tests(script:creation): add some tests and test data

Lain-inrae · Jul 18, 2022 · d7a15c2 · d7a15c2
1 parent d6e6cec
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Showing 7 changed files with 16,467 additions and 11 deletions.
diff --git a/Makefile b/Makefile
@@ -0,0 +1,14 @@
+
+
+## **@AUTHOR**: Lain Pavot - [email protected]
+## **@DATE**: 22/06/2022
+
+
+test:
+	python3 ./history_metadata_extractor.py \
+		-d ./test-data/datasets_attrs.txt \
+		-j ./test-data/jobs_attrs.txt \
+		-o ./test-data/result.html \
+	;
+	firefox ./test-data/result.html
+
diff --git a/manual_test.sh b/manual_test.sh
@@ -0,0 +1,110 @@
+#!/bin/bash
+
+
+
+## **@AUTHOR**: Lain Pavot - [email protected]
+## **@DATE**: 22/06/2022
+
+
+envs_directory=$(pwd)
+envs_directory=/tmp/history_metadata_extractor-envs
+mkdir -p ${envs_directory}
+
+VENV=${envs_directory}/.manual-venv
+CENV=${envs_directory}/.manual-conda
+
+MAMBA_SOLVER=
+## comment to deactivate mamba solver
+MAMBA_SOLVER="--experimental-solver libmamba"
+
+ENV_NAME=history_metadata_extractor
+XML_PATH=./history_metadata_extractor.xml
+SCRIPT_NAME=history_metadata_extractor.py
+output_name=out.html
+options=" \
+  -d ./test-data/datasets_attrs.txt \
+  -j ./test-data/jobs_attrs.txt \
+  -o ./${output_name} \
+"
+expected_result=test-data/out.html
+runner=python3.10
+dependencies=python=3.10.5
+miniconda_version=py37_4.12.0-Linux-x86_64
+
+
+
+if [ ! -e "${VENV}" ];then
+  echo "virtualenv not created yet, creating..."
+  python3 -m virtualenv "${VENV}"
+  echo "venv created"
+else
+  echo "virtualenv already exist: ok"
+fi
+. ${VENV}/bin/activate
+
+if [ ! -e "${CENV}" ];then
+  echo "conda env not created yet, creating..."
+  if [ ! -e ./install_conda.sh ];then
+    wget \
+      -O install_conda.sh \
+      https://repo.anaconda.com/miniconda/Miniconda3-${miniconda_version}.sh \
+    ;
+  fi
+  bash ./install_conda.sh -b -p "${CENV}"
+
+  ${CENV}/bin/conda install -y -n base conda-libmamba-solver
+  ${CENV}/bin/conda create \
+    -y \
+    --quiet \
+    --override-channels \
+    --channel conda-forge \
+    --channel bioconda \
+    --channel defaults \
+    --name "${ENV_NAME}" \
+    ${MAMBA_SOLVER} \
+    ${dependencies}
+  echo "conda env created"
+fi
+
+echo ""
+echo "===== preparing ====="
+
+oldwd=$(pwd)
+tmp=$(mktemp -d)
+echo "Working in ${tmp}"
+files=$(find . -maxdepth 1 -regex "./.+")
+cd "${tmp}"
+echo "creating links..."
+echo "${files}" | xargs -I file ln -s "${oldwd}"/file file
+echo "ready to work"
+
+echo ""
+echo "===== processing ====="
+
+. "${CENV}/bin/activate" "${CENV}/envs/${ENV_NAME}" ;
+
+${runner} ./${SCRIPT_NAME} ${options};
+
+echo ""
+echo "Error code: ${?}" ;
+
+lines=$(diff "${output_name}" "${expected_result}" 2>&1)
+
+echo ""
+echo "===== results ====="
+
+if [ "${lines}" = "" ];then
+  echo "Result equal to expected."
+else
+  echo "Some lines are different:"
+  echo "${lines}"
+fi
+
+echo ""
+echo "===== cleaning ====="
+
+echo "Removing ${tmp}..."
