psdi-data-conversion 0.0.35__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 +18 -13
- psdi_data_conversion/static/content/convertato.htm +40 -33
- psdi_data_conversion/static/content/convertc2x.htm +40 -33
- 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 +80 -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 +0 -6
- 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-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/METADATA +29 -6
- {psdi_data_conversion-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/RECORD +36 -36
- {psdi_data_conversion-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/WHEEL +0 -0
- {psdi_data_conversion-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/entry_points.txt +0 -0
- {psdi_data_conversion-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/licenses/LICENSE +0 -0
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import { commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt } from "./convert_common.js"
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var token = "",
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max_file_size = 0,
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in_ext = "",
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out_ext = "",
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in_str = "",
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out_str = "";
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$(document).ready(function () {
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[token,
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[token, in_str, in_ext, out_str, out_ext] = commonConvertReady("c2x");
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$("#uploadButton").click(submitFile);
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});
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This is the JavaScript which makes the Format and Converter Selection gui work.
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*/
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import { disableDirtyForms, cleanDirtyForms, initDirtyForms, loadServiceMode, loadProductionMode } from "./common.js";
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import {
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getInputFormats, getOutputFormats, getOutputFormatsForInputFormat,
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getInputFormatsForOutputFormat, getConverters, getConverterByName, getLevelChemInfo
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sessionStorage.setItem("token", token);
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sessionStorage.setItem("max_file_size", max_file_size);
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sessionStorage.setItem("max_file_size_ob", max_file_size_ob);
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sessionStorage.setItem("service_mode", service_mode);
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sessionStorage.setItem("production_mode", production_mode);
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sessionStorage.setItem("in_str", "");
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sessionStorage.setItem("out_str", "");
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sessionStorage.setItem("success", "");
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loadServiceMode();
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loadProductionMode();
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$("#fromList").click(populateConversionSuccess);
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$("#toList").click(populateConversionSuccess);
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$("#searchTo").keyup(filterOptions);
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$("#success").click(showConverterDetails);
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$("#resetButton").click(resetAll);
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$("#showButton").click(showQualityDetails);
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initDirtyForms();
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});
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/**
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// Stores chosen formats and switches to the Conversion page
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function goToConversionPage(event) {
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disableDirtyForms();
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var path = ``;
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if ($("#name").html() == "Open Babel") {
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// Populates the "Convert to" selection list
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getOutputFormats().then(formats => populateList(formats, "to"));
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cleanDirtyForms();
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}
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This is the JavaScript which makes the report.htm gui work.
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*/
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import { disableDirtyForms, initDirtyForms } from "./common.js";
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import { getAllFormats, getConverters } from "./data.js";
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var token = "",
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$("#resetButton").click(resetAll);
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$("#resetButton2").click(resetAll);
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$("#reportButton").click(submitUserInput);
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initDirtyForms();
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});
