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ZFIN-9435: UniProt Load Report Improvements #1291

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174bfa3
ZFIN-9435:
rtaylorzfin Dec 19, 2024
cea7558
ZFIN-9435:
rtaylorzfin Dec 19, 2024
5b3003a
ZFIN-9435:
rtaylorzfin Dec 20, 2024
4a1f5e7
ZFIN-9435:
rtaylorzfin Dec 20, 2024
d449731
ZFIN-9435:
rtaylorzfin Dec 20, 2024
446dacf
ZFIN-9435:
rtaylorzfin Dec 20, 2024
8fb2f03
ZFIN-9435:
rtaylorzfin Dec 23, 2024
dfb2de5
ZFIN-9435: Recategorize the SubType of each uniprot load action to in…
rtaylorzfin Jan 15, 2025
922d4ee
Bugfix: move constant
rtaylorzfin Jan 16, 2025
754571b
update analytics jar
rtaylorzfin Jan 16, 2025
8f876b2
Bugfix: update version number of dependency
rtaylorzfin Jan 16, 2025
3041498
More helpful output in case of error
rtaylorzfin Jan 16, 2025
65ef381
debug output
rtaylorzfin Jan 16, 2025
a9a0563
Add throttling
rtaylorzfin Jan 16, 2025
19ca9ef
Make the report prettier -> add ZFIN logo
rtaylorzfin Jan 17, 2025
ce75661
ZFIN-9495: Switched to using the X-Real-IP header in the LogFormat co…
zfinryanm Jan 17, 2025
6398b8f
Change display of reports to use tables instead of lists
rtaylorzfin Jan 17, 2025
6ccc6bb
ZFIN-9488: Enabled more production settings for docker, i.e. franklin.
zfinryanm Jan 17, 2025
d51b4e9
Save ncbi api results so we can audit the history of the run.
rtaylorzfin Jan 17, 2025
cad338f
Cleanup
rtaylorzfin Jan 17, 2025
86256d6
ZFIN-9269 deduplicate pub_pages field in publication table
cmpich Jan 13, 2025
f0008a1
remove duplicated unit test in registration list
cmpich Jan 21, 2025
7ee2c6c
remove dbSNP foregin_db enum
cmpich Jan 21, 2025
db5fdd7
ZFIN-9269 deduplicate pub_pages field in publication table (#1290)
cmpich Jan 21, 2025
0369da8
Update report to use tags instead of multiple subtypes
rtaylorzfin Jan 22, 2025
be71e70
ZFIN-9408: Add company ID to company page. (#1292)
rtaylorzfin Jan 22, 2025
da64bc9
Change default behavior for refseq mismatches due to replacements to …
rtaylorzfin Jan 22, 2025
4b48fa9
Add more information to WARNING action
rtaylorzfin Jan 22, 2025
2bb4869
ZFIN-9505 modify description of unreleased blast database (#1294)
cmpich Jan 22, 2025
9119c57
ZFIN-9491 remove SOAP webservice classes (#1293)
cmpich Jan 22, 2025
4a34ef0
Merge all tomcat10 branch changes into main branch (#1295)
rtaylorzfin Jan 22, 2025
e8d8eac
Merge branch 'zfin-9435' into newmain-9435
rtaylorzfin Jan 22, 2025
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Change default behavior for refseq mismatches due to replacements to …
…ignore those DELETEs
rtaylorzfin committed Jan 22, 2025
commit da64bc92f83cca421bf5937dd6bceab248f116bc
Original file line number Diff line number Diff line change
@@ -85,6 +85,16 @@ private void checkAndUpdateAction(UniProtLoadAction action, Map<String, RichSequ
String details = sb.toString();
action.addTag(UniProtLoadAction.CategoryTag.REPLACED_REFSEQ);
action.addDetails(details);

//default behavior is to not delete a uniprot/gene dblink if the refseq mismatch is due to the refseq getting a replacement
//we expect the difference to reconcile itself over time
if ("true".equals(System.getenv("UNIPROT_DELETE_REPLACED_REFSEQ_FLAG"))) {
log.info("Deleting UniProt accession despite replaced refseq: " + action.getGeneZdbID() + "/" + action.getAccession() + "/" + refseq);
} else {
log.info("Changing action type from DELETE to WARNING due to replaced refseq: " + action.getGeneZdbID() + "/" + action.getAccession());
action.setType(UniProtLoadAction.Type.WARNING);
}

log.debug(details);
}
if ("suppressed".equals(ncbiData.status())) {
@@ -96,15 +106,15 @@ private void checkAndUpdateAction(UniProtLoadAction action, Map<String, RichSequ

private void initializeNcbiRefseqData(Map<String, RichSequenceAdapter> uniProtRecords, List<UniProtLoadAction> deletes) {
//let's get the list of all lost uniprot accessions that exist in the dat file
List<String> losingAccessions = deletes.stream().map(d -> d.getAccession()).toList();
List<String> losingAccessions = deletes.stream().map(UniProtLoadAction::getAccession).toList();
Set<String> accessionsExistingInUniprotFile = uniProtRecords.keySet();
Collection<String> overlap = CollectionUtils.intersection(losingAccessions, accessionsExistingInUniprotFile);

Map<String, Set<String>> refseqsInUniprotByAccession = uniProtRecords
.entrySet()
.stream()
.filter(e -> overlap.contains(e.getKey()))
.collect(Collectors.toMap(e -> e.getKey(), e -> e.getValue().getRefSeqsWithoutVersion()));
.collect(Collectors.toMap(Map.Entry::getKey, e -> e.getValue().getRefSeqsWithoutVersion()));

List<String> refseqs = refseqsInUniprotByAccession.values().stream().flatMap(Collection::stream).toList();