+rm -rf "${tmp}"
+
+echo ""
+echo "Done."
diff --git a/planemo_test.sh b/planemo_test.sh
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+
+## **@AUTHOR**: Lain Pavot - [email protected]
+## **@DATE**: 22/06/2022
+
+VENV=.venv
+TEST_DIR=/tmp/history_metadata_extractor
+
+if [ ! -d ".venv" ];then
+  python3 -m virtualenv ${VENV} ;
+fi
+
+
+. ${VENV}/bin/activate
+
+if [ "$(which planemo)" = "" ];then
+   pip install planemo ;
+fi
+
+
+if [ ! -d "${TEST_DIR}" ];then
+  planemo conda_install --conda_prefix ${TEST_DIR} . ;
+fi
+
+planemo lint --fail_level error ./*.xml || exit 255 ;
+
+planemo test \
+  --install_galaxy \
+  --conda_dependency_resolution \
+  --conda_prefix ${TEST_DIR} \
+  --no_cleanup \
+  --no_wait \
+  --simultaneous_uploads \
+  ${TEST_FLAGS} \
+  history_metadata_extractor.xml \
+;
diff --git a/static/app.template.html b/static/app.template.html
@@ -40,17 +40,17 @@
       style="overflow-y: auto ; height: 100%"
     >
       {table_list}
-    <footer class="d-block py-3">
-      <div class="container text-center">
-        <p>
-          Made with
-          <span id="glitter-generator" title="click for glitter and kawaii >‿<">
-            ❤️
-          </span>
-          by lain.pavot@inrae.fr - feel free to contact me for improvement requests
-        </p>
-      </div>
-    </footer>
+      <footer class="d-block py-3">
+        <div class="container text-center">
+          <p>
+            Made with
+            <span id="glitter-generator" title="click for glitter and kawaii >‿<">
+              ❤️
+            </span>
+            by Lain (mail: lain pavot inrae fr) - feel free to contact me for improvement requests
+          </p>
+        </div>
+      </footer>
     </div>
     <script>
       {javascript}

diff --git a/test-data/datasets_attrs.txt b/test-data/datasets_attrs.txt
@@ -0,0 +1 @@
+[{"annotation": null, "blurb": "2.2 MB", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 07:41:06.150944", "dataset_uuid": "a89e0ed3-253a-4336-bd0d-0bb88e2bbc87", "deleted": false, "designation": null, "encoded_id": "9e77b3d7d0887128", "extension": "rdata", "file_metadata": {}, "file_name": "datasets/test.rdata_1.rdata", "hid": 1, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded rdata file", "metadata": {"dbkey": "?", "version": "2"}, "model_class": "HistoryDatasetAssociation", "name": "test.rdata", "peek": "Compressed binary file", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:57:41.893692", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "82,885 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 14:20:21.414281", "dataset_uuid": "e56a7c62-e129-4c16-b5e3-f50eccbc4da3", "deleted": false, "designation": null, "encoded_id": "9a0ce47bd1734ae7", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragments.tsv_42.tabular", "hid": 42, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded tabular file", "metadata": {"column_names": [], "column_types": ["int", "int", "int", "int", "int", "float", "float", "float", "float", "int", "int", "int", "int", "int"], "columns": 14, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragments.tsv", "peek": "grpid\tpid\tprecursorScanNum\tacquisitionNum\tfileid\tmz\ti\tsnr\tra\tpurity_pass_flag\tintensity_pass_flag\tra_pass_flag\tsnr_pass_flag\tpass_flag\n674\t6641\t217\t218\t3\t78.78297424\t2488.865234\t17.57342471\t55.280578\t1\t1\t1\t1\t1\n674\t6641\t217\t218\t3\t79.78527069\t45.78085709\t0.323250305\t1.016845832\t1\t1\t1\t0\t0\n674\t6641\t217\t218\t3\t80.87423706\t6.168063164\t0.043551572\t0.136999823\t1\t1\t1\t0\t0\n674\t6641\t217\t218\t3\t90.00985718\t229.644455\t1.621477725\t5.100669184\t1\t1\t1\t0\t0\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 09:50:50.774726", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "2,736 lines, 1 comments", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 14:20:21.855053", "dataset_uuid": "686f913c-c854-42ee-aec4-90c357320f8f", "deleted": false, "designation": null, "encoded_id": "eee378ebc66a66f1", "extension": "csv", "file_metadata": {}, "file_name": "datasets/peaklist_precursors.csv_43.csv", "hid": 43, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded csv