Develop (#41)

* Develop backup (#34) * udpate Readme and plugin gpg https://github.com/jodersky/sbt-gpg * downgrade gpg to 0.2.1. 0.2.2 not available ! * remove tagret directory fro repo * remove tagret directory fro repo * update Readme * fix jar publication * covered code for commands * update readme with badge * remove script * change galaxy recipe directory * remove temp file * minor fix for resume * add planemo test * add planemo test * add planemo test * add planemo test * add planemo test * planemo test only master/main/develop * lint planemo + conda test version * lint planemo + conda test version * lint planemo + conda test version * update fix meta.yml * remove conda recipe * clean repo * add sbt-release (#16) * Sbt release (#18) * add sbt-release * valid pom generation * Dockerfile (#20) * target directory for assembly * add dockerized task * add dockerfile * update gitignore * use directory docker * update docker management * fix outputdir assembly * update docker config * remove debug config * Dockerfile (#22) * target directory for assembly * add dockerized task * add dockerfile * update gitignore * use directory docker * update docker management * fix outputdir assembly * update docker config * remove debug config * remove coverage enable * fix dockerfile implementation to run process inside galaxy tools * Uplc tqd to isocor 24 (#26) * update Readme * add MassLynx parser / tests * replace strip with trim * increase coverage. manage bad line def inside array compound * fix coverage * fix coverage * add command/output object and tests * save notes * add galaxy config tools - gcms2isocor openlabcds2csv masslynx2isocor (#27) * add galaxy config tools - gcms2isocor openlabcds2csv masslynx2isocor * fix doc/name bin * downgrade profile galaxy version * fx test masslynx * inverse sample/metabolite in the input isocor file. (#35) * fix (#36) * fix * save * fix coverage * fix typo. increase test precision * increase limit coverage test to 97% ! * fix masslynx2isocor. 0.1.7 * add 0.1.7 jar * update circleci config with planemo conf (#38) * update circleci config with planemo conf * install planemo * fix option planemo * remove docker exemple from planemo test * add jar * decrease coverage mandatory * test artefacts * up * coverage * update with lint * update * Isotopic mass configuration 39 (#40) * features: new method getNumberElementFromFormula to manage isotopic metabolites * save dev * update 0.1.8 * update galaxy tool masslynx2isocor * fix: repair/read formula from isocor Metabolites.dat. close #39 * update galaxy tool masslynx2isocor
p2m2 · May 3, 2022 · ed58b36 · ed58b36
1 parent ff1ab87
commit ed58b36
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Showing 18 changed files with 3,217 additions and 932 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -17,23 +17,33 @@
 #
 version: 2.1
 orbs:
-  node: circleci/node@4.7.0
+  node: circleci/node@5.0.2
 workflows:
   compile-workflow:
     jobs:
       - compile:
           context:
             - DOCKER_CONTEXT
-
       - test_and_coverage_jvm:
           requires:
             - compile
           context:
             - DOCKER_CONTEXT
-
+      - planemo_stage:
+          context:
+            - DOCKER_CONTEXT
+          filters:
+            tags:
+              ignore: /.*/
+            branches:
+              only:
+                - develop
+                - main
+                - master
       - publish_snapshot:
           requires:
             - test_and_coverage_jvm
+            - planemo_stage
           context:
             - DOCKER_CONTEXT
             - CREDENTIAL_CONTEXT
@@ -89,7 +99,15 @@ executors:
           auth:
             username: ${DOCKER_USER}
             password: ${DOCKER_PASS}
-
+
+  python:
+      working_directory: ~/planemo
+      docker:
+        - image: cimg/python:3.10.1  # primary container for the build job
+          auth:
+            username: ${DOCKER_USER}
+            password: ${DOCKER_PASS}
+
   docker-publisher:
       docker:
         - image: circleci/buildpack-deps:stretch
@@ -141,7 +159,45 @@ jobs:
 
       - store_artifacts:
           path: target/test-reports
-
+
+  planemo_stage:
+    executor: python
+    steps:
+      - checkout
+      - setup_remote_docker
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.sbt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+      - run:
+          name: Test P2M2 tools for Galaxy
+          command: |
+            cd galaxy
+            pip install planemo
+            for directory in $(ls -d ls -d */ | awk '!/docker/ {print $0}')
+            do
+              echo " == $directory == "
+              pushd $directory
+              planemo l --fail_level error
+              popd
+            done
+      - run:
+          name: Run on fail status
+          command: |
+            mkdir -p /tmp/html_reports
+            cp $(find ./galaxy/ -name *.html -type f)  /tmp/html_reports/
+            mkdir -p /tmp/json_reports
+            cp $(find ./galaxy/ -name *.json -type f)  /tmp/json_reports/
+          when: on_fail
+
+      - store_artifacts:
+          path: /tmp/html_reports/tool_test_output.html
+          destination: artifacts-planemo-reports-html
+      - store_artifacts:
+          path: /tmp/json_reports/tool_test_output.json
+          destination: artifacts-planemo-reports-json
+
   publish_snapshot:
     executor: openjdk
     steps:

diff --git a/build.sbt b/build.sbt
@@ -15,19 +15,23 @@ scmInfo := Some(
 )
 
 versionScheme := Some("early-semver")
-
-val static_version      = "0.1.7"
+val static_version      = "0.1.8"
 val version_build = scala.util.Properties.envOrElse("PROG_VERSION", static_version )
 
 version :=  version_build
 
-libraryDependencies += "com.lihaoyi" %% "utest" % "0.7.10" % "test"
+libraryDependencies += "com.lihaoyi" %% "utest" % "0.7.11" % "test"
 libraryDependencies += "com.github.scopt" %% "scopt" % "4.0.1"
 
