +692,10 @@ def update(self): continue if GemName.is_preview(artifact.uri): continue - update_artifact_meta(artifact, self._storage_name.file_info.get(artifact.uri)) + if self._lookup._reader: + update_artifact_meta(artifact, self._lookup._reader.file_info.get(artifact.uri)) + else: + update_artifact_meta(artifact, self._storage_name.file_info.get(artifact.uri)) self._update_artifact(artifact) processed = ofr.is_processed(self._storage_name.file_name) if self._instrument in [ @@ -2344,7 +2347,8 @@ def _update_energy(self, chunk, data_product_type, filter_name): 'R600': 3744.0, 'R400': 1918.0, 'R150': 631.0, - # 'B480': 1522.0, # WF - 16-09-22 ## TODO WF - 23-09-22 - need more accurate min/max values + # current best value available from https://gemini.edu/instrumentation/gmos/components#Gratings + 'B480': 1522.0, # WF - 16-09-22 ## TODO WF - 23-09-22 - need more accurate min/max values } # DB 02-12-19 # Found basic info for the Lya395 filter in a published paper. diff --git a/gem2caom2/preview_augmentation.py b/gem2caom2/preview_augmentation.py index 7820295..52d53b6 100644 --- a/gem2caom2/preview_augmentation.py +++ b/gem2caom2/preview_augmentation.py @@ -94,9 +94,14 @@ def visit(observation, **kwargs): clients = kwargs.get('clients') if clients is None or clients.data_client is None: logging.warning('Need a cadc_client to update preview records.') - observable = kwargs.get('observable') - if observable is None: - raise mc.CadcException('Visitor needs a observable parameter.') + reporter = kwargs.get('reporter') + observer = kwargs.get('observable') + if reporter is None and observer is None: + raise mc.CadcException('Visitor needs a reporter or observable parameter.') + if reporter: + observable = reporter._observable + else: + observable = observer storage_name = kwargs.get('storage_name') if storage_name is None: raise mc.CadcException('Visitor needs a storage_name parameter.') diff --git a/gem2caom2/pull_augmentation.py b/gem2caom2/pull_augmentation.py index a38c321..a45ca49 100644 --- a/gem2caom2/pull_augmentation.py +++ b/gem2caom2/pull_augmentation.py @@ -89,9 +89,13 @@ def visit(observation, **kwargs): logging.warning('Need clients to update. Stopping pull visitor.') return reporter = kwargs.get('reporter') - if reporter is None: - raise mc.CadcException('Visitor needs a reporter parameter.') - observable = reporter._observable + observer = kwargs.get('observable') + if reporter is None and observer is None: + raise mc.CadcException('Visitor needs a reporter or observable parameter.') + if reporter: + observable = reporter._observable + else: + observable = observer storage_name = kwargs.get('storage_name') if storage_name is None: raise mc.CadcException('Visitor needs a storage_name parameter.') diff --git a/gem2caom2/tests/data/diskfiles_mock/md.html b/gem2caom2/tests/data/diskfiles_mock/md.html new file mode 100644 index 0000000..5d626fe --- /dev/null +++ b/gem2caom2/tests/data/diskfiles_mock/md.html @@ -0,0 +1,131 @@ + + + + + + + + +FITS header diskfiles table + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Filename↑↓ + Data Label↑↓ + UT Date Time↑↓ + Inst↑↓ + Present + Entry Time + LastMod + File Size + File MD5 + Compressed + Data Size + Data MD5 +
S20240827S0036.fits + +[A] +GS-2024B-DD-103-8-003 + 2024-08-27 00:41:40 + GMOS-S + True + 2024-08-27 03:56:21.223390+00:00 + 2024-08-27 03:56:21.191324+00:00 + 4901634 + 5b03d1510e846953dce1f4aae0d3a491 + True + 14849280 + 250e972fc2cfbebe3acaf918b0a0293b +
S20240827S0035.fits-fits!-md! + +[A] +GS-2024B-DD-103-8-002 + 2024-08-27 00:21:07 + GMOS-S + False + 2024-08-27 03:53:04.068584+00:00 + 2024-08-27 03:53:04.036587+00:00 + 4923541 + de5d0659483d00bb58a5fea9f32254cd + True + 14849280 + 8ea7e29801fec81aa54c966bb3584490 +
S20240827S0035.fits + +[A] +GS-2024B-DD-103-8-002 + 2024-08-27 00:21:07 + GMOS-S + True + 2024-08-27 03:56:43.418974+00:00 + 2024-08-27 03:56:43.391849+00:00 + 4923541 + de5d0659483d00bb58a5fea9f32254cd + True + 14849280 + 8ea7e29801fec81aa54c966bb3584490 +
S20240827S0034.fits + +[A] + +[L] +GS-2024B-DD-103-8-001 + 2024-08-27 00:00:37 + GMOS-S + True + 2024-08-27 03:54:50.692569+00:00 + 2024-08-27 03:54:50.659167+00:00 + 4931086 + e7a70c43b0fd458fc5b81a270359501e + True + 14849280 + 1a8f8b3c07dbde49ffeb8cc9eabed540 +
+ + + + + + + + \ No newline at end of file diff --git a/gem2caom2/tests/data/programs/GN-CAL20220915.xml b/gem2caom2/tests/data/programs/GN-CAL20220915.xml new file mode 100644 index 0000000..1eef58c --- /dev/null +++ b/gem2caom2/tests/data/programs/GN-CAL20220915.xml @@ -0,0 +1,27 @@ + + + + + + + +Detail for Program: GN-CAL20220915 + + + +

