diff --git a/docs/Updating-your-cBioPortal-installation.md b/docs/Updating-your-cBioPortal-installation.md index 6f4d4abc515..2d99e9f0c96 100644 --- a/docs/Updating-your-cBioPortal-installation.md +++ b/docs/Updating-your-cBioPortal-installation.md @@ -4,33 +4,37 @@ As of release **1.1.0** cBioPortal has a Database schema update mechanism which ## First time -The first time you update from release **1.0.4** (or lower) to release **1.1.0** (or higher), you should get a an error banner page after restarting your webserver. The error should state something like: +The first time you update from release **1.0.4** (or lower) to release **1.1.0** (or higher), you should get a an error banner page after restarting your webserver. The error should state something like: ``` -Current DB schema version: xxx +Current DB schema version: xxx DB schema version expected by Portal: yyy ``` -where `xxx` and `yyy` will be different version numbers. -If you get `DB version expected by Portal: 0` (i.e. you are building the new release from source), you need to add a new property to your `application.properties` file which is needed for this check. +where `xxx` and `yyy` will be different version numbers. + +If you get `DB version expected by Portal: 0` (i.e. you are building the new release from source), you need to add a new property to your `application.properties` file which is needed for this check. #### Step1 In your `application.properties` file (e.g. `/src/main/resources/application.properties`) add the following property: + ``` # this is the *expected* DB version (expected by the code). Don't set it manually, it is filled by maven: db.version=${db.version} +genetable.version=${genetable.version} ``` #### Step2 -Compile your code again. After restarting the webserver the page should now state something like: `DB version expected by Portal: 1.1.0` (or higher), while the DB version remains as `Current DB version: -1`. +Compile your code again. After restarting the webserver the page should now state something like: `DB version expected by Portal: 1.1.0` (or higher), while the DB version remains as `Current DB version: -1`. ## Running the migration script First, make sure you have the DB connection properties correctly set in your application.properties file (see [DB connection settings here](/deployment/customization/application.properties-Reference.md#database-settings)). **Dependencies:** the migration script is a Python script that depends on the `mysqlclient` library. If necessary, you can install it with the following commands (example for Ubuntu): + ```console sudo apt-get install python3-dev default-libmysqlclient-dev sudo python3 -m pip install mysqlclient @@ -42,16 +46,20 @@ For macOS, try the following: brew install mysql-connector-c sudo python3 -m pip install mysqlclient ``` + and see if problems occur during installation. To run the migration script first go to the scripts folder -`/core/src/main/scripts` +`/core/src/main/scripts` and then run the following command: + ```console $ python migrate_db.py ``` + This should result in the following output: + ```console WARNING: This script will alter your database! Be sure to back up your data before running. Continue running DB migration? (y/n) y diff --git a/pom.xml b/pom.xml index 00f9153130e..ce883c74d52 100644 --- a/pom.xml +++ b/pom.xml @@ -31,7 +31,7 @@ 2.13.1 - + hgnc_v2023.10.1 1.1.6.RELEASE diff --git a/src/main/java/org/cbioportal/model/Info.java b/src/main/java/org/cbioportal/model/Info.java index beee09b26d7..8c38fef3182 100644 --- a/src/main/java/org/cbioportal/model/Info.java +++ b/src/main/java/org/cbioportal/model/Info.java @@ -10,6 +10,8 @@ public class Info implements Serializable { @NotNull private String dbVersion; @NotNull + private String genetableVersion; + @NotNull private String gitBranch; @NotNull private String gitCommitId; @@ -42,6 +44,14 @@ public String getGitCommitId() { return this.gitCommitId; } + public String getGenetableVersion(){ + return this.genetableVersion; + } + + public void setGenetableVersion(String genetableVersion){ + this.genetableVersion = genetableVersion; + } + public void setGitCommitId(String gitCommitId) { this.gitCommitId = gitCommitId; } diff --git a/src/main/java/org/cbioportal/web/InfoController.java b/src/main/java/org/cbioportal/web/InfoController.java index 59e9352ca5b..6fca1cb9b93 100644 --- a/src/main/java/org/cbioportal/web/InfoController.java +++ b/src/main/java/org/cbioportal/web/InfoController.java @@ -28,6 +28,9 @@ public class InfoController { @Value("${db.version}") private String dbVersion; + + @Value("${genetable.version}") + private String genetableVersion; @Value("${git.branch:not set}") private String gitBranch; @@ -59,15 +62,18 @@ public class InfoController { @Value("${git.dirty:not set}") private String gitDirty; + + @RequestMapping(value = "/api/info", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE) @Operation(description = "Get information about the running instance") @ApiResponse(responseCode = "200", description = "OK", content = @Content(schema = @Schema(implementation = Info.class))) public ResponseEntity getInfo() { - + Info info = new Info(); info.setPortalVersion(portalVersion); info.setDbVersion(dbVersion); + info.setGenetableVersion(genetableVersion); info.setGitBranch(gitBranch); info.setGitCommitId(gitCommitId); info.setGitCommitIdDescribe(gitCommitIdDescribe); @@ -77,6 +83,7 @@ public ResponseEntity getInfo() { info.setGitCommitMessageUserEmail(gitCommitMessageUserEmail); info.setGitCommitMessageUserName(gitCommitMessageUserName); info.isGitDirty(Boolean.valueOf(gitDirty)); + return new ResponseEntity<>(info, HttpStatus.OK); } } diff --git