file", "metadata": {"column_names": ["grpid", "mz", "mzmin", "mzmax", "rt", "rtmin", "rtmax", "into", "intb", "maxo", "sn", "sample", "cid", "filename", "rtminCorrected", "rtmaxCorrected", "inPurity", "pid", "precurMtchID", "precurMtchScan", "precurMtchRT", "precurMtchMZ", "precurMtchPPM", "retentionTime", "fileid", "seqNum", "purity_pass_flag"], "column_types": ["int", "float", "float", "float", "float", "float", "float", "float", "float", "int", "int", "int", "int", "str", "float", "float", "float", "int", "int", "int", "float", "float", "float", "float", "int", "int", "str"], "columns": 27, "comment_lines": 1, "data_lines": 2736, "dbkey": "?", "delimiter": ","}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_precursors.csv", "peek": "\"grpid\",\"mz\",\"mzmin\",\"mzmax\",\"rt\",\"rtmin\",\"rtmax\",\"into\",\"intb\",\"maxo\",\"sn\",\"sample\",\"cid\",\"filename\",\"rtminCorrected\",\"rtmaxCorrected\",\"inPurity\",\"pid\",\"precurMtchID\",\"precurMtchScan\",\"precurMtchRT\",\"precurMtchMZ\",\"precurMtchPPM\",\"retentionTime\",\"fileid\",\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.526099609140227,6641,218,217,64.8261,121.9\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.619848678681211,6642,220,219,65.4511000000\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.644526797604947,6643,222,221,66.0673000000\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.676966047514146,6644,224,223,66.6843,121.9\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-06-28 06:52:20.975613", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "33 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 14:20:22.215516", "dataset_uuid": "e0b52f01-264d-4882-830d-304592fdbd91", "deleted": false, "designation": null, "encoded_id": "7cf499d16bd542b2", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/compounds_pos.txt_44.tabular", "hid": 44, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded tabular file", "metadata": {"column_names": [], "column_types": ["str", "float", "float"], "columns": 3, "comment_lines": 0, "data_lines": 33, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "compounds_pos.txt", "peek": "Compounds\tmz\trt\n2-diethylamino-6-methyl pyrimidin-4-ol one\t182.12879\t345.0\n5-hydroxy-thiabendazole\t218.03826\t315.0\nacetamiprid-N-desmethyl\t209.05885\t526.2\nAcetochlor\t270.12554\t1158.6\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:58:06.876928", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "82,885 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:36.489801", "dataset_uuid": "f2a503b8-0fb7-4d44-aef1-fa3eba565220", "deleted": false, "designation": "outFull", "encoded_id": "1818c0744f54583c", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.BIH4BLOODEXPOSOME_Full.tabular_576.tabular", "hid": 576, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nloading /galaxy/server/database/dependencies/_conda/envs/[email protected]/lib/perl5/site_perl/auto/share/dist/Metabolomics-Fragment-Annotation/BloodExposome_v1_0.txt...\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPea", "metadata": {"column_names": [], "column_types": ["int", "int", "int", "int", "int", "float", "float", "float", "float", "int", "int", "int", "int", "int", "int", "int", "float", "str", "float", "float", "float", "float"], "columns": 22, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.BIH4BLOODEXPOSOME_Full.tabular", "peek": "grpid\tpid\tprecursorScanNum\tacquisitionNum\tfileid\tmz\ti\tsnr\tra\tpurity_pass_flag\tintensity_pass_flag\tra_pass_flag\tsnr_pass_flag\tpass_flag\t_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_N\n674\t6641\t217\t218\t3\t78.78297424\t2488.865234\t17.57342471\t55.280578\t1\t1\t1\t1\t1\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t6641\t217\t218\t3\t79.78527069\t45.78085709\t0.323250305\t1.016845832\t1\t1\t1\t0\t0\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t6641\t217\t218\t3\t80.87423706\t6.168063164\t0.043551572\t0.136999823\t1\t1\t1\t0\t0\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t6641\t217\t218\t3\t90.00985718\t229.644455\t1.621477725\t5.100669184\t1\t1\t1\t0\t0\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 10:20:15.946197", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "82,885 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:36.489807", "dataset_uuid": "e6331c2c-e08e-4730-abcd-637d6ff02c61", "deleted": false, "designation": "outputTab", "encoded_id": "59261f87693eaee6", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.BIH4BLOODEXPOSOME.tabular_577.tabular", "hid": 577, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nloading /galaxy/server/database/dependencies/_conda/envs/[email protected]/lib/perl5/site_perl/auto/share/dist/Metabolomics-Fragment-Annotation/BloodExposome_v1_0.txt...