psdi-data-conversion 0.0.37__py3-none-any.whl → 0.0.38__py3-none-any.whl

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Files changed (21) hide show
  1. psdi_data_conversion/app.py +30 -4
  2. psdi_data_conversion/constants.py +6 -5
  3. psdi_data_conversion/converter.py +13 -6
  4. psdi_data_conversion/converters/base.py +56 -53
  5. psdi_data_conversion/converters/c2x.py +1 -0
  6. psdi_data_conversion/converters/openbabel.py +10 -10
  7. psdi_data_conversion/database.py +335 -113
  8. psdi_data_conversion/main.py +151 -69
  9. psdi_data_conversion/static/javascript/data.js +18 -4
  10. psdi_data_conversion/static/javascript/format.js +22 -9
  11. psdi_data_conversion/templates/index.htm +57 -48
  12. psdi_data_conversion/testing/constants.py +3 -0
  13. psdi_data_conversion/testing/conversion_callbacks.py +2 -1
  14. psdi_data_conversion/testing/conversion_test_specs.py +27 -15
  15. psdi_data_conversion/testing/gui.py +354 -292
  16. psdi_data_conversion/testing/utils.py +35 -16
  17. {psdi_data_conversion-0.0.37.dist-info → psdi_data_conversion-0.0.38.dist-info}/METADATA +88 -4
  18. {psdi_data_conversion-0.0.37.dist-info → psdi_data_conversion-0.0.38.dist-info}/RECORD +21 -21
  19. {psdi_data_conversion-0.0.37.dist-info → psdi_data_conversion-0.0.38.dist-info}/WHEEL +0 -0
  20. {psdi_data_conversion-0.0.37.dist-info → psdi_data_conversion-0.0.38.dist-info}/entry_points.txt +0 -0
  21. {psdi_data_conversion-0.0.37.dist-info → psdi_data_conversion-0.0.38.dist-info}/licenses/LICENSE +0 -0
psdi_data_conversion/testing/conversion_test_specs.py CHANGED
@@ -8,17 +8,17 @@ application, and GUI.
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  from psdi_data_conversion import constants as const
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  from psdi_data_conversion.converters.atomsk import CONVERTER_ATO
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- from psdi_data_conversion.converters.base import (FileConverterAbortException, FileConverterHelpException,
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- FileConverterInputException, FileConverterSizeException)
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+ from psdi_data_conversion.converters.base import (FileConverterAbortException, FileConverterInputException,
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+ FileConverterSizeException)
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  from psdi_data_conversion.converters.c2x import CONVERTER_C2X
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  from psdi_data_conversion.converters.openbabel import CONVERTER_OB, COORD_GEN_KEY, COORD_GEN_QUAL_KEY
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+ from psdi_data_conversion.database import FileConverterDatabaseException
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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 as MCB)
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  from psdi_data_conversion.testing.utils import ConversionTestSpec as Spec
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-
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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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@@ -36,11 +36,16 @@ l_all_test_specs.append(Spec(name="Standard Multiple Tests",
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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",
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+ to_format=["pdb-0",
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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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+ from_format=[None,
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+ None, None, None,
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+ None, None, None,
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+ "pdb-0", "pdb-0", None,
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+ None],
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  converter_name=[CONVERTER_OB,
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  CONVERTER_OB, CONVERTER_OB, CONVERTER_OB,
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  CONVERTER_ATO, CONVERTER_ATO, CONVERTER_ATO,
@@ -65,7 +70,7 @@ 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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- conversion_kwargs={"from_format": "smi"},
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+ from_format="smi",
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  to_format="inchi",
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  callback=archive_callback,
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  ))
@@ -74,8 +79,8 @@ l_all_test_specs.append(Spec(name="Archive",
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  l_all_test_specs.append(Spec(name="Archive (wrong format) - Library and CLA",
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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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+ from_format=["pdb-0", "pdb-0"],
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+ conversion_kwargs=[{}, {"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,
@@ -88,8 +93,8 @@ l_all_test_specs.append(Spec(name="Archive (wrong format) - Library and CLA",
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  l_all_test_specs.append(Spec(name="Archive (wrong format) - GUI",
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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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+ from_format=["pdb-0", "pdb-0"],
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+ conversion_kwargs=[{}, {"strict": True}],
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  expect_success=[False, False],
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  callback=CheckException(ex_type=FileConverterInputException,
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  ex_message=const.ERR_WRONG_EXTENSIONS),
@@ -150,7 +155,7 @@ Not compatible with GUI tests, since the GUI doesn't support quiet mode