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// Included in this file for convenience. When the 'Report' button is clicked, a user's missing conversion report
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// Submits user input
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function submitUserInput() {
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const from = $("#searchFrom").val(),
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to = $("#searchTo").val();
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// Submit feedback
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function submitFeedback(data) {
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disableDirtyForms();
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$.post(`/feedback/`, {
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'token': token,
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'data': JSON.stringify(data)
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display: none;
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}
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.footer__hline hr {
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border-top-style : none;
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border-bottom-style: inset;
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border-bottom-width: 1px;
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}
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/* Convert button and loading spinner */
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.convert-button-and-spinner {
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display : flex;
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}
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.footer__hline hr {
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margin: 0.5rem 0;
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margin : 0.5rem 0;
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height : 2px;
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border-top-style : none;
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border-bottom-style: inset;
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border-bottom-width: 1px;
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}
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.max-width-box .footer__col {
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<script src="https://code.jquery.com/jquery-3.7.1.js" integrity="sha256-eKhayi8LEQwp4NKxN+CfCh+3qOVUtJn3QNZ0TciWLP4="
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crossorigin="anonymous"></script>
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<script src="https://cdn.jsdelivr.net/jquery.dirtyforms/2.0.0/jquery.dirtyforms.min.js"></script>
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{% for item in data %}
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<script>
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const token = "{{item.token}}";
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const max_file_size = "{{item.max_file_size}}";
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const max_file_size_ob = "{{item.max_file_size_ob}}";
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const service_mode = "{{item.service_mode}}";
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const production_mode = "{{item.production_mode}}";
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document.documentElement.setAttribute("service-mode", service_mode);
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</div>
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</div>
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<form name="gui">
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<form name="gui" class="gui">
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<div class="max-width-box">
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<p>Select 'from' and 'to' file formats in the 'Convert from/to' boxes, in either order. Typing where indicated
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filters the options (case insensitive); for example, typing 'can' or 'NON' reduces the number of options to one:
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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 = 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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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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ex_message=const.ERR_WRONG_EXTENSIONS)],
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))
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{"log_mode": const.LOG_STDOUT},
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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=True)],
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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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144
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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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|
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l_all_test_specs.append(Spec(name="Quality note",
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|
+
filename=["quartz.xyz", "ethanol.xyz", "hemoglobin.pdb"],
|
|
156
|
+
to_format=["inchi", "cml", "xyz"],
|
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157
|
+
callback=[quartz_quality_note_callback,
|
|
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|
+
ethanol_quality_note_callback,
|
|
159
|
+
hemoglobin_quality_note_callback],
|
|
160
|
+
))
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|
125
161
|
"""A test conversion which we expect to produce a warning for conversion quality issues, where the connections property