 // Coverage
 
-coverageMinimumStmtTotal := 98
-coverageFailOnMinimum := false
+coverageMinimumStmtTotal := 97
+coverageMinimumBranchTotal := 93
+coverageMinimumStmtPerPackage := 93
+coverageMinimumBranchPerPackage := 93
+coverageMinimumStmtPerFile := 93
+coverageMinimumBranchPerFile := 93
+coverageFailOnMinimum := true
 coverageHighlighting := true
 
 // Publication

diff --git a/galaxy/docker_env_exemple/gcms2isocor.xml b/galaxy/docker_env_exemple/gcms2isocor.xml
@@ -1,9 +1,9 @@
 <tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" version="1.0.0">
     <requirements>	
-        <container type="docker">inraep2m2/p2m2tools:0.1.5</container>
+        <container type="docker">inraep2m2/p2m2tools:0.1.7</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      p2m2tools fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand 
+      p2m2tools fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand
        #for $input in $input_gcms_files
          #if $input
            $input

diff --git a/galaxy/gcms2isocor/P2M2WorkflowsTools-assembly-0.1.4.jar b/galaxy/gcms2isocor/P2M2WorkflowsTools-assembly-0.1.4.jar
diff --git a/galaxy/gcms2isocor/gcms2isocor.xml b/galaxy/gcms2isocor/gcms2isocor.xml
@@ -3,7 +3,7 @@
         <requirement type="package" version="8.0.121">openjdk</requirement> 
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      java -cp '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.4.jar' fr.inrae.metabolomics.p2m2.GCMS2IsocorCommand
+      java -cp '$__tool_directory__/P2M2Tools-assembly-0.1.7.jar' fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand
        #for $input in $input_gcms_files
          #if $input
            $input

diff --git a/...slynx2isocor/P2M2Tools-assembly-0.1.7.jar → ...slynx2isocor/P2M2Tools-assembly-0.1.8.jar b/...slynx2isocor/P2M2Tools-assembly-0.1.7.jar → ...slynx2isocor/P2M2Tools-assembly-0.1.8.jar
diff --git a/galaxy/masslynx2isocor/masslynx2isocor.xml b/galaxy/masslynx2isocor/masslynx2isocor.xml
@@ -1,28 +1,32 @@
-<tool id="masslynx2isocor" name="Conversion MassLynx [Quantify Compound Summary Report] to IsoCor" version="0.1.0" profile="20.09">
+<tool id="masslynx2isocor" name="Conversion MassLynx [Quantify Compound Summary Report] to IsoCor" version="0.1.1" profile="20.09">
     <requirements>
         <requirement type="package" version="8.0.121">openjdk</requirement> 
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      java -cp '$__tool_directory__/P2M2Tools-assembly-0.1.7.jar' fr.inrae.metabolomics.p2m2.command.MassLynx2IsocorCommand
+      java -cp '$__tool_directory__/P2M2Tools-assembly-0.1.8.jar' fr.inrae.metabolomics.p2m2.command.MassLynx2IsocorCommand
        #for $input in $input_masslynx_files
          #if $input
            $input
          #end if
         #end for
-        -d '$input_corr_derivatives' --out '$output_isocor'
+        -d '$input_corr_derivatives' -m '$input_corr_metabolites' --out_13C '$output_isocor_13C' --out_15N '$output_isocor_15N'
     ]]></command>
     <inputs>
         <param type="data" name="input_masslynx_files" multiple="true" format="txt" />
         <param type="data" name="input_corr_derivatives" multiple="false" format="txt" />
+        <param type="data" name="input_corr_metabolites" multiple="false" format="tabular" />
     </inputs>
     <outputs>
-        <data name="output_isocor" format="tabular" />
+        <data name="output_isocor_13C" format="tabular" />
+        <data name="output_isocor_15N" format="tabular" />
     </outputs>
     <tests>
         <test>
             <param name="input_masslynx_files" value="mass_15Ngly.txt"/>
             <param name="input_corr_derivatives" value="correspondence_derivatives.txt"/>
-            <output name="output_isocor" file="input_isocor.tsv"/>
+            <param name="input_corr_metabolites" value="Metabolites.dat"/>
+            <output name="output_isocor_13C" file="isocor_input_13C.tsv"/>
+            <output name="output_isocor_15N" file="isocor_input_15N.tsv"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/galaxy/masslynx2isocor/test-data/Metabolites.dat b/galaxy/masslynx2isocor/test-data/Metabolites.dat
@@ -0,0 +1,25 @@
+name	formula	charge
+His	C6H9N3O2	1
+Asn	C4H8N2O3	1
+SMCSO	C4H9NO3S	1
+Ser	C3H7NO3	1
+Gln	C5H10N2O3	1
+Arg	C6H14N4O2	1
+Gly	C2H5NO2	1
+Asp	C4H7NO4	1
+Glu	C5H9NO4	1
+b-Ala	C3H7NO2	1
+Thr	C4H9NO3	1
+a-Ala	C3H7NO2	1
+GABA	C4H9NO2	1
+Pro	C5H9NO2	1
+SMC	C4H9NO2S	1
+Orn	C5H12N2O2	1
+Lys	C6H14N2O2	1
+Tyr	C9H11NO3	1
+Met	C5H11NO2S	1
+Val	C5H11NO2	1
+Ile	C6H13NO2	1
+Leu	C6H13NO2	1
+Phe	C9H11NO2	1
+Try	C11H12N2O2	1