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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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+ to_format="pdb-0",
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  callback=CheckLogContentsSuccess(["Open Babel Warning",
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  "Failed to kekulize aromatic bonds",])
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  ))
@@ -205,6 +210,7 @@ Not compatible with the GUI, since the GUI can't forcibly delete files uploaded
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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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+ from_format=[None, "mol-0"],
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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,
@@ -246,12 +252,13 @@ l_all_test_specs.append(Spec(name="Errors in logs - GUI",
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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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+ from_format=["ins", "mol-0"],
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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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+ converter_name=[CONVERTER_C2X, 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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+ CheckException(ex_type=FileConverterDatabaseException,
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  ex_message="is not supported")),
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  compatible_with_gui=False,
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  ))
@@ -263,7 +270,8 @@ Not compatible with the GUI, since the GUI only offers valid conversions.
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  l_all_test_specs.append(Spec(name="Blocked conversion - wrong input type",
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  filename="1NE6.mmcif",
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  to_format="cif",
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- conversion_kwargs={"from_format": "pdb", "strict": True},
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+ from_format="pdb-0",
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+ conversion_kwargs={"strict": True},
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  expect_success=False,
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  callback=MCB(CheckFileStatus(expect_output_exists=False,
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  expect_log_exists=None),
@@ -278,7 +286,8 @@ l_all_test_specs.append(Spec(name="Blocked conversion - wrong input type",
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  l_all_test_specs.append(Spec(name="Failed conversion - wrong input type",
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  filename="1NE6.mmcif",
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  to_format="cif",
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- conversion_kwargs={"from_format": "pdb", "strict": False},
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+ from_format="pdb-0",
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+ conversion_kwargs={"strict": False},
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  expect_success=False,
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  callback=MCB(CheckFileStatus(expect_output_exists=False,
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  expect_log_exists=None),
@@ -291,6 +300,8 @@ l_all_test_specs.append(Spec(name="Large files - Library and CLA",
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  filename=["ch3cl-esp.cub", "benzyne.molden", "periodic_dmol3.outmol",
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  "fullRhinovirus.pdb"],
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  to_format=["cdjson", "dmol", "mol", "cif"],
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+ from_format=[None, None, None, "pdb-0"],
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+ conversion_kwargs=[{}, {}, {}, {"strict": False}],
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  converter_name=[CONVERTER_OB, CONVERTER_OB, CONVERTER_OB, CONVERTER_C2X],
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  callback=CheckFileStatus(),
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  compatible_with_gui=False,
@@ -301,6 +312,7 @@ l_all_test_specs.append(Spec(name="Large files - GUI",
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  filename=["ch3cl-esp.cub", "benzyne.molden",
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  "periodic_dmol3.outmol", "fullRhinovirus.pdb"],
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  to_format=["cdjson", "dmol", "mol", "cif"],
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+ from_format=[None, None, None, "pdb-0"],
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  converter_name=[CONVERTER_OB, CONVERTER_OB, CONVERTER_OB, CONVERTER_C2X],
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  expect_success=[False, False, False, True],
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  callback=[CheckException(ex_type=FileConverterInputException),
@@ -319,7 +331,7 @@ max_size_callback = MCB(CheckFileStatus(expect_output_exists=False),
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  ex_status_code=const.STATUS_CODE_SIZE))
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  l_all_test_specs.append(Spec(name="Max size exceeded",
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  filename=["1NE6.mmcif", "caffeine-smi.tar.gz"],
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- to_format="pdb",
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+ to_format="pdb-0",
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  conversion_kwargs=[{"max_file_size": 0.0001}, {"max_file_size": 0.0005}],
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  expect_success=False,
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  callback=max_size_callback,