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Fix import #120

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Fix import #120

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494f77f
fix importing metadata from BrAPI to manage the case of having severa…
aliceboizet Apr 29, 2024
4ddbf84
Merge branch 'master' of github.com:SouthGreenPlatform/Gigwa2 into fi…
aliceboizet Apr 29, 2024
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26 changes: 16 additions & 10 deletions src/main/java/fr/cirad/web/controller/gigwa/GigwaRestController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -260,11 +260,11 @@ public class GigwaRestController extends ControllerInterface {
static public final String VARIANTS_BY_IDS = "/variants/byIds";
static public final String VARIANTS_LOOKUP = "/variants/lookup";
static public final String GENES_LOOKUP = "/genes/lookup";
static public final String GALAXY_HISTORY_PUSH = "/pushToGalaxyHistory";
static public final String GALAXY_HISTORY_PUSH = "/pushToGalaxyHistory";
static public final String DISTINCT_INDIVIDUAL_METADATA = "/distinctIndividualMetadata";
static public final String FILTER_INDIVIDUAL_METADATA = "/filterIndividualsFromMetadata";
static public final String INSTANCE_CONTENT_SUMMARY = "/instanceContentSummary";
static final public String snpclustEditionURL = "/snpclustEditionURL";
static final public String snpclustEditionURL = "/snpclustEditionURL";

/**
* get a unique processID
Expand Down Expand Up @@ -1630,7 +1630,7 @@ public void run() {

if (brapiUrlList.size() > 0) { // we've got BrAPI endpoints to pull metadata from
storeSessionAttributes(session); // in case external source info was just added
HashMap<String /*BrAPI url*/, HashMap<String /*remote germplasmDbId*/, String /*individual*/>> brapiUrlToIndividualsMap = new HashMap<>();
HashMap<String /*BrAPI url*/, HashMap<String /*remote germplasmDbId*/, Set<String> /*individual*/>> brapiUrlToIndividualsMap = new HashMap<>();
if (metadataType.equals("individual")) {
Collection<Individual> individuals = MgdbDao.getInstance().loadIndividualsWithAllMetadata(sModule, sFinalUsername, null, null, null).values();
for (Individual individual : individuals)
Expand All @@ -1648,13 +1648,16 @@ public void run() {
if (brapiUrlToIndividualsMap.get(endPointUrl) == null)
brapiUrlToIndividualsMap.put(endPointUrl, new HashMap<>());

HashMap<String, String> individualsCurrentEndpointHasDataFor = brapiUrlToIndividualsMap.get(endPointUrl);
HashMap<String, Set<String>> individualsCurrentEndpointHasDataFor = brapiUrlToIndividualsMap.get(endPointUrl);
if (individualsCurrentEndpointHasDataFor == null) {
individualsCurrentEndpointHasDataFor = new HashMap<>();
brapiUrlToIndividualsMap.put(endPointUrl, individualsCurrentEndpointHasDataFor);
}

individualsCurrentEndpointHasDataFor.put(extRefIdValue, individual.getId());
if (individualsCurrentEndpointHasDataFor.get(extRefIdValue) == null) {
individualsCurrentEndpointHasDataFor.put(extRefIdValue, new HashSet<>());
}
individualsCurrentEndpointHasDataFor.get(extRefIdValue).add(individual.getId());
}
}
else {
Expand All @@ -1674,13 +1677,16 @@ public void run() {
if (brapiUrlToIndividualsMap.get(endPointUrl) == null)
brapiUrlToIndividualsMap.put(endPointUrl, new HashMap<>());

HashMap<String, String> individualsCurrentEndpointHasDataFor = brapiUrlToIndividualsMap.get(endPointUrl);
HashMap<String, Set<String>> individualsCurrentEndpointHasDataFor = brapiUrlToIndividualsMap.get(endPointUrl);
if (individualsCurrentEndpointHasDataFor == null) {
individualsCurrentEndpointHasDataFor = new HashMap<>();
brapiUrlToIndividualsMap.put(endPointUrl, individualsCurrentEndpointHasDataFor);
}

individualsCurrentEndpointHasDataFor.put(extRefIdValue, sample.getSampleName());
if (individualsCurrentEndpointHasDataFor.get(extRefIdValue) == null) {
individualsCurrentEndpointHasDataFor.put(extRefIdValue, new HashSet<>());
}
individualsCurrentEndpointHasDataFor.get(extRefIdValue).add(sample.getSampleName());
}
}

Expand Down Expand Up @@ -2568,7 +2574,7 @@ public List<Comparable> searchableVariantsLookup(

return null;
}

@ApiIgnore
@RequestMapping(value = BASE_URL + DISTINCT_INDIVIDUAL_METADATA + "/{module}", method = RequestMethod.POST, produces = "application/json")
public LinkedHashMap<String, Set<String>> distinctIndividualMetadata(HttpServletRequest request, HttpServletResponse response, @PathVariable String module, @RequestParam(required = false) final Integer projID, @RequestBody HashMap<String, Object> reqBody) throws IOException {
Expand All @@ -2584,7 +2590,7 @@ public Collection<Individual> filterIndividualMetadata(HttpServletRequest reques
String sUserName = auth != null && auth.getAuthorities().contains(new SimpleGrantedAuthority(IRoleDefinition.ROLE_ADMIN)) ? null : AbstractTokenManager.getUserNameFromAuthentication(auth);
return MgdbDao.getInstance().loadIndividualsWithAllMetadata(module, sUserName, Arrays.asList(projID), null, filters).values();
}

@ApiOperation(authorizations = { @Authorization(value = "AuthorizationToken") }, value = GENES_LOOKUP , notes = "Get genes names ")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success", response = List.class),
@ApiResponse(code = 400, message = "wrong parameters"),
Expand Down Expand Up @@ -2652,6 +2658,6 @@ public List<String> searchableGenesLookup(

i++;
}
return resultObjects;
return resultObjects;
}
}