Remove entityId in schema test (#109)

nf-osi · Jul 11, 2023 · b59eab9 · b59eab9
1 parent c0c2fd9
commit b59eab9
Showing 1 changed file with 43 additions and 44 deletions.
diff --git a/tests/testthat/test_json_schema_utils.R b/tests/testthat/test_json_schema_utils.R
@@ -1,51 +1,50 @@
 test_that("Recursive lookup works with `get_dependency_from_json_schema`", {
   # Note: should make test schema bc test will need to be updated if template changes
   # Define what columns are present in schematic-generated GenomicsAssayTemplate (ignoring "eTag")
-  k <- c("Component",
-         "Filename",
-         "resourceType",
-         "progressReportNumber",
-         "dataType",
-         "assay",
-         "platform",
-         "individualID",
-         "parentSpecimenID",
-         "runType",
-         "libraryPrep",
-         "comments",
-         "age",
-         "ageUnit",
-         "aliquotID",
-         "cellType",
-         "dataSubtype",
-         "diagnosis",
-         "dissociationMethod",
-         "fileFormat",
-         "isCellLine",
-         "isPrimaryCell",
-         "isStranded",
-         "libraryPreparationMethod",
-         "modelSystemName",
-         "nf1Genotype",
-         "nf2Genotype",
-         "nucleicAcidSource",
-         "organ",
-         "readDepth",
-         "readLength",
-         "readPair",
-         "readPairOrientation",
-         "readStrandOrigin",
-         "sex",
+  k <- c("age",                             
+         "ageUnit",                         
+         "aliquotID",                       
+         "assay",                           
+         "cellType",                        
+         "comments",                        
+         "Component",                      
+         "dataSubtype",                     
+         "dataType",                        
+         "diagnosis",                       
+         "dissociationMethod",              
+         "fileFormat",                      
+         "Filename",                        
+         "individualID",                   
+         "isCellLine",                      
+         "isPrimaryCell",                   
+         "isStranded",                      
+         "isXenograft",                     
+         "libraryPrep",                     
+         "libraryPreparationMethod",        
+         "modelSystemName",                
+         "nf1Genotype",                     
+         "nf2Genotype",                     
+         "nucleicAcidSource",               
+         "organ",                           
+         "parentSpecimenID",                
+         "platform",                        
+         "progressReportNumber",           
+         "readDepth",                       
+         "readLength",                      
+         "readPair",                        
+         "readPairOrientation",             
+         "readStrandOrigin",                
+         "resourceType",                    
+         "runType",                        
+         "sex",                             
          "species",
-         "specimenID",
-         "specimenPreparationMethod",
-         "tissue",
-         "tumorType",
-         "entityId",
-         "transplantationType",
-         "transplantationRecipientSpecies",
-         "transplantationRecipientTissue",
-         "isXenograft")
+         "specimenID",                      
+         "specimenPreparationMethod",       
+         "tissue",                          
+         "transplantationRecipientSpecies", 
+         "transplantationRecipientTissue", 
+         "transplantationType",             
+         "tumorType")
 
   k_test <- get_dependency_from_json_schema(id = "bts:GenomicsAssayTemplate") 
   testthat::expect_equal(sort(k), sort(k_test))