Merge pull request #89 from PNNL-CompBio/schema-build

Adding in tests to build schema to database

.github/workflows/docker.yml

@@ -56,25 +56,6 @@ jobs:
          tags: sgosline/srp-exposome:latest
          push: true
 
-  build-push-db:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3     
-      - name: Login to DockerHub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push dbschema
-        uses: docker/build-push-action@v3
-        with:
-         file: dbSchema/Dockerfile
-         tags: sgosline/srp-dbschema:latest
-         push: true      
-
   build-push-exp:
     runs-on: ubuntu-latest
     steps:

build_script.py

@@ -70,6 +70,13 @@ def runSampMap(is_sample=False,drcfiles=[],smap='',cid='',\
     print(cmd)
     os.system(cmd)
     print('ls -la .')
+    ##now we validate the files that came out.
+    dblist=['/tmp/samples.csv','/tmp/chemicals.csv','/tmp/samplesToChemicals.csv']
+    for ftype in ['ChemXYCoords.csv','DoseResponse.csv','BMDs.csv']:
+        dblist.append('/tmp/zebrafishChem'+ftype)
+        dblist.append('/tmp/zebrafishSamp'+ftype)
+    runSchemaCheck(dblist)
+
 
 def runExposome(chem_id_file):
     '''
@@ -78,6 +85,7 @@ def runExposome(chem_id_file):
     cmd = 'Rscript exposome/exposome_summary_stats.R '+chem_id_file
     print(cmd)
     os.system(cmd)
+    runSchemaCheck(['/tmp/exposomeGeneStats.csv'])
 
 def runExpression(gex,chem,ginfo):
     '''
@@ -86,13 +94,18 @@ def runExpression(gex,chem,ginfo):
     cmd = 'Rscript zfExp/parseGexData.R '+gex+' '+chem+' '+ginfo
     print(cmd)
     os.system(cmd)
+    runSchemaCheck(['/tmp/srpDEGPathways.csv','/tmp/srpDEGStats.csv','/tmp/allGeneEx.csv'])
 
 def runSchemaCheck(dbfiles=[]):
     '''
     run schema checking
     '''
-    ##TODO: make this work with files as arguments
-    cmd = 'python dbSchema/main.py'
+    ##TODO: make this work with internal calls
+    for filename in dbfiles:
+        classname = os.path.basename(filename).split('.')[0]
+        cmd = 'linkml-validate --schema srpAnalytics.yaml '+filename+' --target-class '+classname
+        print(cmd)
+        os.system(cmd)
 
 def main():
     '''
@@ -106,7 +119,7 @@ def main():
     # file parsing - collects all files we might need for the tool below
     ####
     ##first find the morphology and behavior pairs for chemical sources
-    chemdf = df.loc[df.sample_type=='chemical']
+    chemdf = df.loc[df.sample_type=='chemical'] 
     morph = chemdf.loc[chemdf.data_type=='morphology']
     beh = chemdf.loc[chemdf.data_type=='behavior']
     tupes =[]