diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 10b8e52a..cb19f55e 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -49,6 +49,11 @@ jobs: cd SBML ./validateAll.sh + - name: Test test_suite output regeneration + run: | + cd test_suite + ./test_results_regeneration.sh + - name: Final version info run: | omv list -V # list installed engines diff --git a/test_suite/README.md b/test_suite/README.md new file mode 100644 index 00000000..cbb3715f --- /dev/null +++ b/test_suite/README.md @@ -0,0 +1,19 @@ +# Tabulates results of validation tests on SBML test suite + +The `process_test_suite.py` script currently runs three tests from pyneuroml on all SBML files that match the input glob argument given to it: validate SBML, validate SBML (with strict unit checks activated), validate SEDML. The SEDML file is assumed to have the same name as the SBML file except the `.xml` extension must to changed to `-sedml.xml`. The output is a markdown file containing a simple table of the results obtained on each file, where each test result is recorded as either a `pass` or `FAIL`. + +- First download the [zipfile](https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip) (or the latest equivalent) of the [SBML test suite](https://github.com/sbmlteam/sbml-test-suite) that includes [SEDML](https://github.com/SED-ML/sed-ml) files. + +- Extract to any convenient location, for example using the `unzip` command: + +``` +unzip semantic_tests_with_sedml_and_graphs.v3.4.0.zip +``` + +- Then run the `process_test_suite.py` tool, pointing it towards the extracted test files, for example if the extraction folder is at `/home/vagrant/test_suite_files/semantic` and the `process_test_suite.py` script is in the current directory: + +``` +./process_test_suite.py --suite-path /home/vagrant/test_suite_files/semantic --suite-glob '*/*-sbml-l3v2.xml' --output-file results.md +``` + +- Use the `--help` option for more details or see the process script source code. \ No newline at end of file diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py new file mode 100755 index 00000000..68966865 --- /dev/null +++ b/test_suite/process_test_suite.py @@ -0,0 +1,134 @@ +#!/usr/bin/env python3 + +""" +produce a markdown table of the results of running various tests on the SBML Test Suite + +get this version of the test suite that includes sedml versions or the sedml validation will fail: +https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip +""" + +import os +import glob +from pyneuroml.sbml import validate_sbml_files +from pyneuroml.sedml import validate_sedml_files + +def parse_arguments(): + "Parse command line arguments" + + import argparse + + parser = argparse.ArgumentParser( + description="Run various tests on the SBML Test Suite (or any similar set of SBML/SEDML files)" + ) + + parser.add_argument( + "--suite-path", + action="store", + type=str, + default=".", + help="Path to test suite directory, eg '~/repos/sbml-test-suite/cases/semantic'", + ) + + parser.add_argument( + "--suite-glob", + action="store", + type=str, + default="000*/*-sbml-l3v2.xml", + help="Shell-style glob matching test suite file(s) within suite_path, eg '000*/*-sbml-l3v2.xml'", + ) + + parser.add_argument( + "--suite-url-base", + action="store", + type=str, + default="https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic", + help="Base of the URL-to-suite-test-cases link to embed in results, use '' empty string to disable links", + ) + + parser.add_argument( + "--output-file", + action="store", + type=str, + default="results.md", + help="Path to file results will be written to, any parent directories must exist, eg ./results.md", + ) + + return parser.parse_args() + +#strings to use to represent passed and failed tests +okay = "pass" +fail = "FAIL" +def pass_or_fail(result): + ''' + convert True into "pass" and False into "fail" + as otherwise it's not obvious in the table what True and False mean + ''' + global okay,fail + + return okay if result else fail + + +def add_case_url(case,fpath,url_base): + ''' + insert URL link to original test case file online + effectively replaces args.suite_path with args.suite_url_base + this should produce a valid link for all the main intended use cases + of testing the sbml test suite using the default args + but will not handle all possible variations of globs and base directories + in which case it should be disabled by setting --suite-url-base='' + ''' + + url = os.path.join(url_base,fpath) + new_item = f'[{case}]({url})' + return new_item + +def process_cases(args): + """ + process the test cases and write results out as a markdown table + with links to the test case files online (as noted above the sedml files are actually in a zip file) + with a summary of how many cases were tested and how many tests failed + """ + + header = "|case|valid-sbml|valid-sbml-units|valid-sedml|" + sep = "|---|---|---|---|" + summary="|cases={n_cases}|fails={n_failing[valid_sbml]}|fails={n_failing[valid_sbml_units]}|fails={n_failing[valid_sedml]}|" + row = "|{case}|{valid_sbml}|{valid_sbml_units}|{valid_sedml}|" + + with open(args.output_file, "w") as fout: + #accumulate output in memory so we can put the nifty summary at the top + #instead of at the end of a very long table + output = [] + output.append(header) + output.append(sep) + output.append("") + n_cases = 0 + n_failing = {"valid_sbml":0, "valid_sbml_units":0, "valid_sedml":0 } + + os.chdir(args.suite_path) + for fpath in sorted(glob.glob(args.suite_glob)): + sedml_path = fpath.replace(".xml", "-sedml.xml") + print(fpath) + assert os.path.isfile(fpath) + assert os.path.isfile(sedml_path) + case = os.path.basename(fpath) + if args.suite_url_base != '': case = add_case_url(case,fpath,args.suite_url_base) + valid_sbml = pass_or_fail(validate_sbml_files([fpath], strict_units=False)) + valid_sbml_units = pass_or_fail(validate_sbml_files([fpath], strict_units=True)) + valid_sedml = pass_or_fail(validate_sedml_files([sedml_path])) + output.append(row.format(**locals())) + + #tally results so we can provide a summary + global okay,fail + n_cases +=1 + if valid_sbml != okay: n_failing["valid_sbml"] += 1 + if valid_sbml_units != okay: n_failing["valid_sbml_units"] += 1 + if valid_sedml != okay: n_failing["valid_sedml"] += 1 + + output[2] = summary.format(**locals()) + for line in output: fout.write(line+'\n') + + +if __name__ == "__main__": + args = parse_arguments() + + process_cases(args) diff --git a/test_suite/results.md b/test_suite/results.md new file mode 100644 index 00000000..f5e012f5 --- /dev/null +++ b/test_suite/results.md @@ -0,0 +1,1693 @@ +|case|valid-sbml|valid-sbml-units|valid-sedml| +|---|---|---|---| +|cases=1690|fails=1|fails=5|fails=0| 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+|[01760-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01760/01760-sbml-l3v2.xml)|pass|pass|pass| +|[01761-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01761/01761-sbml-l3v2.xml)|pass|pass|pass| +|[01762-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01762/01762-sbml-l3v2.xml)|pass|pass|pass| +|[01763-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01763/01763-sbml-l3v2.xml)|pass|pass|pass| +|[01766-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01766/01766-sbml-l3v2.xml)|pass|pass|pass| +|[01767-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01767/01767-sbml-l3v2.xml)|pass|pass|pass| +|[01768-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01768/01768-sbml-l3v2.xml)|pass|pass|pass| +|[01769-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01769/01769-sbml-l3v2.xml)|pass|pass|pass| +|[01770-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01770/01770-sbml-l3v2.xml)|pass|pass|pass| +|[01771-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01771/01771-sbml-l3v2.xml)|pass|pass|pass| +|[01772-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01772/01772-sbml-l3v2.xml)|pass|pass|pass| +|[01773-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01773/01773-sbml-l3v2.xml)|pass|pass|pass| +|[01774-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01774/01774-sbml-l3v2.xml)|pass|pass|pass| +|[01775-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01775/01775-sbml-l3v2.xml)|pass|pass|pass| +|[01776-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01776/01776-sbml-l3v2.xml)|pass|pass|pass| +|[01777-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01777/01777-sbml-l3v2.xml)|pass|pass|pass| +|[01778-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01778/01778-sbml-l3v2.xml)|pass|pass|pass| +|[01779-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01779/01779-sbml-l3v2.xml)|pass|pass|pass| +|[01780-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01780/01780-sbml-l3v2.xml)|pass|pass|pass| +|[01781-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01781/01781-sbml-l3v2.xml)|pass|pass|pass| +|[01782-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01782/01782-sbml-l3v2.xml)|pass|pass|pass| +|[01783-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01783/01783-sbml-l3v2.xml)|pass|pass|pass| +|[01799-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01799/01799-sbml-l3v2.xml)|pass|pass|pass| +|[01800-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01800/01800-sbml-l3v2.xml)|pass|pass|pass| +|[01801-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01801/01801-sbml-l3v2.xml)|pass|pass|pass| +|[01802-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01802/01802-sbml-l3v2.xml)|pass|pass|pass| +|[01803-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01803/01803-sbml-l3v2.xml)|pass|pass|pass| +|[01804-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01804/01804-sbml-l3v2.xml)|pass|pass|pass| +|[01805-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01805/01805-sbml-l3v2.xml)|pass|pass|pass| +|[01806-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01806/01806-sbml-l3v2.xml)|pass|pass|pass| +|[01807-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01807/01807-sbml-l3v2.xml)|pass|pass|pass| +|[01808-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01808/01808-sbml-l3v2.xml)|pass|pass|pass| +|[01809-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01809/01809-sbml-l3v2.xml)|pass|pass|pass| +|[01810-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01810/01810-sbml-l3v2.xml)|pass|pass|pass| +|[01811-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01811/01811-sbml-l3v2.xml)|pass|pass|pass| +|[01812-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01812/01812-sbml-l3v2.xml)|pass|pass|pass| +|[01813-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01813/01813-sbml-l3v2.xml)|pass|pass|pass| +|[01814-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01814/01814-sbml-l3v2.xml)|pass|pass|pass| +|[01815-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01815/01815-sbml-l3v2.xml)|pass|pass|pass| +|[01816-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01816/01816-sbml-l3v2.xml)|pass|pass|pass| +|[01817-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01817/01817-sbml-l3v2.xml)|pass|pass|pass| +|[01818-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01818/01818-sbml-l3v2.xml)|pass|pass|pass| +|[01819-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01819/01819-sbml-l3v2.xml)|pass|pass|pass| +|[01820-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01820/01820-sbml-l3v2.xml)|pass|pass|pass| +|[01821-sbml-l3v2.xml](https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01821/01821-sbml-l3v2.xml)|pass|pass|pass| diff --git a/test_suite/test_results_regeneration.sh b/test_suite/test_results_regeneration.sh new file mode 100755 index 00000000..843741e0 --- /dev/null +++ b/test_suite/test_results_regeneration.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +# +# test that the results.md file can be regenerated +# + +set -ex + +sudo apt-get install wget unzip --fix-missing --yes +wget https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip +unzip semantic_tests_with_sedml_and_graphs.v3.4.0.zip +./process_test_suite.py --suite-path ./semantic --suite-glob '*/*-sbml-l3v2.xml' --output-file ./test_results.md