Trm 30823 UniParc proteome redundant fasta #249

LeonardoGonzales · 2024-12-09T14:53:24Z

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…t data

# Conflicts: # controlled-vocabulary/src/test/resources/xdb/dr_ord # core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParser.java # core-parser/src/test/java/org/uniprot/core/parser/fasta/UniParcFastaParserTest.java

# Conflicts: # xml-parser/src/main/java/org/uniprot/core/xml/uniparc/UniParcDBCrossReferenceConverter.java

ahmadshadab · 2024-12-11T10:53:28Z

I am going to merge with main before review.

ahmadshadab · 2024-12-13T09:28:25Z

core-domain/src/main/java/org/uniprot/core/uniparc/UniParcDatabase.java

+    VECTORBASE(3500, "VectorBase", false, false),
+    VEGA(3600, "VEGA", true, false,  "https://vega.sanger.ac.uk/id/%id"),
+    WORMBASE_PARASITE(3700, "WBParaSite", true, true, "https://parasite.wormbase.org/id/%id"),
+    WORMBASE(3800, "WormBase", true, true,"https://wormbase.org/db/seq/protein?name=%id;class=CDS");



How do we know if a database is source? Could you please add source of this information in this class?

Jie provided the list of databases that are sources in UniParc.

ahmadshadab · 2024-12-13T09:31:05Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

+
+    private static final Set<UniParcDatabase> uniProtDatabases = Set.of(
+            UniParcDatabase.SWISSPROT, UniParcDatabase.TREMBL, UniParcDatabase.SWISSPROT_VARSPLIC);
+


Use uppercase for const.

ahmadshadab · 2024-12-13T09:49:18Z

core-domain/src/main/java/org/uniprot/core/uniparc/UniParcCrossReference.java

@@ -11,6 +11,8 @@
 */
 public interface UniParcCrossReference extends CrossReference<UniParcDatabase> {



We should add formula and an example how we construct source. :: and eg. ABC01415:UP000005640:Chromosome 1

ahmadshadab · 2024-12-13T09:55:25Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

+                    hasActive = true;
+                }
+            } else {
+                sourceXrefs.add(xref);


Here we are assuming that database type other than uniProtDatabases are source xref. But in UniParcDatabase,java i can see other non-source xrefs e.g. EPO, FLYbase. Will they not be added as sourceXrefs?

We are doing a filter in the REST side (we filter proteome Id). I can add an else if for sources if you prefer

ahmadshadab · 2024-12-13T09:56:18Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

@@ -0,0 +1,134 @@
+package org.uniprot.core.parser.fasta.uniparc;


We should add few comments in this class.

ahmadshadab · 2024-12-13T10:17:21Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

+    }
+
+    private static StringBuilder getFastaHeader(List<UniParcCrossReference> xrefs, boolean hasActive, String id, String proteomeId, boolean isSource) {
+        Set<String> proteinName = new LinkedHashSet<>();


Use plural name for collection proteinNames and components

ahmadshadab · 2024-12-13T10:19:28Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

+        if(!component.isEmpty()){
+            sb.append(":").append(String.join("|", component));
+        }
+        return sb;


We can move "|" to a constant.

ahmadshadab · 2024-12-13T10:23:20Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

+        if(!sourceIds.isEmpty()){
+            sb.append(" SS=").append(String.join("|", sourceIds));
+        }
+        sb.append(" PC=").append(proteomeId);


proteomeId can be null

ahmadshadab · 2024-12-13T10:25:07Z

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java

+                                            component.add(ids[2]);
+                                        }
+                                    }
+                                });


Extract the logic for processing xref.getProperties() into a helper method, simplifying the loop body.
We should keep the lambda small. we can extract the for(source:sources) logic another method.

ahmadshadab · 2024-12-13T10:31:15Z

xml-parser/src/main/java/org/uniprot/core/xml/CrossReferenceConverterUtils.java

@@ -47,6 +49,9 @@ public static void populateUniParcCrossReferenceBuilder(String propertyType, Str
            case PROPERTY_UNIPROTKB_ACCESSION:
                builder.propertiesAdd(PROPERTY_UNIPROTKB_ACCESSION, propertyValue);
                break;
+            case PROPERTY_SOURCES:
+                builder.propertiesAdd(PROPERTY_SOURCES, propertyValue);
+                break;
            default:


We have not covered this case in test case.

LeonardoGonzales added 21 commits March 12, 2024 13:59

First Version of FASTA with sequence sources

5ffb871

Updated second Version of FASTA with sequence sources

805dd62

Merge branch 'main' into TRM-30823-REDUNDANT-FASTA

d4fb112

Add exploratory options source ids and proteome and proteome componen…

5d93997

…t data

Merge branch 'main' into TRM-30823-REDUNDANT-FASTA

65f50d6

Fix exploratory options source ids and proteome and proteome componen…

5f11138

…t data

Merge branch 'main' into TRM-30823-REDUNDANT-FASTA

ac82972

add SWISSPROT_VARSPLIC database

01e806c

Merge branch 'main' into TRM-30823-REDUNDANT-FASTA

7a6b247

Add stream to uniparc proteome endpoint

2cb4648

Merge branch 'main' into TRM-30823-REDUNDANT-FASTA

cad6c55

Merge changes

fc381eb

add sequence source for proteome fasta

149a8cf

Merge branch 'uniparc_light_vd_v2' into TRM-30823-REDUNDANT-FASTA_TST

01539d9

Improvements in the fasta Format parser and sources attribute

335954d

Merge branch 'main' into TRM-30823-REDUNDANT-FASTA_TST

97d68a9

# Conflicts: # xml-parser/src/main/java/org/uniprot/core/xml/uniparc/UniParcDBCrossReferenceConverter.java

improve test in UniParcProteomeFastaParser.java

a13cefc

improve uniparc xref voldemort index

606d6ef

code format

47003db

improve fasta details

6e1c554

LeonardoGonzales requested a review from ahmadshadab December 9, 2024 14:53

ahmadshadab reviewed Dec 13, 2024

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Trm 30823 UniParc proteome redundant fasta #249

Trm 30823 UniParc proteome redundant fasta #249

LeonardoGonzales commented Dec 9, 2024

ahmadshadab commented Dec 11, 2024

ahmadshadab Dec 13, 2024

LeonardoGonzales Dec 13, 2024

ahmadshadab Dec 13, 2024

ahmadshadab Dec 13, 2024 •

edited

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ahmadshadab Dec 13, 2024

LeonardoGonzales Dec 13, 2024

ahmadshadab Dec 13, 2024

ahmadshadab Dec 13, 2024

ahmadshadab Dec 13, 2024

ahmadshadab Dec 13, 2024

ahmadshadab Dec 13, 2024

ahmadshadab Dec 13, 2024


		private static final Set<UniParcDatabase> uniProtDatabases = Set.of(
		UniParcDatabase.SWISSPROT, UniParcDatabase.TREMBL, UniParcDatabase.SWISSPROT_VARSPLIC);

		@@ -11,6 +11,8 @@
		*/
		public interface UniParcCrossReference extends CrossReference<UniParcDatabase> {

		@@ -0,0 +1,134 @@
		package org.uniprot.core.parser.fasta.uniparc;

Trm 30823 UniParc proteome redundant fasta #249

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Trm 30823 UniParc proteome redundant fasta #249

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LeonardoGonzales commented Dec 9, 2024

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ahmadshadab Dec 13, 2024 • edited Loading

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ahmadshadab Dec 13, 2024 •

edited

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