psdi-data-conversion 0.0.33__py3-none-any.whl → 0.0.36__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- psdi_data_conversion/app.py +23 -3
- psdi_data_conversion/constants.py +2 -0
- psdi_data_conversion/converter.py +16 -6
- psdi_data_conversion/converters/atomsk.py +3 -1
- psdi_data_conversion/converters/base.py +99 -39
- psdi_data_conversion/converters/c2x.py +3 -1
- psdi_data_conversion/converters/openbabel.py +40 -1
- psdi_data_conversion/database.py +5 -0
- psdi_data_conversion/main.py +18 -10
- psdi_data_conversion/static/content/accessibility.htm +5 -5
- psdi_data_conversion/static/content/convert.htm +31 -15
- psdi_data_conversion/static/content/convertato.htm +46 -28
- psdi_data_conversion/static/content/convertc2x.htm +47 -28
- psdi_data_conversion/static/content/documentation.htm +4 -4
- psdi_data_conversion/static/content/download.htm +4 -1
- psdi_data_conversion/static/content/feedback.htm +4 -4
- psdi_data_conversion/static/content/index-versions/psdi-common-header.html +1 -1
- psdi_data_conversion/static/content/psdi-common-header.html +1 -1
- psdi_data_conversion/static/content/report.htm +9 -7
- psdi_data_conversion/static/javascript/common.js +20 -0
- psdi_data_conversion/static/javascript/convert.js +1 -2
- psdi_data_conversion/static/javascript/convert_common.js +100 -7
- psdi_data_conversion/static/javascript/convertato.js +1 -2
- psdi_data_conversion/static/javascript/convertc2x.js +1 -2
- psdi_data_conversion/static/javascript/format.js +12 -0
- psdi_data_conversion/static/javascript/report.js +6 -0
- psdi_data_conversion/static/styles/format.css +13 -0
- psdi_data_conversion/static/styles/psdi-common.css +5 -2
- psdi_data_conversion/templates/index.htm +4 -1
- psdi_data_conversion/testing/conversion_test_specs.py +240 -149
- psdi_data_conversion/testing/utils.py +22 -7
- {psdi_data_conversion-0.0.33.dist-info → psdi_data_conversion-0.0.36.dist-info}/METADATA +29 -6
- {psdi_data_conversion-0.0.33.dist-info → psdi_data_conversion-0.0.36.dist-info}/RECORD +36 -36
- {psdi_data_conversion-0.0.33.dist-info → psdi_data_conversion-0.0.36.dist-info}/WHEEL +0 -0
- {psdi_data_conversion-0.0.33.dist-info → psdi_data_conversion-0.0.36.dist-info}/entry_points.txt +0 -0
- {psdi_data_conversion-0.0.33.dist-info → psdi_data_conversion-0.0.36.dist-info}/licenses/LICENSE +0 -0
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@@ -15,194 +15,285 @@ from psdi_data_conversion.converters.openbabel import CONVERTER_OB, COORD_GEN_KE
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from psdi_data_conversion.testing.conversion_callbacks import (CheckArchiveContents, CheckException, CheckLogContents,
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CheckLogContentsSuccess, CheckFileStatus,
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CheckStderrContents, CheckStdoutContents,
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MatchOutputFile, MultiCallback)
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from psdi_data_conversion.testing.utils import ConversionTestSpec
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"""
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MatchOutputFile, MultiCallback as MCB)
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from psdi_data_conversion.testing.utils import ConversionTestSpec as Spec
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l_all_test_specs: list[Spec] = []
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"""All test specs defined in this file"""
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l_all_test_specs.append(Spec(name="Basic",
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filename=["1NE6.mmcif", "standard_test.cdxml",
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"hemoglobin.pdb", "aceticacid.mol", "nacl.cif",
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"hemoglobin.pdb", "hemoglobin.pdb", "nacl.cif",
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"hemoglobin.pdb", "hemoglobin.pdb", "nacl.cif",
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"ethanol.xyz"],
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to_format=["pdb", "inchi",
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"cif", "mol2", "xyz",
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"cif", "xyz", "xyz",
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"cif", "xyz", "xyz",
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"cml"],
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converter_name=[CONVERTER_OB, CONVERTER_OB,
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CONVERTER_OB, CONVERTER_OB, CONVERTER_OB,
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CONVERTER_ATO, CONVERTER_ATO, CONVERTER_ATO,
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CONVERTER_C2X, CONVERTER_C2X, CONVERTER_C2X,
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CONVERTER_OB],
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callback=MCB(CheckFileStatus(),
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CheckLogContentsSuccess()),
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))
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"""A basic set of test conversions which we expect to succeed without issue, running conversions with each of the
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Open Babel, Atomsk, and c2x converters"""
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archive_callback =
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archive_callback = MCB(CheckFileStatus(),
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CheckArchiveContents(l_filename_bases=["caffeine-no-flags",
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"caffeine-ia",
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"caffeine-ia-ox",
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"caffeine-ia-okx",
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"caffeine-ia-okx-oof4",
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"caffeine-ia-okx-oof4l5",],
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to_format="inchi"))
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l_all_test_specs.append(Spec(name="Archive",
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filename=["caffeine-smi.zip",
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"caffeine-smi.tar",
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"caffeine-smi.tar.gz"],
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to_format="inchi",
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callback=archive_callback,
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))
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"""A test of converting a archives of files"""
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l_all_test_specs.append(Spec(name="Archive (wrong format)",
