updated tests to use list for all objects category and type fields

smaht-dac · Oct 31, 2023 · fd77a9b · fd77a9b
1 parent 3fc75e5
commit fd77a9b
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Showing 15 changed files with 55 additions and 36 deletions.
diff --git a/pipeline_utils/__main__.py b/pipeline_utils/__main__.py
@@ -20,8 +20,8 @@
 
 # Variables
 PIPELINE_DEPLOY = 'pipeline_deploy'
-CONSORTIA_ALIAS = 'CONSORTIUM'
-SUBMISSION_CENTERS_ALIAS = 'SUBMISSION_CENTER'
+CONSORTIA_ALIAS = ['smaht_consortium']
+SUBMISSION_CENTERS_ALIAS = ['smaht_dac']
 KEYS_ALIAS = '~/.cgap-keys.json'
 MAIN_ALIAS = 'main'
 BUILDER_ALIAS = '<ff-env>-pipeline-builder'
@@ -51,9 +51,9 @@ def main(args=None):
     pipeline_deploy_parser.add_argument('--account', required=False, help='AWS account to use for deployment')
     pipeline_deploy_parser.add_argument('--region', required=False, help='AWS account region to use for deployment')
     pipeline_deploy_parser.add_argument('--consortia', required=False, nargs='+', help='List of consortia to use for deployment',
-                                                       default=[CONSORTIA_ALIAS])
+                                                       default=CONSORTIA_ALIAS)
     pipeline_deploy_parser.add_argument('--submission-centers', required=False, nargs='+', help='List of centers to use for deployment',
-                                                                default=[SUBMISSION_CENTERS_ALIAS])
+                                                                default=SUBMISSION_CENTERS_ALIAS)
 
     pipeline_deploy_parser.add_argument('--post-software', action='store_true', help='POST|PATCH Software objects')
     pipeline_deploy_parser.add_argument('--post-file-format', action='store_true', help='POST|PATCH FileFormat objects')

diff --git a/pipeline_utils/schemas/yaml_file_reference.py b/pipeline_utils/schemas/yaml_file_reference.py
@@ -28,8 +28,11 @@
             }
         },
         'type': {
-            schema.DESCRIPTION: 'Type of the FileReference',
-            schema.TYPE: schema.STRING
+            schema.DESCRIPTION: 'Types of the FileReference',
+            schema.TYPE: schema.ARRAY,
+            schema.ITEMS: {
+                schema.TYPE: schema.STRING
+            }
         },
         'version': {
             schema.DESCRIPTION: 'Version of the FileReference',

diff --git a/tests/repo_correct/portal_objects/file_format.yaml b/tests/repo_correct/portal_objects/file_format.yaml
@@ -5,9 +5,9 @@ extension: bam
 description: format to represent aligned reads
 secondary_formats:
   - bai
-file_types:
-  - FileReference
-  - FileProcessed
+# file_types:
+#   - FileReference
+#   - FileProcessed
 status: shared
 
 ---

diff --git a/tests/repo_correct/portal_objects/file_reference.yaml b/tests/repo_correct/portal_objects/file_reference.yaml
@@ -12,15 +12,19 @@ secondary_files:
 status: uploading
 uuid: 1936f246-22e1-45dc-bb5c-9cfd55537fe7
 accession: GAPFIXRDPDK5
-category: Sequencing Reads
-type: Unaligned Reads
+category:
+  - Sequencing Reads
+type:
+  - Unaligned Reads
 
 ---
 
 # hg38 fasta (MINIMAL)
 name: reference_genome
-category: Sequencing Reads
-type: Aligned Reads
+category:
+  - Sequencing Reads
+type:
+  - Aligned Reads
 description: hg38 full reference genome plus decoy for CGAP, fasta format
 format: fa
 version: hg38
diff --git a/tests/repo_correct/portal_objects/software.yaml b/tests/repo_correct/portal_objects/software.yaml
@@ -5,15 +5,17 @@ version: 4.1.2
 title: gatk 4.1.2
 source_url: 'http:/broad'
 description: gatk software package
-category: Aligner
+category:
+  - Aligner
 
 ---
 
 # picard (MINIMAL)
 #   + uuid
 #   + accession
 name: picard
-category: Variant Caller
+category:
+  - Variant Caller
 commit: 324ePT
 uuid: efdac7ec-7da3-4f23-9056-7a04abbc5e8b
 accession: GAPMKF1LL29K
diff --git a/tests/repo_correct/portal_objects/workflows/A_gatk-HC.yaml b/tests/repo_correct/portal_objects/workflows/A_gatk-HC.yaml
@@ -3,7 +3,8 @@
 name: gatk-HaplotypeCaller
 description: Run HaplotypeCaller from gatk package
 
-category: Annotation
+category:
+  - Annotation
 
 runner:
   language: wdl

diff --git a/tests/repo_correct/portal_objects/workflows/B_minimal-gatk-HC.yaml b/tests/repo_correct/portal_objects/workflows/B_minimal-gatk-HC.yaml
@@ -20,4 +20,5 @@ output:
 uuid: 1936f246-22e1-45dc-bb5c-9cfd55537fe9
 accession: GAPFIXRDPDK1
 