|
|
126
162
|
isn't present in the input and has to be extrapolated, and the 2D and 3D coordinates properties aren't present in the
|
|
127
163
|
output and will be lost"""
|
|
128
164
|
|
|
129
|
-
|
|
130
|
-
|
|
165
|
+
l_all_test_specs.append(Spec(name="Cleanup input",
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166
|
+
conversion_kwargs={"delete_input": True},
|
|
167
|
+
callback=CheckFileStatus(expect_input_exists=False),
|
|
168
|
+
))
|
|
131
169
|
"""A test that the input file to a conversion is deleted when cleanup is requested"""
|
|
132
170
|
|
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133
|
-
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134
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135
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138
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139
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|
140
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-
|
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141
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-
|
|
142
|
-
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|
143
|
-
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|
144
|
-
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|
145
|
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|
146
|
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|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
"
|
|
152
|
-
|
|
153
|
-
|
|
154
|
-
|
|
155
|
-
|
|
156
|
-
|
|
157
|
-
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
|
|
162
|
-
|
|
171
|
+
l_all_test_specs.append(Spec(name="Failed conversion - bad input file",
|
|
172
|
+
filename=["quartz_err.xyz", "cyclopropane_err.mol"],
|
|
173
|
+
to_format=["inchi", "xyz"],
|
|
174
|
+
expect_success=False,
|
|
175
|
+
converter_name=[CONVERTER_OB, CONVERTER_C2X],
|
|
176
|
+
callback=[MCB(CheckFileStatus(expect_output_exists=False,
|
|
177
|
+
expect_log_exists=None),
|
|
178
|
+
CheckException(ex_type=FileConverterAbortException,
|
|
179
|
+
ex_message="Problems reading an XYZ file")),
|
|
180
|
+
MCB(CheckFileStatus(expect_output_exists=False,
|
|
181
|
+
expect_log_exists=None),
|
|
182
|
+
CheckException(ex_type=FileConverterAbortException,
|
|
183
|
+
ex_message="Aborting: mol file contains no atoms"))],
|
|
184
|
+
))
|
|
185
|
+
"""A test that a conversion that fails due to an unreadable input file will properly fail"""
|
|
186
|
+
|
|
187
|
+
quartz_error_ob_callback = CheckLogContents(["ERROR",
|
|
188
|
+
"Problems reading an XYZ file: Could not read line #11, file error"])
|
|
189
|
+
l_all_test_specs.append(Spec(name="Errors in logs",
|
|
190
|
+
filename="quartz_err.xyz",
|
|
191
|
+
to_format="inchi",
|
|
192
|
+
converter_name=CONVERTER_OB,
|
|
193
|
+
expect_success=False,
|
|
194
|
+
callback=quartz_error_ob_callback,
|
|
195
|
+
))
|
|
196
|
+
"""A test that when a conversion fails, logs are still produced and contain the expected error message"""
|
|
197
|
+
|
|
198
|
+
l_all_test_specs.append(Spec(name="Failed conversion - invalid conversion",
|
|
199
|
+
filename=["Fapatite.ins", "nacl.mol"],
|
|
200
|
+
to_format=["cml", "xyz"],
|
|
201
|
+
expect_success=False,
|
|
202
|
+
converter_name=[CONVERTER_OB, CONVERTER_ATO],
|
|
203
|
+
callback=MCB(CheckFileStatus(expect_output_exists=False,
|
|
204
|
+
expect_log_exists=None),
|
|
205
|
+
CheckException(ex_type=FileConverterHelpException,
|
|
206
|
+
ex_message="is not supported")),
|
|
207
|
+
))
|
|
208
|
+
"""A test that a conversion that fails due an unsupported conversion will properly fail"""
|
|
209
|
+
|
|
210
|
+
l_all_test_specs.append(Spec(name="Failed Conversion - wrong input type",
|
|
211
|
+
filename="1NE6.mmcif",
|
|
212
|
+
to_format="cif",
|
|
213
|
+
conversion_kwargs={"from_format": "pdb"},
|
|
214
|
+
expect_success=False,
|
|
215
|
+
callback=MCB(CheckFileStatus(expect_output_exists=False,
|
|
216
|
+
expect_log_exists=None),
|
|
217
|
+
CheckException(ex_type=FileConverterAbortException,
|
|
218
|
+
ex_message="not a valid {} file")),
|
|
219
|
+
))
|
|
220
|
+
"""A test that a conversion which fails due to the wrong input file type will properly fail"""
|
|
221
|
+
|
|
222
|
+
l_all_test_specs.append(Spec(name="Large files",
|
|
223
|
+
filename=["ch3cl-esp.cub", "benzyne.molden", "periodic_dmol3.outmol",
|
|
224
|
+
"fullRhinovirus.pdb"],
|
|
225
|
+
to_format=["cdjson", "dmol", "mol", "cif"],
|
|
226
|
+
converter_name=[CONVERTER_OB, CONVERTER_OB, CONVERTER_OB, CONVERTER_C2X],
|
|
227
|
+
callback=CheckFileStatus(),
|
|
228
|
+
))
|
|
229
|
+
|
|
230
|
+
max_size_callback = MCB(CheckFileStatus(expect_output_exists=False),
|
|
231
|
+
CheckLogContents("file exceeds maximum size"),
|
|
232
|
+
CheckException(ex_type=FileConverterSizeException,
|
|
233
|
+
ex_message="exceeds maximum size",
|
|
234
|
+
ex_status_code=const.STATUS_CODE_SIZE))
|
|
235
|
+
l_all_test_specs.append(Spec(name="Max size exceeded",
|
|
236
|
+
filename=["1NE6.mmcif", "caffeine-smi.tar.gz"],
|
|
237
|
+
to_format="pdb",
|
|
238
|
+
conversion_kwargs=[{"max_file_size": 0.0001}, {"max_file_size": 0.0005}],
|
|
239
|
+
expect_success=False,
|
|
240
|
+
callback=max_size_callback,
|
|
241
|
+
compatible_with_cla=False,
|
|
242
|
+
))
|
|
163
243
|
"""A set of test conversion that the maximum size constraint is properly applied. In the first test, the input file
|
|
164
244
|
will be greater than the maximum size, and the test should fail as soon as it checks it. In the second test, the input
|
|
165
245
|
archive is smaller than the maximum size, but the unpacked files in it are greater, so it should fail midway through.
|
|
166
246
|
|
|
167
|
-
|
|
247
|
+
Not compatible with CLA tests, since the CLA doesn't allow the imposition of a maximum size.
