target_repository

elixir-europe · Nov 5, 2024 · e39fdfc · e39fdfc
1 parent ea16333
commit e39fdfc
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Showing 9 changed files with 26 additions and 26 deletions.
diff --git a/mars-cli/mars_lib/models/repository_response.py b/mars-cli/mars_lib/models/repository_response.py
@@ -51,7 +51,7 @@ class RepositoryResponse(BaseModel):
     @field_validator("target_repository")
     def validate_target_repository(cls, v: str) -> str:
         if v not in [item.value for item in TargetRepository]:
-            raise ValueError(f"Invalid 'target repository' value: '{v}'")
+            raise ValueError(f"Invalid 'target_repository' value: '{v}'")
         return v
 
     @classmethod

diff --git a/mars-cli/mars_lib/target_repo.py b/mars-cli/mars_lib/target_repo.py
@@ -1,7 +1,7 @@
 from enum import Enum
 
 
-TARGET_REPO_KEY = "target repository"
+TARGET_REPO_KEY = "target_repository"
 
 
 class TargetRepository(str, Enum):

diff --git a/mars-cli/tests/test_isa_json.py b/mars-cli/tests/test_isa_json.py
@@ -121,28 +121,28 @@ def test_target_repo_comment_validator():
         "comments": [
             {
                 "@id": "comment_003",
-                "name": "target repository",
+                "name": "target_repository",
                 "value": TargetRepository.ENA,
             },
             {
                 "@id": "comment_004",
-                "name": "target repository",
+                "name": "target_repository",
                 "value": TargetRepository.METABOLIGHTS,
             },
         ],
     }
 
     assert Assay.model_validate(valid_assay_json)
     with pytest.raises(
-        ValidationError, match="Invalid 'target repository' value: 'my special repo'"
+        ValidationError, match="Invalid 'target_repository' value: 'my special repo'"
     ):
         Assay.model_validate(invalid_assay_json)
 
-    with pytest.raises(ValidationError, match="'target repository' comment is missing"):
+    with pytest.raises(ValidationError, match="'target_repository' comment is missing"):
         Assay.model_validate(second_invalid_assay_json)
 
     with pytest.raises(
-        ValidationError, match="Multiple 'target repository' comments found"
+        ValidationError, match="Multiple 'target_repository' comments found"
     ):
         Assay.model_validate(third_invalid_assay_json)
 

diff --git a/test-data/ISA-BH2023-ALL/i_investigation.txt b/test-data/ISA-BH2023-ALL/i_investigation.txt
@@ -69,7 +69,7 @@ Study Assay Technology Type	mass spectrometry	NMR spectroscopy	NMR spectroscopy
 Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/CHMO_0000470	http://purl.obolibrary.org/obo/CHMO_0000591	http://purl.obolibrary.org/obo/CHMO_0000591		
 Study Assay Technology Type Term Source REF	MSIO	MSIO	MSIO	MSIO	MSIO
 Study Assay Technology Platform					
-Comment[target repository]	metabolights	metabolights	metabolights	ega	arrayexpress
+Comment[target_repository]	metabolights	metabolights	metabolights	ega	arrayexpress
 STUDY PROTOCOLS
 Study Protocol Name	cell culture and isotopic labeling	intracellular metabolite extraction	extracellular metabolite extraction	liquid chromatography mass spectrometry	1D 13C NMR spectroscopy for isotopomer analysis	1D 13C NMR spectroscopy for metabolite profiling	MS metabolite identification	NMR metabolite identification	mRNA extraction	gDNA extraction	gDNA library preparation	mRNA library preparation	sequencing	transcription analysis	CNV analysis	13C SIRM MS and NMR integrative analysis
 Study Protocol Type	sample collection	metabolite extraction	metabolite extraction	mass spectrometry	nmr spectroscopy	nmr spectroscopy	metabolite identification	data transformation	material separation	material separation	library construction	library construction	nucleic acid sequencing	data transformation	data transformation	data transformation

diff --git a/test-data/ISA-BH2023-ALL/isa-bh2023-all.json b/test-data/ISA-BH2023-ALL/isa-bh2023-all.json
@@ -60,7 +60,7 @@
                     ],
                     "comments": [
                     {
-                        "name": "target repository",
+                        "name": "target_repository",
                         "value": "metabolights"
                     }
                     ],
@@ -858,7 +858,7 @@
                     "characteristicCategories": [],
                     "comments": [
                     {
-                        "name": "target repository",
+                        "name": "target_repository",
                         "value": "metabolights"
                     }
                     ],
@@ -2735,7 +2735,7 @@
                     "characteristicCategories": [],
                     "comments": [
                     {
-                        "name": "target repository",
+                        "name": "target_repository",
                         "value": "metabolights"
                     }
                     ],
@@ -3429,7 +3429,7 @@
                     ],
                     "comments": [
                     {
-                        "name": "target repository",
+                        "name": "target_repository",
                         "value": "eva"
                     }
                     ],
@@ -4749,7 +4749,7 @@
                     ],
                     "comments": [
                     {
-                        "name": "target repository",
+                        "name": "target_repository",
                         "value": "ena"
                     }
                     ],