-category: Feature Calling
+category:
+  - Feature Calling
diff --git a/tests/repo_error/portal_objects/file_format.yaml b/tests/repo_error/portal_objects/file_format.yaml
@@ -6,9 +6,9 @@ extension: bam
 description: format to represent aligned reads
 secondary_formats:
   - bai
-file_types:
-  - FileReference
-  - FileProcessed
+# file_types:
+#   - FileReference
+#   - FileProcessed
 status: shared
 
 ---

diff --git a/tests/repo_error/portal_objects/file_reference.yaml b/tests/repo_error/portal_objects/file_reference.yaml
@@ -12,15 +12,19 @@ secondary_files:
 status: uploading
 uuid: 1936f246-22e1-45dc-bb5c-9cfd55537fe7
 accession: GAPFIXRDPDK5
-category: Sequencing Reads
-type: Unaligned Reads
+category:
+  - Sequencing Reads
+type:
+  - Unaligned Reads
 
 ---
 
 # hg38 fasta (MINIMAL)
 name: reference_genome
-category: Sequencing Reads
-type: Aligned Reads
+category:
+  - Sequencing Reads
+type:
+  - Aligned Reads
 description: hg38 full reference genome plus decoy for CGAP, fasta format
 format: fa
 version: hg38
diff --git a/tests/repo_error/portal_objects/software.yaml b/tests/repo_error/portal_objects/software.yaml
@@ -5,15 +5,17 @@ name: gatk
 title: gatk 4.1.2
 source_url: 'http:/broad'
 description: gatk software package
-category: Aligner
+category:
+  - Aligner
 
 ---
 
 # picard (MINIMAL)
 #   + uuid
 #   + accession
 name: picard
-category: Variant Caller
+category:
+  - Variant Caller
 commit: 324ePT
 uuid: efdac7ec-7da3-4f23-9056-7a04abbc5e8b
 accession: GAPMKF1LL29K
diff --git a/tests/repo_error/portal_objects/workflows/A_gatk-HC.yaml b/tests/repo_error/portal_objects/workflows/A_gatk-HC.yaml
@@ -3,7 +3,8 @@
 name: gatk-HaplotypeCaller
 description: Run HaplotypeCaller from gatk package
 
-category: Annotation
+category:
+  - Annotation
 
 runner:
   language: wdl

diff --git a/tests/repo_error/portal_objects/workflows/B_minimal-gatk-HC.yaml b/tests/repo_error/portal_objects/workflows/B_minimal-gatk-HC.yaml
@@ -21,4 +21,5 @@ output:
 uuid: 1936f246-22e1-45dc-bb5c-9cfd55537fe9
 accession: GAPFIXRDPDK1
 
-category: Feature Calling
+category:
+  - Feature Calling
diff --git a/tests/test_yaml_file_reference.py b/tests/test_yaml_file_reference.py
@@ -22,8 +22,8 @@ def test_file_reference():
                 "consortia": ["cgap-core"],
                 "status": "uploading",
                 "uuid": "1936f246-22e1-45dc-bb5c-9cfd55537fe7",
-                "data_category": "Sequencing Reads",
-                "data_type": "Unaligned Reads"
+                "data_category": ["Sequencing Reads"],
+                "data_type": ["Unaligned Reads"]
             },
             {
                 "aliases": ["cgap-core:FileReference-reference_genome_hg38"],
@@ -33,8 +33,8 @@ def test_file_reference():
                 "submission_centers": ["hms-dbmi"],
                 "consortia": ["cgap-core"],
                 "status": None,
-                "data_category": "Sequencing Reads",
-                "data_type": "Aligned Reads"
+                "data_category": ["Sequencing Reads"],
+                "data_type": ["Aligned Reads"]
             }
         ]
 

diff --git a/tests/test_yaml_software.py b/tests/test_yaml_software.py
@@ -21,7 +21,7 @@ def test_software():
                 "source_url": "http:/broad",
                 "title": "gatk 4.1.2",
                 "version": "4.1.2",
-                "category": "Aligner"
+                "category": ["Aligner"]
             },
             {
                 "accession": "GAPMKF1LL29K",
@@ -32,7 +32,7 @@ def test_software():
                 "consortia": ["cgap-core"],
                 "title": "picard [324ePT]",
                 "uuid": "efdac7ec-7da3-4f23-9056-7a04abbc5e8b",
-                "category": "Variant Caller"
+                "category": ["Variant Caller"]
             }
         ]
 

diff --git a/tests/test_yaml_workflow.py b/tests/test_yaml_workflow.py
@@ -17,7 +17,7 @@ def test_workflow():
                 "aliases": ["cgap-core:Workflow-gatk-HaplotypeCaller_v1.0.0"],
                 "name": "gatk-HaplotypeCaller",
                 "version": "v1.0.0",
-                "category": "Annotation",
+                "category": ["Annotation"],
                 "arguments": [
                     {
                       "argument_format": "bam",
@@ -65,7 +65,7 @@ def test_workflow():
             },
             {
                 "accession": "GAPFIXRDPDK1",
-                "category": "Feature Calling",
+                "category": ["Feature Calling"],
                 "aliases": ["cgap-core:Workflow-gatk-HaplotypeCaller_v1.0.0"],
                 "name": "gatk-HaplotypeCaller",
                 "version": "v1.0.0",