Merge pull request #82 from icgc-argo/[email protected]

[release]
icgc-argo · Jun 26, 2023 · 931468e · 931468e
2 parents 2eae399 + c52a2d4
commit 931468e
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Showing 15 changed files with 72 additions and 6 deletions.
diff --git a/sanity-check/main.nf b/sanity-check/main.nf
@@ -24,7 +24,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.1'
+version = '0.1.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.sanity-check'

diff --git a/sanity-check/main.py b/sanity-check/main.py
@@ -58,7 +58,7 @@ def main():
             args.clinical_url,
             args.api_token
         )
-        
+
         final_metadata=compile_metadata(
             metadata,
             clinical_metadata
@@ -67,14 +67,15 @@ def main():
                 final_metadata,
                 args.submission_song_url
         )
+
         if not args.force:
             check_analysis_exists(
                 final_metadata,
                 args.submission_song_url
             )
 
         update_tsv(final_metadata,"updated_"+args.experiment_info_tsv)
-        
+
 
 def load_tsv(experiment_info_tsv):
     metadata_dict = {}
@@ -145,12 +146,39 @@ def get_clinical(metadata,clinical_url,api_token):
 
         sample_ind=[ele for ele,sample in enumerate(response.json()['specimens'][specimen_ind[0]]['samples']) if sample['sampleId']==return_metadata['sample_id']]
         if len(sample_ind)!=1:
-            sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s'  was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id'],))
+            sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s'  was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id']))
         return_metadata['sample_type']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['sampleType']
         return_metadata['submitter_sample_id']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['submitterId']
 
+    if return_metadata['tumour_normal_designation']=="Tumour":
+        #WGS, WXS, RNA-Seq, Bisulfite-Seq, ChIP-Seq, Targeted-Seq
+        if metadata.get("submitter_matched_normal_sample_id"):
+            check_normal_sample_exists(metadata,response.json())
+        else:
+            if metadata.get("experimental_strategy") in ['WGS', 'WXS']:
+                sys.exit("Null entry for `submitter_matched_normal_sample_id` detected. For tumour `experiment_strategy` type %s ,this field is required and must reference a registered normal sample." % (metadata.get("experimental_strategy")))
+
     return return_metadata
 
+
+
+def check_normal_sample_exists(metadata,clinical_metadata):
+    submitter_id=metadata['submitter_matched_normal_sample_id']
+
+    return_id=None
+    tumourNormalDesignation=None
+
+    for specimen in clinical_metadata['specimens']:
+        for samples in specimen['samples']:
+            if samples['submitterId']==submitter_id:
+                return_id=samples['submitterId']
+                tumourNormalDesignation=specimen["tumourNormalDesignation"]
+    if return_id==None:
+        sys.exit("'submitter_matched_normal_sample_id':%s was not found in study. Please verify '%s' has been registered." % (submitter_id,submitter_id))
+    if tumourNormalDesignation=="Tumour":
+        sys.exit("'submitter_matched_normal_sample_id':%s detected as tumour instead of normal. Please verify correct sample." % (submitter_id))
+
+
 def compile_metadata(metadata,clinical_metadata):
 
     ###Over-write metadata with clinical_metadata

diff --git a/sanity-check/pkg.json b/sanity-check/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "sanity-check",
-    "version": "0.1.1",
+    "version": "0.1.2",
     "description": "Data submission sanity checks including verifying info from Clinical API",
     "main": "main.nf",
     "deprecated": false,

diff --git a/sanity-check/tests/checker.nf b/sanity-check/tests/checker.nf
@@ -29,7 +29,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.1'
+version = '0.1.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.sanity-check'

diff --git a/sanity-check/tests/input/bad1_tumour_example.tsv b/sanity-check/tests/input/bad1_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4
diff --git a/sanity-check/tests/input/bad2_tumour_example.tsv b/sanity-check/tests/input/bad2_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1		QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4
diff --git a/sanity-check/tests/input/comparison_good1_tumour_example.tsv b/sanity-check/tests/input/comparison_good1_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count	gender	specimen_tissue_source	tumour_normal_designation	specimen_type	sample_type
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN1	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4	Female	Urine	Tumour	Metastatic tumour - metastasis to distant location	Total RNA
diff --git a/sanity-check/tests/input/comparison_good2_tumour_example.tsv b/sanity-check/tests/input/comparison_good2_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count	gender	specimen_tissue_source	tumour_normal_designation	specimen_type	sample_type
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1		QCMG	ILLUMINA	Illumina HiSeq 2000	Targeted-Seq		4	Female	Urine	Tumour	Metastatic tumour - metastasis to distant location	Total RNA
diff --git a/sanity-check/tests/input/comparison_good_tumour_example.tsv b/sanity-check/tests/input/comparison_good_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count	gender	specimen_tissue_source	tumour_normal_designation	specimen_type	sample_type
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN1	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4	Female	Urine	Tumour	Metastatic tumour - metastasis to distant location	Total RNA
diff --git a/sanity-check/tests/input/good1_tumour_example.tsv b/sanity-check/tests/input/good1_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN1	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4
diff --git a/sanity-check/tests/input/good2_tumour_example.tsv b/sanity-check/tests/input/good2_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1		QCMG	ILLUMINA	Illumina HiSeq 2000	Targeted-Seq		4
diff --git a/sanity-check/tests/local_bad_tumour_badRef_example.json b/sanity-check/tests/local_bad_tumour_badRef_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/bad1_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good_example.tsv"
+}
diff --git a/sanity-check/tests/local_bad_tumour_nullWGS_example.json b/sanity-check/tests/local_bad_tumour_nullWGS_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/bad2_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good_example.tsv"
+}
diff --git a/sanity-check/tests/local_good_tumour_ts_example.json b/sanity-check/tests/local_good_tumour_ts_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/good2_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good2_tumour_example.tsv"
+}
diff --git a/sanity-check/tests/local_good_tumour_wgs_example.json b/sanity-check/tests/local_good_tumour_wgs_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/good1_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good1_tumour_example.tsv"
+}