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filename="caffeine-smi.zip",
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to_format="inchi",
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conversion_kwargs=[{"from_format": "pdb"},
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{"from_format": "pdb", "strict": True}],
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expect_success=[True, False],
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callback=[CheckStderrContents(const.ERR_WRONG_EXTENSIONS),
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CheckException(ex_type=FileConverterInputException,
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ex_message=const.ERR_WRONG_EXTENSIONS)],
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))
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"""A test that if the user provides the wrong input format for files in an archive, and error will be output to stderr
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"""
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l_all_test_specs.append(Spec(name="Log mode",
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conversion_kwargs=[{"log_mode": const.LOG_NONE},
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{"log_mode": const.LOG_STDOUT},
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{"log_mode": const.LOG_SIMPLE},
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{"log_mode": const.LOG_FULL},
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{"log_mode": const.LOG_FULL_FORCE},],
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callback=[CheckFileStatus(expect_log_exists=False,
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expect_global_log_exists=False),
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CheckFileStatus(expect_log_exists=False,
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expect_global_log_exists=False),
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CheckFileStatus(expect_log_exists=True,
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expect_global_log_exists=False),
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CheckFileStatus(expect_log_exists=True,
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expect_global_log_exists=True),
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CheckFileStatus(expect_log_exists=True,
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expect_global_log_exists=True)],
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compatible_with_gui=False,
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))
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"""Tests that the different log modes have the desired effects on logs
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Not compatible with GUI tests, since the GUI requires the log mode to always be "Full"
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"""
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l_all_test_specs.append(Spec(name="Stdout",
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conversion_kwargs={"log_mode": const.LOG_STDOUT},
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callback=CheckStdoutContents(l_strings_to_exclude=["ERROR", "exception",
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"Exception"],
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l_regex_to_find=[r"File name:\s*nacl",
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const.DATETIME_RE_RAW]
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),
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compatible_with_gui=False,
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))
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"""Test that the log is output to stdout when requested
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Not compatible with GUI tests, since the GUI requires the log mode to always be "Full"
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"""
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l_all_test_specs.append(Spec(name="Quiet",
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conversion_kwargs={"log_mode": const.LOG_NONE},
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callback=CheckStdoutContents(l_regex_to_exclude=r"."),
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compatible_with_gui=False,
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))
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"""Test that nothing is output to stdout when quiet mode is enabled
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Not compatible with GUI tests, since the GUI doesn't support quiet mode
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"""
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l_all_test_specs.append(Spec(name="Open Babel Warning",
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filename="1NE6.mmcif",
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to_format="pdb",
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callback=CheckLogContentsSuccess(["Open Babel Warning",
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"Failed to kekulize aromatic bonds",])
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))
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"""A test that confirms expected warnings form Open Babel are output and captured in the log"""
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invalid_converter_callback =
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invalid_converter_callback = MCB(CheckFileStatus(expect_output_exists=False,
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expect_log_exists=False),
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CheckException(ex_type=FileConverterInputException,
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ex_message="Converter {} not recognized"))
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l_all_test_specs.append(Spec(name="Invalid Converter",
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converter_name="INVALID",
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expect_success=False,
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callback=invalid_converter_callback,
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))
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"""A test that a proper error is returned if an invalid converter is requested"""
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quartz_quality_note_callback = CheckLogContentsSuccess(["WARNING",
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const.QUAL_NOTE_OUT_MISSING.format(const.QUAL_2D_LABEL),
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const.QUAL_NOTE_OUT_MISSING.format(const.QUAL_3D_LABEL),
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const.QUAL_NOTE_IN_MISSING.format(const.QUAL_CONN_LABEL)])