\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPea", "metadata": {"column_names": [], "column_types": ["int", "int", "float", "str", "float", "float", "float", "float"], "columns": 8, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.BIH4BLOODEXPOSOME.tabular", "peek": "_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_NEG_MODE_\t_ANNOTATION_IN_POS_MODE_\t_ANNOTATION_FORMULA_\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 10:20:15.946200", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "queued", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:48.681710", "dataset_uuid": "519086d9-8e01-4fb5-a086-debfb1113ca8", "deleted": false, "designation": "variableMetadata", "encoded_id": "b379da601dbce29e", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/HR2_formula_TSV_580.tabular", "hid": 580, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": null, "metadata": {"column_names": [], "column_types": [], "columns": 0, "comment_lines": 0, "data_lines": 0, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "HR2 formula_TSV", "peek": null, "state": "running", "tags": [], "tool_version": null, "update_time": "2022-07-11 08:56:52.263881", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "queued", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:48.681717", "dataset_uuid": "23538dc5-a51a-4455-bf2a-abbadf110ca7", "deleted": false, "designation": "hr2ResView", "encoded_id": "e86562c804ca5387", "extension": "html", "file_metadata": {}, "file_name": "datasets/HR2_formula_VIEW_581.html", "hid": 581, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": null, "metadata": {"data_lines": 0, "dbkey": "?"}, "model_class": "HistoryDatasetAssociation", "name": "HR2 formula_VIEW", "peek": null, "state": "running", "tags": [], "tool_version": null, "update_time": "2022-07-11 08:56:52.263881", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "0 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:57:48.400497", "dataset_uuid": "a91187da-b53a-4622-a733-a57962de08c5", "deleted": false, "designation": "GolmOutTab", "encoded_id": "681d5df1cc46e913", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.GOLM.tabular_593.tabular", "hid": 593, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nCan't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/datab", "metadata": {"column_names": [], "column_types": ["str"], "columns": 1, "comment_lines": 0, "data_lines": 0, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.GOLM.tabular", "peek": "", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:57:58.708891", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "0 bytes", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:57:48.400509", "dataset_uuid": "5c3b230f-5a9d-4580-93b7-d2096e96de92", "deleted": false, "designation": "GolmOutWeb", "encoded_id": "fa68e87a50af12b3", "extension": "html", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.GOLM_WEB.html_594.html", "hid": 594, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nCan't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/datab", "metadata": {"data_lines": 0, "dbkey": "?"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.GOLM_WEB.html", "peek": "HTML file", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:57:58.708894", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "0 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:57:48.400515", "dataset_uuid": "2619df53-ccee-4de4-b16d-521e81212987", "deleted": false, "designation": "GolmOutXlsx", "encoded_id": "5c30ceded02186bf", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.GOLM.txt_595.tabular", "hid": 595, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nCan't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/datab", "metadata": {"column_names": [], "column_types": ["str"], "columns": 1, "comment_lines": 0, "data_lines": 0, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.GOLM.txt", "peek": "", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 09:50:19.923606", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "error", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:58:27.161061", "dataset_uuid": "25758f79-9a34-47f8-9bb4-b4896d8efadc", "deleted": false, "designation": "out_file1", "encoded_id": "79c7ce84f3ac839b", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/Compute_on_data_42_602.tabular", "hid": 602, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nFile \"/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/626658afe4cb/column_maker/column_maker.py\", line 107\n    exec code\n    ^^^^^^^^^\nSyntaxError: Missing parentheses in call to 'exec'. Did you mean exec(...)?", "metadata": {"column_names": [], "column_types": ["int", "int", "int", "int", "int", "float", "float", "float", "float", "int", "int", "int", "int", "int"], "columns": 14, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "Compute on data 42", "peek": "no peek", "state": "error", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:58:32.766199", "validated_state": "unknown", "validated_state_message": null, "visible": true}]