Program: GN-CAL20220915

+ + + + + +
Title:GN-CAL20220915
PI:
Co-I(s):
+

Abstract

+
+No abstract +
+ + + + + \ No newline at end of file From 6c362c35ae07124e2bfb94485bc7e6a807b08571 Mon Sep 17 00:00:00 2001 From: Sharon Goliath Date: Tue, 10 Dec 2024 14:00:52 -0800 Subject: [PATCH 5/5] fix(data_source.py): ensure the file metadata is in the FileInfo dataclass format --- gem2caom2/data_source.py | 10 +++++++++- gem2caom2/tests/test_data_source.py | 6 ++++++ 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/gem2caom2/data_source.py b/gem2caom2/data_source.py index a92f5a6..f9606ec 100644 --- a/gem2caom2/data_source.py +++ b/gem2caom2/data_source.py @@ -70,6 +70,9 @@ from collections import defaultdict, deque, OrderedDict from datetime import datetime +from cadcdata import FileInfo +from caom2utils.blueprints import _to_int +from caom2utils.data_util import get_file_type from caom2pipe import client_composable as clc from caom2pipe import data_source_composable as dsc from caom2pipe.manage_composable import build_uri, CaomName, ISO_8601_FORMAT, make_datetime, query_endpoint_session @@ -284,7 +287,12 @@ def get_time_box_work(self, prev_exec_dt, exec_dt): for value in values: file_name = value.get('filename') storage_name = self._storage_name_ctor(file_name, self._filter_cache) - storage_name.file_info[storage_name.destination_uris[0]] = value + storage_name.file_info[storage_name.destination_uris[0]] = FileInfo( + id=file_name, + size=_to_int(value.get('data_size')), + md5sum=value.get('data_md5'), + file_type=get_file_type(file_name), + ) repaired_data_label = repair_data_label(file_name, value.get('datalabel')) storage_name.obs_id = repaired_data_label entries.append(dsc.RunnerMeta(storage_name, entry_dt)) diff --git a/gem2caom2/tests/test_data_source.py b/gem2caom2/tests/test_data_source.py index 217bdaf..e14ba8b 100644 --- a/gem2caom2/tests/test_data_source.py +++ b/gem2caom2/tests/test_data_source.py @@ -218,6 +218,12 @@ def test_diskfiles_incremental_source_md(query_mock, test_config): assert test_last_entry.storage_entry.file_name == 'S20240827S0035.fits', 'wrong 2nd file' assert test_last_entry.entry_dt == datetime(2024, 8, 27, 3, 56, 43, 418974), 'wrong last datetime' assert test_last_entry.storage_entry.obs_id == 'GS-2024B-DD-103-8-002', 'wrong last obs id' + test_file_info = test_last_entry.storage_entry.file_info.get('gemini:GEMINI/S20240827S0035.fits') + assert test_file_info is not None, 'file info' + assert test_file_info.id == 'S20240827S0035.fits', 'file info id' + assert test_file_info.size == 14849280, 'file info size' + assert test_file_info.md5sum == '8ea7e29801fec81aa54c966bb3584490', 'file info checksum' + assert test_file_info.file_type == 'application/fits', 'file info type' assert test_reporter.capture_todo.called, 'capture_todo' assert test_reporter.capture_todo.call_count == 1, 'wrong number of capture_todo calls' assert not test_subject.max_records_encountered(), 'limit warning'