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ethanol_quality_note_callback = CheckLogContentsSuccess(["WARNING",
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"Potential data loss or extrapolation",
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const.QUAL_NOTE_IN_MISSING.format(const.QUAL_CONN_LABEL)])
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hemoglobin_quality_note_callback = CheckLogContentsSuccess(["WARNING",
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"Potential data loss or extrapolation",
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const.QUAL_NOTE_OUT_MISSING.format(const.QUAL_CONN_LABEL)])
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l_all_test_specs.append(Spec(name="Quality note",
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filename=["quartz.xyz", "ethanol.xyz", "hemoglobin.pdb"],
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to_format=["inchi", "cml", "xyz"],
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callback=[quartz_quality_note_callback,
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ethanol_quality_note_callback,
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hemoglobin_quality_note_callback],
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))
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"""A test conversion which we expect to produce a warning for conversion quality issues, where the connections property
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output and will be lost"""
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l_all_test_specs.append(Spec(name="Cleanup input",
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conversion_kwargs={"delete_input": True},
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callback=CheckFileStatus(expect_input_exists=False),
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))
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l_all_test_specs.append(Spec(name="Failed conversion - bad input file",
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filename=["quartz_err.xyz", "cyclopropane_err.mol"],
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to_format=["inchi", "xyz"],
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expect_success=False,
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converter_name=[CONVERTER_OB, CONVERTER_C2X],
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callback=[MCB(CheckFileStatus(expect_output_exists=False,
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expect_log_exists=None),
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CheckException(ex_type=FileConverterAbortException,
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ex_message="Problems reading an XYZ file")),
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MCB(CheckFileStatus(expect_output_exists=False,
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expect_log_exists=None),
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CheckException(ex_type=FileConverterAbortException,
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ex_message="Aborting: mol file contains no atoms"))],
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))
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"""A test that a conversion that fails due to an unreadable input file will properly fail"""
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quartz_error_ob_callback = CheckLogContents(["ERROR",
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"Problems reading an XYZ file: Could not read line #11, file error"])
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l_all_test_specs.append(Spec(name="Errors in logs",
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filename="quartz_err.xyz",
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to_format="inchi",
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converter_name=CONVERTER_OB,
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expect_success=False,
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callback=quartz_error_ob_callback,
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))
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"""A test that when a conversion fails, logs are still produced and contain the expected error message"""
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l_all_test_specs.append(Spec(name="Failed conversion - invalid conversion",
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filename=["Fapatite.ins", "nacl.mol"],
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to_format=["cml", "xyz"],
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expect_success=False,
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converter_name=[CONVERTER_OB, CONVERTER_ATO],
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callback=MCB(CheckFileStatus(expect_output_exists=False,
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expect_log_exists=None),
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CheckException(ex_type=FileConverterHelpException,
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COORD_GEN_QUAL_KEY: "fastest"}},
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COORD_GEN_QUAL_KEY: "best"}}
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"""A set of tests which checks that coordinate generation options are processed correctly, by matching tests using them
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to expected output files"""
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"""All test specs which are compatible with being run on the GUI"""
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(as if using zip on the multiple lists) to test each element in turn.
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"""
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name: str
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filename: str | Iterable[str] = "nacl.cif"
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"""The name of the input file, relative to the input test data location, or a list thereof"""
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to_format: str | Iterable[str] = "pdb"
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"""The format to test converting the input file to, or a list thereof"""
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"""The name of the converter to be used for the test, or a list thereof"""
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conversion_kwargs: dict[str, Any] | Iterable[dict[str, Any]] = field(default_factory=dict)
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should take as its only argument a `ConversionTestInfo` and return a string. The string should be empty if the check
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is passed and should explain the failure otherwise."""
