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o2r-project / o2r-meta

Metadata toolsuite for an extract-map-validate workflow supporting reproducible research
Apache License 2.0
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Fix relative mainfile path #101

Closed nuest closed 6 years ago

nuest commented 6 years ago

Failing test:

======================================================================================== FAILURES =========================================================================================
________________________________________________________________________________ test_minimal[subprocess] _________________________________________________________________________________

script_runner = <ScriptRunner subprocess>, tmpdir = local('/tmp/pytest-of-daniel/pytest-2/test_minimal_subprocess_0')

    def test_minimal(script_runner, tmpdir):
        ret = script_runner.run('python3', 'o2rmeta.py', '-debug', 'extract',
            '-i', 'extract/tests/minimal',
            '-o', str(tmpdir),
            '-xo', '-m')
        print(ret.stdout)
        print(ret.stderr)

        assert ret.success, "process should return success"
        assert ret.stderr == '', "stderr should be empty"
        assert "total files processed: 2" in ret.stdout, "should process 2 files"

        metadata = json.load(open(os.path.join(str(tmpdir), 'metadata_raw.json')))
        assert metadata['displayfile'] == "extract/tests/minimal/display.html"
>       assert metadata['mainfile'] == "extract/tests/minimal/main.Rmd"
E       AssertionError: assert 'main.Rmd' == 'extract/tests/minimal/main.Rmd'
E         - main.Rmd
E         + extract/tests/minimal/main.Rmd

extract/tests/test_extract_maindisplay.py:52: AssertionError
---------------------------------------------------------------------------------- Captured stdout call -----------------------------------------------------------------------------------
[o2rmeta] 20180321.132704 received arguments: {'basedir': None, 'outputdir': '/tmp/pytest-of-daniel/pytest-2/test_minimal_subprocess_0', 'modexml': False, 'metafiles': True, 'outputtostdout': False, 'stayoffline': True, 'ercid': None, 'formats': False, 'inputdir': 'extract/tests/minimal', 'debug': True, 'tool': 'extract'}
[o2rmeta] 20180321.132704 launching extractor
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_bagittxt.ParseBagitTxt object at 0x7f4dc45e22e8>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_candidatefiles.ParseCandidateFiles object at 0x7f4dc45e2320>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_geojson.ParseGeojson object at 0x7f4dc45e2470>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_netcdf.ParseNetcdf object at 0x7f4dc45e26a0>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_ogc_shp.ParseGeopackage object at 0x7f4dc45e2710>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_rmd.ParseRmd object at 0x7f4dc45e2c88>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_rdata.ParseRData object at 0x7f4dc45e2e80>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_yaml.ParseYaml object at 0x7f4dc45f3710>
[o2rmeta][debug: extract.metaextract @ register_parsers] 20180321.132705 <parsers.parse_erc_config.ParseErcConfig object at 0x7f4db44bf630>
[o2rmeta] 20180321.132705 <class 'parsers.parse_rdata.ParseRData'> unavailable (No module named 'rpy2')
[o2rmeta][debug: extract.metaextract @ start] 20180321.132705 extracted from: extract/tests/minimal/display.html
[o2rmeta] 20180321.132705 skipping orcid lookup (http disabled)
[o2rmeta] 20180321.132705 <class 'parsers.parse_rdata.ParseRData'> unavailable (No module named 'rpy2')
[o2rmeta][debug: extract.metaextract @ start] 20180321.132705 extracted from: extract/tests/minimal/main.Rmd
[o2rmeta] 20180321.132705 total files processed: 2
[o2rmeta] 20180321.132705 total extraction errors: 0
[o2rmeta] 20180321.132705 total skipped files: 0
[o2rmeta] 20180321.132705 2.4951 KB written to ../../../../../tmp/pytest-of-daniel/pytest-2/test_minimal_subprocess_0/metadata_raw.json
[o2rmeta] 20180321.132705 skipping erc spec download (http disabled)

See also https://github.com/o2r-project/o2r-meta/pull/100

nuest commented 6 years ago

Test is not failing anymore.