|
|
168
248
|
"""
|
|
169
249
|
|
|
170
250
|
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
|
|
176
|
-
|
|
177
|
-
|
|
178
|
-
|
|
179
|
-
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
184
|
-
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
|
|
188
|
-
|
|
189
|
-
|
|
251
|
+
l_all_test_specs.append(Spec(name="Format args",
|
|
252
|
+
filename="caffeine.inchi",
|
|
253
|
+
to_format="smi",
|
|
254
|
+
conversion_kwargs=[{},
|
|
255
|
+
{"data": {"from_flags": "a"}},
|
|
256
|
+
{"data": {"from_flags": "a", "to_flags": "x"}},
|
|
257
|
+
{"data": {"from_flags": "a", "to_flags": "kx"}},
|
|
258
|
+
{"data": {"from_flags": "a", "to_flags": "kx",
|
|
259
|
+
"to_options": "f4"}},
|
|
260
|
+
{"data": {"from_flags": "a", "to_flags": "kx",
|
|
261
|
+
"to_options": "f4 l5"}}
|
|
262
|
+
],
|
|
263
|
+
callback=[MatchOutputFile("caffeine.smi"),
|
|
264
|
+
MatchOutputFile("caffeine_a_in.smi"),
|
|
265
|
+
MatchOutputFile("caffeine_a_in_x_out.smi"),
|
|
266
|
+
MatchOutputFile("caffeine_a_in_kx_out.smi"),
|
|
267
|
+
MatchOutputFile("caffeine_a_in_kx_f4_out.smi"),
|
|
268
|
+
MatchOutputFile("caffeine_a_in_kx_f4_l5_out.smi")
|
|
269
|
+
]
|
|
270
|
+
))
|
|
190
271
|
"""A set of tests which checks that format args (for how to read from and write to specific file formats) are processed
|
|
191
272
|
correctly, by matching tests using them to expected output files"""
|
|
192
273
|
|
|
193
274
|
|
|
194
|
-
|
|
195
|
-
|
|
196
|
-
|
|
197
|
-
|
|
198
|
-
|
|
199
|
-
|
|
200
|
-
|
|
201
|
-
|
|
202
|
-
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
|
|
206
|
-
|
|
275
|
+
l_all_test_specs.append(Spec(name="Coord gen",
|
|
276
|
+
filename="caffeine.inchi",
|
|
277
|
+
to_format="xyz",
|
|
278
|
+
conversion_kwargs=[{},
|
|
279
|
+
{"data": {COORD_GEN_KEY: "Gen2D",
|
|
280
|
+
COORD_GEN_QUAL_KEY: "fastest"}},
|
|
281
|
+
{"data": {COORD_GEN_KEY: "Gen3D",
|
|
282
|
+
COORD_GEN_QUAL_KEY: "best"}}
|
|
283
|
+
],
|
|
284
|
+
callback=[MatchOutputFile("caffeine.xyz"),
|
|
285
|
+
MatchOutputFile("caffeine-2D-fastest.xyz"),
|
|
286
|
+
MatchOutputFile("caffeine-3D-best.xyz"),
|
|
287
|
+
]
|
|
288
|
+
))
|
|
207
289
|
"""A set of tests which checks that coordinate generation options are processed correctly, by matching tests using them
|
|
208
290
|
to expected output files"""
|
|
291
|
+
|
|
292
|
+
l_library_test_specs = [x for x in l_all_test_specs if x.compatible_with_library]
|
|
293
|
+
"""All test specs which are compatible with being run on the Python library"""
|
|
294
|
+
|
|
295
|
+
l_cla_test_specs = [x for x in l_all_test_specs if x.compatible_with_cla]
|
|
296
|
+
"""All test specs which are compatible with being run on the command-line application"""
|
|
297
|
+
|
|
298
|
+
l_gui_test_specs = [x for x in l_all_test_specs if x.compatible_with_gui]
|
|
299
|
+
"""All test specs which are compatible with being run on the GUI"""
|