diff --git a/test-data/ISA-BH2023-Gx/i_investigation.txt b/test-data/ISA-BH2023-Gx/i_investigation.txt
@@ -69,7 +69,7 @@ Study Assay Technology Type	nucleic acid sequencing
 Study Assay Technology Type Term Accession Number	
 Study Assay Technology Type Term Source REF	MSIO
 Study Assay Technology Platform	
-Comment[target repository]	ega
+Comment[target_repository]	ega
 STUDY PROTOCOLS
 Study Protocol Name	cell culture and isotopic labeling	intracellular metabolite extraction	extracellular metabolite extraction	liquid chromatography mass spectrometry	1D 13C NMR spectroscopy for isotopomer analysis	1D 13C NMR spectroscopy for metabolite profiling	MS metabolite identification	NMR metabolite identification	mRNA extraction	gDNA extraction	gDNA library preparation	mRNA library preparation	sequencing	transcription analysis	CNV analysis	13C SIRM MS and NMR integrative analysis
 Study Protocol Type	sample collection	metabolite extraction	metabolite extraction	mass spectrometry	nmr spectroscopy	nmr spectroscopy	metabolite identification	data transformation	material separation	material separation	library construction	library construction	nucleic acid sequencing	data transformation	data transformation	data transformation

diff --git a/test-data/ISA-BH2023-Mx/i_investigation.txt b/test-data/ISA-BH2023-Mx/i_investigation.txt
@@ -69,7 +69,7 @@ Study Assay Technology Type	mass spectrometry	NMR spectroscopy	NMR spectroscopy
 Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/CHMO_0000470	http://purl.obolibrary.org/obo/CHMO_0000591	http://purl.obolibrary.org/obo/CHMO_0000591
 Study Assay Technology Type Term Source REF	MSIO	MSIO	MSIO
 Study Assay Technology Platform			
-Comment[target repository]	metabolights	metabolights	metabolights
+Comment[target_repository]	metabolights	metabolights	metabolights
 STUDY PROTOCOLS
 Study Protocol Name	cell culture and isotopic labeling	intracellular metabolite extraction	extracellular metabolite extraction	liquid chromatography mass spectrometry	1D 13C NMR spectroscopy for isotopomer analysis	1D 13C NMR spectroscopy for metabolite profiling	MS metabolite identification	NMR metabolite identification	mRNA extraction	gDNA extraction	gDNA library preparation	mRNA library preparation	sequencing	transcription analysis	CNV analysis	13C SIRM MS and NMR integrative analysis
 Study Protocol Type	sample collection	metabolite extraction	metabolite extraction	mass spectrometry	nmr spectroscopy	nmr spectroscopy	metabolite identification	data transformation	material separation	material separation	library construction	library construction	nucleic acid sequencing	data transformation	data transformation	data transformation

diff --git a/test-data/ISA-BH2023-Tx/i_investigation.txt b/test-data/ISA-BH2023-Tx/i_investigation.txt
@@ -69,7 +69,7 @@ Study Assay Technology Type	nucleic acid sequencing
 Study Assay Technology Type Term Accession Number	
 Study Assay Technology Type Term Source REF	MSIO
 Study Assay Technology Platform	
-Comment[target repository]	arrayexpress
+Comment[target_repository]	arrayexpress
 STUDY PROTOCOLS
 Study Protocol Name	cell culture and isotopic labeling	intracellular metabolite extraction	extracellular metabolite extraction	liquid chromatography mass spectrometry	1D 13C NMR spectroscopy for isotopomer analysis	1D 13C NMR spectroscopy for metabolite profiling	MS metabolite identification	NMR metabolite identification	mRNA extraction	gDNA extraction	gDNA library preparation	mRNA library preparation	sequencing	transcription analysis	CNV analysis	13C SIRM MS and NMR integrative analysis
 Study Protocol Type	sample collection	metabolite extraction	metabolite extraction	mass spectrometry	nmr spectroscopy	nmr spectroscopy	metabolite identification	data transformation	material separation	material separation	library construction	library construction	nucleic acid sequencing	data transformation	data transformation	data transformation

diff --git a/test-data/biosamples-input-isa.json b/test-data/biosamples-input-isa.json
@@ -675,7 +675,7 @@
             ],
             "comments": [
               {
-                "name": "target repository",
+                "name": "target_repository",
                 "value": "ena"
               }
             ],
@@ -974,27 +974,27 @@
             "dataFiles": [
               {
                 "@id": "#data/334",
-                "name": "fake2.bam",
+                "name": "RD file 1b",
                 "type": "Raw Data File",
                 "comments": [
                   {
-                    "name": "file type",
-                    "value": "bam"
+                    "name": "file_name",
+                    "value": "ENA_TEST2.R2.fastq.gz"
                   },
                   {
-                    "name": "file checksum",
-                    "value": "9840f585055afc37de353706fd31a377"
+                    "name": "file_type",
+                    "value": "fastq"
                   },
                   {
-                    "name": "submission date",
-                    "value": ""
+                    "name": "file checksum",
+                    "value": "69c903251902c1e0b75331f70e531012"
                   },
                   {
-                    "name": "status",
+                    "name": "accession",
                     "value": ""
                   },
                   {
-                    "name": "accession",
+                    "name": "submission date",
                     "value": ""
                   }
                 ]