diff -r 4682dcff7e2f -r cca2b6c3ae61 fill_ctd.py --- a/fill_ctd.py Thu Sep 03 16:23:50 2020 +0000 +++ b/fill_ctd.py Thu Sep 24 09:56:27 2020 +0000 @@ -150,6 +150,8 @@ # transform values from json that correspond to # - old style booleans (string + restrictions) -> transformed to a str +# - new style booleans that get a string (happens for hidden parameters [-test]) +# are transformed to a bool # - unrestricted ITEMLIST which are represented as strings # ("=quoted and space separated) in Galaxy -> transform to lists # - optional data input parameters that have defaults and for which no @@ -164,7 +166,7 @@ except KeyError: # few tools use dashes in parameters which are automatically replaced # by underscores by Galaxy. in these cases the dictionary needs to be - # updated + # updated (better: then dash and the underscore variant are in the dict) # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529 try: lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)] @@ -172,12 +174,16 @@ except KeyError: continue else: - setInDict(args, lineage, val) + setInDict(args, p.get_lineage(name_only=True), val) if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]): v = getFromDict(args, p.get_lineage(name_only=True)) setInDict(args, p.get_lineage(name_only=True), str(v).lower()) - + elif p.type is bool: + v = getFromDict(args, p.get_lineage(name_only=True)) + if isinstance(v, str): + v = (v.lower() == "true") + setInDict(args, p.get_lineage(name_only=True), v) elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange): v = getFromDict(args, p.get_lineage(name_only=True)) if type(v) is str: diff -r 4682dcff7e2f -r cca2b6c3ae61 generate.sh --- a/generate.sh Thu Sep 03 16:23:50 2020 +0000 +++ b/generate.sh Thu Sep 24 09:56:27 2020 +0000 @@ -67,6 +67,7 @@ patch PepNovoAdapter.xml < PepNovoAdapter.patch patch OMSSAAdapter.xml < OMSSAAdapter.patch +patch -p0 <404-urls.patch # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool diff -r 4682dcff7e2f -r cca2b6c3ae61 hardcoded_params.json --- a/hardcoded_params.json Thu Sep 03 16:23:50 2020 +0000 +++ b/hardcoded_params.json Thu Sep 24 09:56:27 2020 +0000 @@ -164,7 +164,7 @@ "tools": ["PhosphoScoring"] }, { "CTD:type": "output-prefix", - "CTD:required": "true", + "CTD:required": true, "CTD:restrictions": "mzml", "tools": ["MzMLSplitter"] }, { @@ -234,13 +234,14 @@ "#": "output-prefix", "out_path": [{ "CTD:type": "output-prefix", - "CTD:required": "true", + "CTD:required": true, "CTD:restrictions": "idXML", "tools": ["IDRipper"] }], "outputDirectory": [{ "CTD:type": "output-prefix", - "CTD:required": "true", + "CTD:advanced": false, + "CTD:required": true, "CTD:restrictions": "mzml", "tools": ["OpenSwathFileSplitter"] }] diff -r 4682dcff7e2f -r cca2b6c3ae61 macros_autotest.xml --- a/macros_autotest.xml Thu Sep 03 16:23:50 2020 +0000 +++ b/macros_autotest.xml Thu Sep 24 09:56:27 2020 +0000 @@ -1475,6 +1475,8 @@ + + @@ -26315,4 +26317,4 @@ - + diff -r 4682dcff7e2f -r cca2b6c3ae61 macros_discarded_auto.xml --- a/macros_discarded_auto.xml Thu Sep 03 16:23:50 2020 +0000 +++ b/macros_discarded_auto.xml Thu Sep 24 09:56:27 2020 +0000 @@ -7,7 +7,7 @@ - + diff -r 4682dcff7e2f -r cca2b6c3ae61 macros_test.xml --- a/macros_test.xml Thu Sep 03 16:23:50 2020 +0000 +++ b/macros_test.xml Thu Sep 24 09:56:27 2020 +0000 @@ -293,7 +293,7 @@ - + diff -r 4682dcff7e2f -r cca2b6c3ae61 test-data.sh --- a/test-data.sh Thu Sep 03 16:23:50 2020 +0000 +++ b/test-data.sh Thu Sep 24 09:56:27 2020 +0000 @@ -18,6 +18,11 @@ export OPENMSENV="$tmp/OpenMS$VERSION-env" export CTDCONVERTER="$tmp/CTDConverter" +if [[ -z "$1" ]]; then + autotests="/dev/null" +else + autotests="$1" +fi if type conda > /dev/null; then true @@ -28,11 +33,6 @@ fi eval "$(conda shell.bash hook)" -if [[ -z "$1" ]]; then - autotests="/dev/null" -else - autotests="$1" -fi ############################################################################### ## get @@ -88,7 +88,7 @@ git pull origin topic/cdata cd - fi -export PYTHONPATH=$(pwd)/CTDopts +# export PYTHONPATH=$(pwd)/CTDopts ############################################################################### ## copy all the test data files to test-data @@ -96,6 +96,8 @@ ## prepare_test_data ############################################################################### echo "Get test data" +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete + cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ @@ -211,20 +213,17 @@ cd - || exit -# # # exit - ############################################################################### ## auto generate tests ############################################################################### - -echo "Write test macros to "$autotests -echo "" > $autotests +echo "Write test macros to $autotests" +echo "" > "$autotests" for i in $(ls *xml |grep -v macros) do b=$(basename "$i" .xml) - get_tests2 "$b" >> $autotests + get_tests2 "$b" >> "$autotests" done -echo "" >> $autotests +echo "" >> "$autotests" echo "Create test data links" link_tmp_files @@ -232,9 +231,16 @@ # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests +# -> OpenSwathFileSplitter IDRipper MzMLSplitter +# +# Furthermore we remove tests for tools without binaries in conda +# -> MSFragger MaRaClusterAdapter NovorAdapter +# +# not able to specify composite test data +# -> SpectraSTSearchAdapter if [[ ! -z "$1" ]]; then echo "" > macros_discarded_auto.xml - for i in OpenSwathFileSplitter IDRipper MzMLSplitter + for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter do echo "" >> macros_discarded_auto.xml xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml @@ -242,7 +248,7 @@ xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp mv tmp macros_autotest.xml done - >&2 "discarded autogenerated macros for curation in macros_discarded_auto.xml" + >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" fi conda deactivate