Merge pull request #173 from prjemian/158-validate-report-option

support validate's report option

.flake8

@@ -18,4 +18,4 @@ exclude =
 # some in test cases
 max-line-length = 115
 # TODO: re-enable E501 error
-ignore: E226,E402,E501,E741,F401,F403,F811,W503,W504
+ignore: E226,E231,E402,E501,E741,F401,F403,F811,W503,W504

.github/workflows/upload_new_tag_to_pypi.yml

@@ -35,10 +35,9 @@ jobs:
       run: >-
         twine check dist/*
 
-
-    - name: Publish distribution 📦 to PyPI
+    - name: Publish 📦 to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

docs/source/validate.rst

@@ -6,14 +6,14 @@ Validation
 
 .. toctree::
    :hidden:
-   
+
    data_file_validation
    nxdl_file_validation
 
 *Validation* is the process of comparing an object with a standard.
 An important aspect of validation is the report of each aspect tested and whether
 or not it complies with the standard.  This is a useful and necessary step when
-composing NeXus HDF5 data files or software that will read NeXus data files and when 
+composing NeXus HDF5 data files or software that will read NeXus data files and when
 building NeXus Definition Language (NXDL) files.
 
 In NeXus, three basic types of object can be validated:
@@ -34,26 +34,19 @@ validate a NeXus file
 
 .. code-block:: console
    :linenos:
-   
-   usage: punx validate [-h] [--report REPORT] [-l [LOGFILE]] [-i INTEREST]
-                        infile
-   
+
+   usage: punx validate [-h] [--report REPORT] infile
+
    positional arguments:
-     infile                HDF5 or NXDL file name
-   
+     infile           HDF5 or NXDL file name
+
    optional arguments:
-     -h, --help            show this help message and exit
-     --report REPORT       select which validation findings to report, choices:
-                           COMMENT,ERROR,NOTE,OK,TODO,UNUSED,WARN
-     -l [LOGFILE], --logfile [LOGFILE]
-                           log output to file (default: no log file)
-     -i INTEREST, --interest INTEREST
-                           logging interest level (1 - 50), default=1 (Level 1)
+     -h, --help       show this help message and exit
+    --report REPORT  select which validation findings to report, choices: COMMENT,ERROR,NOTE,OK,OPTIONAL,TODO,UNUSED,WARN (separate with comma if more
+                     than one, do not use white space)
 
 The **REPORT** findings are as presented in the table above for each validation step.
 
-The logging **INTEREST** levels are for output from the program, 
-
 ..
 	For now, refer to the source code documentation: :ref:`source.validate`.
 

punx/main.py

@@ -222,7 +222,7 @@ def func_validate(args):
     report_choices, trouble = [], []
     for c in args.report.upper().split(","):
         if c in finding.VALID_STATUS_DICT:
-            report_choices.append(finding.VALID_STATUS_DICT[c])
+            report_choices.append(c)
         else:
             trouble.append(c)
     if len(trouble) > 0:
@@ -244,7 +244,7 @@ def func_validate(args):
         exit_message(str(_exc))
 
     # report the findings from the validation
-    validator.print_report()
+    validator.print_report(statuses=report_choices)
 
 
 def _install(cm, grr, ref, use_user_cache=True, force=False):
@@ -430,8 +430,11 @@ def parse_command_line_arguments():
     p_sub.add_argument("infile", help="HDF5 or NXDL file name")
     p_sub.set_defaults(func=func_validate)
     reporting_choices = ",".join(sorted(finding.VALID_STATUS_DICT.keys()))
-    help_text = "select which validation findings to report, choices: "
-    help_text += reporting_choices
+    help_text = (
+        "select which validation findings to report, "
+        f"choices: {reporting_choices}"
+        " (separate with comma if more than one, do not use white space)"
+    )
     p_sub.add_argument("--report", default=reporting_choices, help=help_text)
     # TODO: add_logging_argument(p_sub)
 

punx/tests/test_validate.py

@@ -440,7 +440,7 @@ def TODO_test_axes_attribute_2D__fail(hfile):
         ds = dg.create_dataset("y", data=vec)
         ds.attrs["units"] = "mm"
 
