Start CI unit test for uploadInputBag

.gitlab-ci.yml

@@ -7,6 +7,7 @@ before_script:
   - mkdir -p ~/.deriva
   - mkdir -p ~/.bdbag
 
+
 stages:
   - unit
   - aggregation
@@ -14,6 +15,7 @@ stages:
   - integration
   - consistency
 
+
 getBag:
   stage: unit
   only:
@@ -136,7 +138,6 @@ downsampleData:
   - singularity run 'docker://bicf/seqtk:2.0.1_indev' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
   - pytest -m downsampleData
 
-
 alignData:
   stage: unit
   only:
@@ -164,7 +165,6 @@ alignData:
       - version_samtools.txt
     expire_in: 7 days
 
-
 dedupData:
   stage: unit
   only:
@@ -262,22 +262,48 @@ dataQC:
     - merge_requests
   script:
   - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
-  - for i in {"chr8","chr4","chrY"}; do
-    echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
+  - >
+    for i in {"chr8","chr4","chrY"}; do
+      echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"
+    done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - pytest -m dataQC
 
 outputBag:
   stage: unit
   only:
     - push
-    - tags
-  except:
     - merge_requests
   script:
   - mkdir test
   - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag test --archiver zip
   - pytest -m outputBag
 
+outputBag:
+  stage: unit
+  only:
+    - push
+    - tags
+  except:
+    - merge_requests
+  script:
+  - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
+  - hatrac=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o TEST)
+  - >
+    if [ -z "${hatrac}" ]; then
+      singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${source} mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST
+    fi
+  - echo "THIS IS A TEST FILE" > test.txt
+  - md5=$(md5sum ./test.txt | awk '{ print $1 }')
+  - size=$(wc -c < ./test.txt)
+  - exist=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5})
+  - >
+    if [ "\${exist}" == "[]" ]; then
+      cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org": {' | grep -o '\"cookie\": \".*\"')
+      cookie=${cookie:11:-1}
+      loc=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt)
+      inputBag_rid=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie})
+    fi
+  - #pytest -m uploadInputBag
 
 generateVersions:
   stage: aggregation