Merge pull request #155 from icgc-argo-workflows/payload-gen-seq-experiment@0.6.0.1

edsu7 · web-flow · commit fde82e19f70e · 2022-08-09T17:27:01.000-04:00
[release]
diff --git a/payload-gen-seq-experiment/main.py b/payload-gen-seq-experiment/main.py
@@ -58,8 +58,9 @@
 
 TSV_FIELDS['file']={}
 TSV_FIELDS['file']["core"]=['type', 'name', 'size', 'md5sum', 'path', 'format']
-TSV_FIELDS['file']["conditional"]=["EGAS","EGAC","EGAP","EGAN","EGAR","EGAX","EGAZ","EGAD","EGAB","EGAF"]
-
+TSV_FIELDS['file']["conditional"]=[
+    "ega_file_id","ega_dataset_id","ega_experiment_id","ega_sample_id","ega_study_id",
+    "ega_run_id","ega_policy_id","ega_analysis_id","ega_submission_id","ega_dac_id"]
 
 
 
diff --git a/payload-gen-seq-experiment/tests/input/208c5ea6-c17a-4a63-981e-4bb91d3119f2.sequencing_experiment.payload.json b/payload-gen-seq-experiment/tests/input/208c5ea6-c17a-4a63-981e-4bb91d3119f2.sequencing_experiment.payload.json
@@ -81,8 +81,7 @@
       "dataType": "Submitted Reads",
       "info": {
         "data_category": "Sequencing Reads"
-      },
-      "EGAF": "EGAF000001"
+      }
     }
   ]
 }
diff --git a/payload-gen-seq-experiment/tests/input/file.v3.tsv b/payload-gen-seq-experiment/tests/input/file.v3.tsv
@@ -1,2 +1,2 @@
-type	name	format	size	md5sum	path	EGAF
+type	name	format	size	md5sum	path	ega_file_id
 file	test_rg_3.bam	BAM	14911	178f97f7b1ca8bfc28fd5586bdd56799	test_rg_3.bam	EGAF000001
diff --git a/tests/data/cab531fd-dc75-462f-8a73-fb7fcbf73185.sequencing_experiment.payload.uniform_id_added.json b/tests/data/cab531fd-dc75-462f-8a73-fb7fcbf73185.sequencing_experiment.payload.uniform_id_added.json
@@ -122,7 +122,7 @@
     {
       "submitterSampleId": "HCC1143_FASTQ_INPUT",
       "matchedNormalSubmitterSampleId": "HCC1143_BAM_INPUT",
-      "sampleType": "DNA",
+      "sampleType": "Total DNA",
       "specimen": {
         "submitterSpecimenId": "HCC1143_FASTQ_INPUT",
         "tumourNormalDesignation": "Cell line - derived from tumour",

Original file line number	Diff line number	Diff line change
`@@ -81,8 +81,7 @@`
`81`	`81`	`"dataType": "Submitted Reads",`
`82`	`82`	`"info": {`
`83`	`83`	`"data_category": "Sequencing Reads"`
`84`		`- },`
`85`		`- "EGAF": "EGAF000001"`
	`84`	`+ }`
`86`	`85`	`}`
`87`	`86`	`]`
`88`	`87`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`		`-type name format size md5sum path EGAF`
	`1`	`+type name format size md5sum path ega_file_id`
`2`	`2`	`file test_rg_3.bam BAM 14911 178f97f7b1ca8bfc28fd5586bdd56799 test_rg_3.bam EGAF000001`
Original file line number	Diff line number	Diff line change
`@@ -122,7 +122,7 @@`
`122`	`122`	`{`
`123`	`123`	`"submitterSampleId": "HCC1143_FASTQ_INPUT",`
`124`	`124`	`"matchedNormalSubmitterSampleId": "HCC1143_BAM_INPUT",`
`125`		`- "sampleType": "DNA",`
	`125`	`+ "sampleType": "Total DNA",`
`126`	`126`	`"specimen": {`
`127`	`127`	`"submitterSpecimenId": "HCC1143_FASTQ_INPUT",`
`128`	`128`	`"tumourNormalDesignation": "Cell line - derived from tumour",`