diff --git a/test-data/jobs_attrs.txt b/test-data/jobs_attrs.txt
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		[{"annotation": null, "blurb": "2.2 MB", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 07:41:06.150944", "dataset_uuid": "a89e0ed3-253a-4336-bd0d-0bb88e2bbc87", "deleted": false, "designation": null, "encoded_id": "9e77b3d7d0887128", "extension": "rdata", "file_metadata": {}, "file_name": "datasets/test.rdata_1.rdata", "hid": 1, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded rdata file", "metadata": {"dbkey": "?", "version": "2"}, "model_class": "HistoryDatasetAssociation", "name": "test.rdata", "peek": "Compressed binary file", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:57:41.893692", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "82,885 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 14:20:21.414281", "dataset_uuid": "e56a7c62-e129-4c16-b5e3-f50eccbc4da3", "deleted": false, "designation": null, "encoded_id": "9a0ce47bd1734ae7", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragments.tsv_42.tabular", "hid": 42, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded tabular file", "metadata": {"column_names": [], "column_types": ["int", "int", "int", "int", "int", "float", "float", "float", "float", "int", "int", "int", "int", "int"], "columns": 14, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragments.tsv", "peek": "grpid\tpid\tprecursorScanNum\tacquisitionNum\tfileid\tmz\ti\tsnr\tra\tpurity_pass_flag\tintensity_pass_flag\tra_pass_flag\tsnr_pass_flag\tpass_flag\n674\t6641\t217\t218\t3\t78.78297424\t2488.865234\t17.57342471\t55.280578\t1\t1\t1\t1\t1\n674\t6641\t217\t218\t3\t79.78527069\t45.78085709\t0.323250305\t1.016845832\t1\t1\t1\t0\t0\n674\t6641\t217\t218\t3\t80.87423706\t6.168063164\t0.043551572\t0.136999823\t1\t1\t1\t0\t0\n674\t6641\t217\t218\t3\t90.00985718\t229.644455\t1.621477725\t5.100669184\t1\t1\t1\t0\t0\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 09:50:50.774726", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "2,736 lines, 1 comments", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 14:20:21.855053", "dataset_uuid": "686f913c-c854-42ee-aec4-90c357320f8f", "deleted": false, "designation": null, "encoded_id": "eee378ebc66a66f1", "extension": "csv", "file_metadata": {}, "file_name": "datasets/peaklist_precursors.csv_43.csv", "hid": 43, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded csv file", "metadata": {"column_names": ["grpid", "mz", "mzmin", "mzmax", "rt", "rtmin", "rtmax", "into", "intb", "maxo", "sn", "sample", "cid", "filename", "rtminCorrected", "rtmaxCorrected", "inPurity", "pid", "precurMtchID", "precurMtchScan", "precurMtchRT", "precurMtchMZ", "precurMtchPPM", "retentionTime", "fileid", "seqNum", "purity_pass_flag"], "column_types": ["int", "float", "float", "float", "float", "float", "float", "float", "float", "int", "int", "int", "int", "str", "float", "float", "float", "int", "int", "int", "float", "float", "float", "float", "int", "int", "str"], "columns": 27, "comment_lines": 1, "data_lines": 2736, "dbkey": "?", "delimiter": ","}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_precursors.csv", "peek": "\"grpid\",\"mz\",\"mzmin\",\"mzmax\",\"rt\",\"rtmin\",\"rtmax\",\"into\",\"intb\",\"maxo\",\"sn\",\"sample\",\"cid\",\"filename\",\"rtminCorrected\",\"rtmaxCorrected\",\"inPurity\",\"pid\",\"precurMtchID\",\"precurMtchScan\",\"precurMtchRT\",\"precurMtchMZ\",\"precurMtchPPM\",\"retentionTime\",\"fileid\",\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.526099609140227,6641,218,217,64.8261,121.9\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.619848678681211,6642,220,219,65.4511000000\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.644526797604947,6643,222,221,66.0673000000\n\"674\",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,\"HBMSPE21_024.mzML\",62.750400858841,78.0434285273669,0.676966047514146,6644,224,223,66.6843,121.9\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-06-28 