From 0a12fe82d2f178ad76c2c08dd80677a46fcf511f Mon Sep 17 00:00:00 2001 From: alx652 Date: Thu, 24 Oct 2024 16:02:54 -0400 Subject: [PATCH 1/3] asmisc_smsid_in_report --- .../java/gsrs/module/substance/exporters/DefaultColumns.java | 1 + .../DefaultSubstanceSpreadsheetExporterFactory.java | 5 ++++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultColumns.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultColumns.java index 0569cdb9..ce2b24c5 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultColumns.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultColumns.java @@ -31,6 +31,7 @@ public enum DefaultColumns implements Column { RECORD_ACCESS_GROUPS, RXCUI, PUBCHEM, + SMSID, MPNS, GRIN, INGREDIENT_TYPE, diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java index 4a4b76b5..79fe63aa 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java @@ -132,7 +132,7 @@ public Map> createColumnRecipes(Parameters Map> defaultRecipeMap= new LinkedHashMap<>(); - // UUID, APPROVAL_ID, PT, RN, EC, NCIT, RXCUI PUBCHEM EPA_CompTox CATALOG_OF_LIFE ITIS NCBI PLANTS POWO GRIN MPNS INN_ID DAILYMED MF INCHIKEY SMILES INGREDIENT_TYPE + // UUID, APPROVAL_ID, PT, RN, EC, NCIT, RXCUI PUBCHEM SMSID EPA_CompTox CATALOG_OF_LIFE ITIS NCBI PLANTS POWO GRIN MPNS INN_ID DAILYMED MF INCHIKEY SMILES INGREDIENT_TYPE defaultRecipeMap.put(DefaultColumns.UUID, SingleColumnValueRecipe.create(DefaultColumns.UUID, (s, cell) -> cell.write(s.getOrGenerateUUID()))); defaultRecipeMap.put(DefaultColumns.APPROVAL_ID, SingleColumnValueRecipe.create(DefaultColumns.APPROVAL_ID, (s, cell) -> cell.writeString(s.getApprovalID()))); @@ -157,6 +157,9 @@ public Map> createColumnRecipes(Parameters defaultRecipeMap.put(DefaultColumns.RXCUI, new CodeSystemRecipe(DefaultColumns.RXCUI, "RXCUI")); defaultRecipeMap.put(DefaultColumns.PUBCHEM, new CodeSystemRecipe(DefaultColumns.PUBCHEM, "PUBCHEM")); + defaultRecipeMap.put(DefaultColumns.SMSID, new CodeSystemRecipe(DefaultColumns.SMSID, "SMS_ID").replaceColumnName(DefaultColumns.SMSID + .name(),"SMSID")); + defaultRecipeMap.put(DefaultColumns.EPA_CompTox, new CodeSystemRecipe(DefaultColumns.EPA_CompTox, "EPA CompTox")); defaultRecipeMap.put(DefaultColumns.CATALOGUE_OF_LIFE, ParentSourceMaterialRecipeWrapper.wrap(new CodeSystemRecipe(DefaultColumns.CATALOGUE_OF_LIFE, "CATALOGUE OF LIFE"),params.getScrubber())); From a696d424ea20ef11259d7d69ed1e055b57a52d65 Mon Sep 17 00:00:00 2001 From: alx652 Date: Thu, 24 Oct 2024 16:11:49 -0400 Subject: [PATCH 2/3] add comment --- .../exporters/DefaultSubstanceSpreadsheetExporterFactory.java | 1 + 1 file changed, 1 insertion(+) diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java index 79fe63aa..ecdc0291 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java @@ -157,6 +157,7 @@ public Map> createColumnRecipes(Parameters defaultRecipeMap.put(DefaultColumns.RXCUI, new CodeSystemRecipe(DefaultColumns.RXCUI, "RXCUI")); defaultRecipeMap.put(DefaultColumns.PUBCHEM, new CodeSystemRecipe(DefaultColumns.PUBCHEM, "PUBCHEM")); + // In controlled vocab, the display is SMSID, but the value is SMS_ID, want report column to be SMSID defaultRecipeMap.put(DefaultColumns.SMSID, new CodeSystemRecipe(DefaultColumns.SMSID, "SMS_ID").replaceColumnName(DefaultColumns.SMSID .name(),"SMSID")); From 1566dce447bf5339ac00f980f8c4c05adb3d8eab Mon Sep 17 00:00:00 2001 From: alx652 Date: Thu, 24 Oct 2024 16:12:57 -0400 Subject: [PATCH 3/3] add comment --- .../exporters/DefaultSubstanceSpreadsheetExporterFactory.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java index ecdc0291..af0b4dfd 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java @@ -157,7 +157,7 @@ public Map> createColumnRecipes(Parameters defaultRecipeMap.put(DefaultColumns.RXCUI, new CodeSystemRecipe(DefaultColumns.RXCUI, "RXCUI")); defaultRecipeMap.put(DefaultColumns.PUBCHEM, new CodeSystemRecipe(DefaultColumns.PUBCHEM, "PUBCHEM")); - // In controlled vocab, the display is SMSID, but the value is SMS_ID, want report column to be SMSID + // In controlled vocab, the display is SMSID, but the value is SMS_ID, want report column header to be SMSID defaultRecipeMap.put(DefaultColumns.SMSID, new CodeSystemRecipe(DefaultColumns.SMSID, "SMS_ID").replaceColumnName(DefaultColumns.SMSID .name(),"SMSID"));