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"""Whether or not this test spec is compatible with being run through the GUI, default True"""
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def __post_init__(self):
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lists, and set up initial values
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# To ease maintainability, we get the list of this class's attributes automatically from its __dict__, excluding
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# any which start with an underscore
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not (attr_name.startswith("_") or
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attr_name == "name" or
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attr_name.startswith("compatible"))]
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"""The format to test converting the input file to"""
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"""The name of the converter to be used for the test"""
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conversion_kwargs: dict[str, Any] = field(default_factory=dict)
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@@ -279,7 +294,7 @@ def _run_single_test_conversion_with_library(test_spec: SingleConversionTestSpec
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if test_spec.expect_success:
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upload_dir=input_dir,
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**test_spec.conversion_kwargs)
|
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@@ -288,7 +303,7 @@ def _run_single_test_conversion_with_library(test_spec: SingleConversionTestSpec
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with pytest.raises(Exception) as exc_info:
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**test_spec.conversion_kwargs)
|
|
@@ -359,7 +374,7 @@ def _run_single_test_conversion_with_cla(test_spec: SingleConversionTestSpec,
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|
|
@@ -369,7 +384,7 @@ def _run_single_test_conversion_with_cla(test_spec: SingleConversionTestSpec,
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|
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@@ -1,6 +1,6 @@
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1
1
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Metadata-Version: 2.1
|
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2
2
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Name: psdi_data_conversion
|
|
3
|
-
Version: 0.0.
|
|
3
|
+
Version: 0.0.36
|
|
4
4
|
Summary: Chemistry file format conversion service, provided by PSDI
|
|
5
5
|
Project-URL: Homepage, https://data-conversion.psdi.ac.uk/
|
|
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6
|
Project-URL: Documentation, https://psdi-uk.github.io/psdi-data-conversion/
|
|
@@ -403,13 +403,21 @@ In addition to the dependencies listed above, this project uses the assets made
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|
### Installation
|
|
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|
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|
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|
-
The CLA and Python library are installed together. This
|
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+
The CLA and Python library are installed together. This project is available on PyPI, and so can be installed via pip with:
|
|
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|
+
|
|
408
|
+
```bash
|
|
409
|
+
pip install psdi-data-conversion
|
|
410
|
+
```
|
|
411
|
+
|
|
412
|
+
If you wish to install from source, this can be done most easily by cloning the project and then executing:
|
|
407
413
|
|
|
408
414
|
```bash
|
|
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415
|
pip install .
|
|
410
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|
```
|
|
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|
|
|
412
|
-
|
|
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|
+
from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
|
|
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|
+
|
|
420
|
+
**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
|
|
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|
|
|
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|
Depending on your system, it may not be possible to install packages in this manner without creating a virtual environment to do so in. You can do this by first installing the `venv` module for Python3 with e.g.:
|
|
415
423
|
|
|
@@ -572,15 +580,23 @@ Enter https://data-conversion.psdi.ac.uk/ in a browser. Guidance on usage is giv
|
|
|
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|
|
|
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|
### Installation and Setup
|
|
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|
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|
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|
-
|
|
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|
+
This project is available on PyPI, and so can be installed via pip, including the necessary dependencies for the GUI, with:
|
|
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|
+
|
|
585
|
+
```bash
|
|
586
|
+
pip install psdi-data-conversion'[gui]'
|
|
587
|
+
```
|
|
588
|
+
|
|
589
|
+
If you wish to install the project locally from source, this can be done most easily by cloning the project and then executing:
|
|
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590
|
|
|
577
591
|
```bash
|
|
578
592
|
pip install .'[gui]'
|
|
579
593
|
```
|
|
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|
|
|
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|
-
If
|
|
595
|
+
**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
|
|
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|
|
|
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|
-
If
|
|
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|
+
If your system does not allow installation in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
|
|
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|
+
|
|
599
|
+
If you've installed this repository from source, you can use the provided `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
|
|
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|
|
|
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|
```bash
|
|
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#!/bin/bash
|
|
@@ -590,6 +606,13 @@ if [ -z $MAX_FILESIZE ]; then
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|
|
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|
export MAX_FILESIZE=0
|
|
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607
|
fi
|
|
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|
|
|
609
|
+
# The envvar MAX_FILESIZE_OB can be used to set the maximum allowed filesize in MB for the Open Babel converter - 0
|
|
610
|
+
# indicates no maximum. This is currently set to 1 MB by default as the converter seems to hang above this limit (not
|
|
611
|
+
# even allowing the process to be cancelled). This can be changed in the future if this is patched
|
|
612
|
+
if [ -z $MAX_FILESIZE_OB ]; then
|
|
613
|
+
export MAX_FILESIZE_OB=1
|
|
614
|
+
fi
|
|
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|
+
|
|
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|
# Logging control - "full" sets server-style logging, which is necessary to produce the output logs with the expected
|
|
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|
# names. This should not be changed, or else errors will occur
|
|
595
618
|
export LOG_MODE=full
|