06:52:20.975613", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "33 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-06-23 14:20:22.215516", "dataset_uuid": "e0b52f01-264d-4882-830d-304592fdbd91", "deleted": false, "designation": null, "encoded_id": "7cf499d16bd542b2", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/compounds_pos.txt_44.tabular", "hid": 44, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "uploaded tabular file", "metadata": {"column_names": [], "column_types": ["str", "float", "float"], "columns": 3, "comment_lines": 0, "data_lines": 33, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "compounds_pos.txt", "peek": "Compounds\tmz\trt\n2-diethylamino-6-methyl pyrimidin-4-ol one\t182.12879\t345.0\n5-hydroxy-thiabendazole\t218.03826\t315.0\nacetamiprid-N-desmethyl\t209.05885\t526.2\nAcetochlor\t270.12554\t1158.6\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:58:06.876928", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "82,885 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:36.489801", "dataset_uuid": "f2a503b8-0fb7-4d44-aef1-fa3eba565220", "deleted": false, "designation": "outFull", "encoded_id": "1818c0744f54583c", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.BIH4BLOODEXPOSOME_Full.tabular_576.tabular", "hid": 576, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nloading /galaxy/server/database/dependencies/_conda/envs/[email protected]/lib/perl5/site_perl/auto/share/dist/Metabolomics-Fragment-Annotation/BloodExposome_v1_0.txt...\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPea", "metadata": {"column_names": [], "column_types": ["int", "int", "int", "int", "int", "float", "float", "float", "float", "int", "int", "int", "int", "int", "int", "int", "float", "str", "float", "float", "float", "float"], "columns": 22, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.BIH4BLOODEXPOSOME_Full.tabular", "peek": "grpid\tpid\tprecursorScanNum\tacquisitionNum\tfileid\tmz\ti\tsnr\tra\tpurity_pass_flag\tintensity_pass_flag\tra_pass_flag\tsnr_pass_flag\tpass_flag\t_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_N\n674\t6641\t217\t218\t3\t78.78297424\t2488.865234\t17.57342471\t55.280578\t1\t1\t1\t1\t1\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t6641\t217\t218\t3\t79.78527069\t45.78085709\t0.323250305\t1.016845832\t1\t1\t1\t0\t0\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t6641\t217\t218\t3\t80.87423706\t6.168063164\t0.043551572\t0.136999823\t1\t1\t1\t0\t0\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t6641\t217\t218\t3\t90.00985718\t229.644455\t1.621477725\t5.100669184\t1\t1\t1\t0\t0\t674\t0\t0\tNA\tNA\tNA\tNA\tNA\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 10:20:15.946197", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "82,885 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:36.489807", "dataset_uuid": "e6331c2c-e08e-4730-abcd-637d6ff02c61", "deleted": false, "designation": "outputTab", "encoded_id": "59261f87693eaee6", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.BIH4BLOODEXPOSOME.tabular_577.tabular", "hid": 577, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nloading /galaxy/server/database/dependencies/_conda/envs/[email protected]/lib/perl5/site_perl/auto/share/dist/Metabolomics-Fragment-Annotation/BloodExposome_v1_0.txt...\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPea", "metadata": {"column_names": [], "column_types": ["int", "int", "float", "str", "float", "float", "float", "float"], "columns": 8, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.BIH4BLOODEXPOSOME.tabular", "peek": "_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_NEG_MODE_\t_ANNOTATION_IN_POS_MODE_\t_ANNOTATION_FORMULA_\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n674\t0\t0\tNA\tNA\tNA\tNA\tNA\n", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 10:20:15.946200", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "queued", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:48.681710", "dataset_uuid": "519086d9-8e01-4fb5-a086-debfb1113ca8", "deleted": false, "designation": "variableMetadata", "encoded_id": "b379da601dbce29e", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/HR2_formula_TSV_580.tabular", "hid": 580, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": null, "metadata": {"column_names": [], "column_types": [], "columns": 0, "comment_lines": 0, "data_lines": 0, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "HR2 formula_TSV", "peek": null, "state": "running", "tags": [], "tool_version": null, "update_time": "2022-07-11 08:56:52.263881", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "queued", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:56:48.681717", "dataset_uuid": "23538dc5-a51a-4455-bf2a-abbadf110ca7", "deleted": false, "designation": "hr2ResView", "encoded_id": "e86562c804ca5387", "extension": "html", "file_metadata": {}, "file_name": "datasets/HR2_formula_VIEW_581.html", "hid": 581, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": null, "metadata": {"data_lines": 0, "dbkey": "?"}, "model_class": "HistoryDatasetAssociation", "name": "HR2 formula_VIEW", "peek": null, "state": "running", "tags": [], "tool_version": null, "update_time": "2022-07-11 08:56:52.263881", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "0 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:57:48.400497", "dataset_uuid": "a91187da-b53a-4622-a733-a57962de08c5", "deleted": false, "designation": "GolmOutTab", "encoded_id": "681d5df1cc46e913", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.GOLM.tabular_593.tabular", "hid": 593, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nCan't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/datab", "metadata": {"column_names": [], "column_types": ["str"], "columns": 1, "comment_lines": 0, "data_lines": 0, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.GOLM.tabular", "peek": "", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:57:58.708891", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "0 bytes", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:57:48.400509", "dataset_uuid": "5c3b230f-5a9d-4580-93b7-d2096e96de92", "deleted": false, "designation": "GolmOutWeb", "encoded_id": "fa68e87a50af12b3", "extension": "html", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.GOLM_WEB.html_594.html", "hid": 594, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nCan't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/datab", "metadata": {"data_lines": 0, "dbkey": "?"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.GOLM_WEB.html", "peek": "HTML file", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:57:58.708894", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "0 lines", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:57:48.400515", "dataset_uuid": "2619df53-ccee-4de4-b16d-521e81212987", "deleted": false, "designation": "GolmOutXlsx", "encoded_id": "5c30ceded02186bf", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/peaklist_fragmen.GOLM.txt_595.tabular", "hid": 595, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nCan't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/datab", "metadata": {"column_names": [], "column_types": ["str"], "columns": 1, "comment_lines": 0, "data_lines": 0, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "peaklist_fragmen.GOLM.txt", "peek": "", "state": "ok", "tags": [], "tool_version": "", "update_time": "2022-07-11 09:50:19.923606", "validated_state": "unknown", "validated_state_message": null, "visible": true}, {"annotation": null, "blurb": "error", "copied_from_history_dataset_association_id_chain": [], "create_time": "2022-07-11 08:58:27.161061", "dataset_uuid": "25758f79-9a34-47f8-9bb4-b4896d8efadc", "deleted": false, "designation": "out_file1", "encoded_id": "79c7ce84f3ac839b", "extension": "tabular", "file_metadata": {}, "file_name": "datasets/Compute_on_data_42_602.tabular", "hid": 602, "history_encoded_id": "2ed2d0cb9d9fff8e", "info": "\nFile \"/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/626658afe4cb/column_maker/column_maker.py\", line 107\n exec code\n ^^^^^^^^^\nSyntaxError: Missing parentheses in call to 'exec'. Did you mean exec(...)?", "metadata": {"column_names": [], "column_types": ["int", "int", "int", "int", "int", "float", "float", "float", "float", "int", "int", "int", "int", "int"], "columns": 14, "comment_lines": 0, "data_lines": 82885, "dbkey": "?", "delimiter": "\t"}, "model_class": "HistoryDatasetAssociation", "name": "Compute on data 42", "peek": "no peek", "state": "error", "tags": [], "tool_version": "", "update_time": "2022-07-11 08:58:32.766199", "validated_state": "unknown", "validated_state_message": null, "visible": true}]