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Merge branch 'release-3.2.x' into TASK-6255
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Resolve conflicts:
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@jtarraga
jtarraga committed Aug 13, 2024
2 parents d94e6c2 + bf2a0d8 commit f031313
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Showing 43 changed files with 1,274 additions and 1,191 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/pull-request-approved.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,5 +15,5 @@ jobs:
uses: ./.github/workflows/test-analysis.yml
needs: build
with:
test_profile: runShortTests,runMediumTests,runLongTests
test_profile: runShortTests,runMediumTests
secrets: inherit
2 changes: 1 addition & 1 deletion opencga-app/app/misc/clients/javascript_client_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ def get_method_definition(self, category, endpoint):
f'"{self.get_endpoint_subcategory()}"' if self.subcategory else "null",
self.get_endpoint_id2() if self.get_endpoint_id2() else "null",
f'"{self.get_endpoint_action()}"' if self.get_endpoint_action() else "null",
"data" if self.has_body() else False,
"data" if self.has_body() else ("null" if self.get_endpoint_method(endpoint).lower() == "post" else False),
query_string_params
] if s)
return (f' {self.get_method_doc(endpoint)}'
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44 changes: 22 additions & 22 deletions ...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,9 +130,9 @@ private RestResponse<ObjectMap> installCatalog() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), InstallationParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "secretKey",commandOptions.secretKey, true);
putNestedIfNotEmpty(beanParams, "password",commandOptions.password, true);
putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
putNestedIfNotEmpty(beanParams, "secretKey", commandOptions.secretKey, true);
putNestedIfNotEmpty(beanParams, "password", commandOptions.password, true);
putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);

installationParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -161,7 +161,7 @@ private RestResponse<ObjectMap> jwtCatalog() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), JWTParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "secretKey",commandOptions.secretKey, true);
putNestedIfNotEmpty(beanParams, "secretKey", commandOptions.secretKey, true);

jWTParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand All @@ -186,11 +186,11 @@ private RestResponse<User> createUsers() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), UserCreateParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
putNestedIfNotEmpty(beanParams, "password",commandOptions.password, true);
putNestedIfNotEmpty(beanParams, "organization",commandOptions.organization, true);
putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);
putNestedIfNotEmpty(beanParams, "password", commandOptions.password, true);
putNestedIfNotEmpty(beanParams, "organization", commandOptions.organization, true);

userCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -219,11 +219,11 @@ private RestResponse<User> importUsers() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), UserImportParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "authenticationOriginId",commandOptions.authenticationOriginId, true);
putNestedIfNotNull(beanParams, "id",commandOptions.id, true);
putNestedIfNotNull(beanParams, "resourceType",commandOptions.resourceType, true);
putNestedIfNotEmpty(beanParams, "study",commandOptions.study, true);
putNestedIfNotEmpty(beanParams, "studyGroup",commandOptions.studyGroup, true);
putNestedIfNotEmpty(beanParams, "authenticationOriginId", commandOptions.authenticationOriginId, true);
putNestedIfNotNull(beanParams, "id", commandOptions.id, true);
putNestedIfNotNull(beanParams, "resourceType", commandOptions.resourceType, true);
putNestedIfNotEmpty(beanParams, "study", commandOptions.study, true);
putNestedIfNotEmpty(beanParams, "studyGroup", commandOptions.studyGroup, true);

userImportParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -287,12 +287,12 @@ private RestResponse<Group> syncUsers() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), GroupSyncParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "authenticationOriginId",commandOptions.authenticationOriginId, true);
putNestedIfNotEmpty(beanParams, "from",commandOptions.from, true);
putNestedIfNotEmpty(beanParams, "to",commandOptions.to, true);
putNestedIfNotEmpty(beanParams, "study",commandOptions.study, true);
putNestedIfNotNull(beanParams, "syncAll",commandOptions.syncAll, true);
putNestedIfNotNull(beanParams, "force",commandOptions.force, true);
putNestedIfNotEmpty(beanParams, "authenticationOriginId", commandOptions.authenticationOriginId, true);
putNestedIfNotEmpty(beanParams, "from", commandOptions.from, true);
putNestedIfNotEmpty(beanParams, "to", commandOptions.to, true);
putNestedIfNotEmpty(beanParams, "study", commandOptions.study, true);
putNestedIfNotNull(beanParams, "syncAll", commandOptions.syncAll, true);
putNestedIfNotNull(beanParams, "force", commandOptions.force, true);

groupSyncParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -322,8 +322,8 @@ private RestResponse<Group> usersUpdateGroups() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), UserUpdateGroup.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotNull(beanParams, "studyIds",commandOptions.studyIds, true);
putNestedIfNotNull(beanParams, "groupIds",commandOptions.groupIds, true);
putNestedIfNotNull(beanParams, "studyIds", commandOptions.studyIds, true);
putNestedIfNotNull(beanParams, "groupIds", commandOptions.groupIds, true);

userUpdateGroup = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down
62 changes: 31 additions & 31 deletions ...main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -140,12 +140,12 @@ private RestResponse<Job> runBwa() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), BwaWrapperParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "fastaFile",commandOptions.fastaFile, true);
putNestedIfNotEmpty(beanParams, "fastq1File",commandOptions.fastq1File, true);
putNestedIfNotEmpty(beanParams, "fastq2File",commandOptions.fastq2File, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotNull(beanParams, "bwaParams",commandOptions.bwaParams, true);
putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "fastaFile", commandOptions.fastaFile, true);
putNestedIfNotEmpty(beanParams, "fastq1File", commandOptions.fastq1File, true);
putNestedIfNotEmpty(beanParams, "fastq2File", commandOptions.fastq2File, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
putNestedMapIfNotEmpty(beanParams, "bwaParams", commandOptions.bwaParams, true);

bwaWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -184,9 +184,9 @@ private RestResponse<Job> runCoverageIndex() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), CoverageIndexParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "bamFileId",commandOptions.bamFileId, true);
putNestedIfNotEmpty(beanParams, "baiFileId",commandOptions.baiFileId, true);
putNestedIfNotNull(beanParams, "windowSize",commandOptions.windowSize, true);
putNestedIfNotEmpty(beanParams, "bamFileId", commandOptions.bamFileId, true);
putNestedIfNotEmpty(beanParams, "baiFileId", commandOptions.baiFileId, true);
putNestedIfNotNull(beanParams, "windowSize", commandOptions.windowSize, true);

coverageIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -225,9 +225,9 @@ private RestResponse<Job> coverageQcGeneCoverageStatsRun() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), AlignmentGeneCoverageStatsParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "bamFile",commandOptions.bamFile, true);
putNestedIfNotNull(beanParams, "genes",commandOptions.genes, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotEmpty(beanParams, "bamFile", commandOptions.bamFile, true);
putNestedIfNotNull(beanParams, "genes", commandOptions.genes, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);

alignmentGeneCoverageStatsParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -323,9 +323,9 @@ private RestResponse<Job> runDeeptools() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), DeeptoolsWrapperParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotNull(beanParams, "deeptoolsParams",commandOptions.deeptoolsParams, true);
putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
putNestedMapIfNotEmpty(beanParams, "deeptoolsParams", commandOptions.deeptoolsParams, true);

deeptoolsWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -364,9 +364,9 @@ private RestResponse<Job> runFastqc() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), FastqcWrapperParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "inputFile",commandOptions.inputFile, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotNull(beanParams, "fastqcParams",commandOptions.fastqcParams, true);
putNestedIfNotEmpty(beanParams, "inputFile", commandOptions.inputFile, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
putNestedMapIfNotEmpty(beanParams, "fastqcParams", commandOptions.fastqcParams, true);

fastqcWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -405,8 +405,8 @@ private RestResponse<Job> runIndex() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), AlignmentIndexParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "fileId",commandOptions.fileId, true);
putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
putNestedIfNotEmpty(beanParams, "fileId", commandOptions.fileId, true);
putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);

alignmentIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -445,9 +445,9 @@ private RestResponse<Job> runPicard() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), PicardWrapperParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotNull(beanParams, "picardParams",commandOptions.picardParams, true);
putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
putNestedMapIfNotEmpty(beanParams, "picardParams", commandOptions.picardParams, true);

picardWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -486,10 +486,10 @@ private RestResponse<Job> runQc() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), AlignmentQcParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "bamFile",commandOptions.bamFile, true);
putNestedIfNotEmpty(beanParams, "skip",commandOptions.skip, true);
putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotEmpty(beanParams, "bamFile", commandOptions.bamFile, true);
putNestedIfNotEmpty(beanParams, "skip", commandOptions.skip, true);
putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);

alignmentQcParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -560,10 +560,10 @@ private RestResponse<Job> runSamtools() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), SamtoolsWrapperParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "inputFile",commandOptions.inputFile, true);
putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
putNestedIfNotNull(beanParams, "samtoolsParams",commandOptions.samtoolsParams, true);
putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
putNestedIfNotEmpty(beanParams, "inputFile", commandOptions.inputFile, true);
putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
putNestedMapIfNotEmpty(beanParams, "samtoolsParams", commandOptions.samtoolsParams, true);

samtoolsWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down
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