-        dg.attrs["axes"] = utils.string_list_to_hdf5(["x,y", ])
+        dg.attrs["axes"] = utils.string_list_to_hdf5(["x,y",])
         dg.attrs["x_indices"] = [0]
         dg.attrs["y_indices"] = [1]
 
@@ -654,4 +654,54 @@ def TODO_test_default_plot_v1_fail(hfile):
     # TODO:
 
 
+@pytest.mark.parametrize(
+    "infile, report, observations",
+    [
+        ["writer_1_3.hdf5", "TODO", 7],
+        ["writer_1_3.hdf5", "NOTE", 1],
+        ["writer_1_3.hdf5", "NOTE,TODO", 7 + 1],
+        ["writer_2_1.hdf5", "note", 0],
+        ["writer_2_1.hdf5", "TODO", 11],
+        ["1998spheres.h5", "ERROR", 2],
+        ["02_03_setup.h5", "NOTE,OPTIONAL,ERROR", 98 + 70 + 0],
+        ["prj_test.nexus.hdf5", "", 121],
+    ],
+)
+def test_report_option(infile, report, observations, capsys):
+    full_file_name = os.path.join(EXAMPLE_DATA_DIR, infile)
+    assert os.path.exists(full_file_name)
+
+    if report == "":
+        report = ",".join(finding.VALID_STATUS_DICT.keys())
+    reported_statuses = report.upper().split(",")
+    for s in reported_statuses:
+        assert s in finding.VALID_STATUS_DICT
+
+    validator = validate.Data_File_Validator()
+    validator.validate(full_file_name)
+    validator.print_report(statuses=reported_statuses)
+    captured = capsys.readouterr()
+    lines = captured.out.splitlines()
+    assert len(lines) > 17  # length of 2nd table
+
+    count = 0
+    for line in captured.out.splitlines()[6:]:
+        if (
+            # only look at content lines in first table
+            len(line.strip()) == 0
+            or line.startswith("==")
+            or line.startswith("data file")
+            or line.startswith("NeXus definitions")
+            or line.startswith("findings")
+            or line.startswith("address")
+        ):
+            continue
+        if line.startswith("summary statistics"):
+            # end when 2nd (summary) table starts
+            break
+        assert line.split()[1] in reported_statuses
+        count += 1
+    assert count == observations
+
+
 # Note: class Test_Example_data is already handled by test_data_files.py

punx/validate.py

@@ -169,10 +169,12 @@ def finding_summary(self, report_statuses=None):
             summary[f.status] += 1
         return summary
 
-    def print_report(self):
+    def print_report(self, statuses=None):
         """
-        print a validation report
+        Print a validation report.
         """
+        reported_statuses = statuses or list(finding.VALID_STATUS_DICT.keys())
+
         print("data file: " + self.fname)
         print(
             "NeXus definitions ({}): {}, dated {}, sha={}\n".format(
@@ -195,14 +197,13 @@ def sort_validations(f):
         for label in "address status test comments".split():
             t.addLabel(label)
         for f in sorted(self.validations, key=sort_validations):
-            if f.status == finding.OPTIONAL:
-                continue  # enable if you like verbose reports
-            row = []
-            row.append(f.h5_address)
-            row.append(f.status)
-            row.append(f.test_name)
-            row.append(f.comment)
-            t.addRow(row)
+            if str(f.status) in reported_statuses:
+                row = []
+                row.append(f.h5_address)
+                row.append(f.status)
+                row.append(f.test_name)
+                row.append(f.comment)
+                t.addRow(row)
         print(str(t))
 
         summary = self.finding_summary()