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Add SMSID to report (Display SMSID, but actual code is SMS_ID) #377

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merged 3 commits into from
Oct 24, 2024
Merged

Add SMSID to report (Display SMSID, but actual code is SMS_ID) #377

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asmisc_smsid_in_report
alx652 Oct 24, 2024
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alx652 Oct 24, 2024
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alx652 Oct 24, 2024
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1 change: 1 addition & 0 deletions ...-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultColumns.java
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Expand Up @@ -31,6 +31,7 @@ public enum DefaultColumns implements Column {
RECORD_ACCESS_GROUPS,
RXCUI,
PUBCHEM,
SMSID,
MPNS,
GRIN,
INGREDIENT_TYPE,
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6 changes: 5 additions & 1 deletion ...main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java
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Expand Up @@ -132,7 +132,7 @@ public Map<Column, ColumnValueRecipe<Substance>> createColumnRecipes(Parameters
Map<Column, ColumnValueRecipe<Substance>> 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())));
Expand All @@ -157,6 +157,10 @@ public Map<Column, ColumnValueRecipe<Substance>> 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 header to be SMSID
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()));

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