a/src/main/resources/db-scripts/cgds.sql b/src/main/resources/db-scripts/cgds.sql index 2971b3d1be6..001803c2f4b 100644 --- a/src/main/resources/db-scripts/cgds.sql +++ b/src/main/resources/db-scripts/cgds.sql @@ -711,7 +711,8 @@ CREATE TABLE `allele_specific_copy_number` ( -- -------------------------------------------------------- CREATE TABLE `info` ( `DB_SCHEMA_VERSION` varchar(24), - `GENESET_VERSION` varchar(24) + `GENESET_VERSION` varchar(24), + `GENE_TABLE_VERSION` varchar(24) ); -- -------------------------------------------------------- @@ -755,5 +756,5 @@ CREATE TABLE `resource_study` ( ); -- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml -INSERT INTO info VALUES ('2.13.1', NULL); +INSERT INTO info VALUES ('2.13.1','hgnc_v2023.10.1', NULL ); diff --git a/src/main/resources/db-scripts/migration.sql b/src/main/resources/db-scripts/migration.sql index 78c0d25ea14..0f2783c3426 100644 --- a/src/main/resources/db-scripts/migration.sql +++ b/src/main/resources/db-scripts/migration.sql @@ -1027,4 +1027,6 @@ ALTER TABLE `clinical_event_data` MODIFY COLUMN `VALUE` varchar(3000) NOT NULL; CREATE INDEX idx_clinical_event_key ON clinical_event_data (`KEY`); CREATE INDEX idx_clinical_event_value ON clinical_event_data (`VALUE`); CREATE INDEX idx_sample_stable_id ON sample (`STABLE_ID`); +ALTER TABLE `info` ADD COLUMN `GENE_TABLE_VERSION` varchar(24); +UPDATE `info` SET `GENE_TABLE_VERSION`="hgnc_v2023.10.1"; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.1"; \ No newline at end of file diff --git a/src/main/resources/legacy-api.json b/src/main/resources/legacy-api.json index 2239a91b458..d866eddb6ec 100644 --- a/src/main/resources/legacy-api.json +++ b/src/main/resources/legacy-api.json @@ -1 +1,4551 @@ -{"swagger":"2.0","info":{"description":"A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.","version":"1.0 (beta). Backwards compatibility will be maintained (after 1.0 release)","title":"cBioPortal web Public API [Beta]","contact":{"name":"cBioPortal","url":"https://www.cbioportal.org","email":"cbioportal@googlegroups.com"},"license":{"name":"License","url":"https://github.com/cBioPortal/cbioportal/blob/master/LICENSE"}},"host":"www.cbioportal.org","basePath":"/api","tags":[{"name":"Cancer Types"},{"name":"Studies"},{"name":"Patients"},{"name":"Samples"},{"name":"Sample Lists"},{"name":"Clinical Attributes"},{"name":"Clinical Data"},{"name":"Molecular Data"},{"name":"Molecular Profiles"},{"name":"Mutations"},{"name":"Discrete Copy Number Alterations"},{"name":"Copy Number Segments"},{"name":"Genes"},{"name":"Gene Panels"},{"name":"Generic Assays"},{"name":"Generic Assay Data"},{"name":"Info"},{"name":"Gene Panel Data","description":" "},{"name":"Server running status","description":"This end point does not require authentication"},{"name":"Treatments","description":" 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["application/json"], + "parameters": [ + { + "in": "body", + "name": "genePanelIds", + "description": "List of Gene Panel IDs", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/GenePanel" } + } + } + } + } + }, + "/gene-panels/{genePanelId}": { + "get": { + "tags": ["Gene Panels"], + "summary": "Get gene panel", + "operationId": "getGenePanelUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "genePanelId", + "in": "path", + "description": "Gene Panel ID e.g. NSCLC_UNITO_2016_PANEL", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/GenePanel" } + } + } + } + }, + "/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}": { + "get": { + "tags": ["Generic Assay Data"], + "summary": "Get generic_assay_data in a molecular profile", + "operationId": "getGenericAssayDataInMolecularProfileUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "genericAssayStableId", + "in": "path", + "description": "Generic Assay stable ID", + "required": true, + "type": "string" + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayData" + } + } + } + } + } + }, + "/generic-assay-meta/generic-assay/{genericAssayStableId}": { + "get": { + "tags": ["Generic Assays"], + "summary": "Fetch meta data for generic-assay by ID", + "operationId": "getGenericAssayMeta_gaUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "genericAssayStableId", + "in": "path", + "description": "Generic Assay stable ID", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayMeta" + } + } + } + } + } + }, + "/generic-assay-meta/{molecularProfileId}": { + "get": { + "tags": ["Generic Assays"], + "summary": "Fetch meta data for generic-assay by ID", + "operationId": "getGenericAssayMetaUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayMeta" + } + } + } + } + } + }, + "/generic_assay_data/fetch": { + "post": { + "tags": ["Generic Assay Data"], + "summary": "Fetch generic_assay_data", + "operationId": "fetchGenericAssayDataInMultipleMolecularProfilesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "genericAssayDataMultipleStudyFilter", + "description": "List of Molecular Profile ID and Sample ID pairs or List of MolecularProfile IDs and Generic Assay IDs", + "required": true, + "schema": { + "$ref": "#/definitions/GenericAssayDataMultipleStudyFilter" + } + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayData" + } + } + } + } + } + }, + "/generic_assay_data/{molecularProfileId}/fetch": { + "post": { + "tags": ["Generic Assay Data"], + "summary": "fetch generic_assay_data in a molecular profile", + "operationId": "fetchGenericAssayDataInMolecularProfileUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "genericAssayDataFilter", + "description": "List of Sample IDs/Sample List ID and Generic Assay IDs", + "required": true, + "schema": { "$ref": "#/definitions/GenericAssayFilter" } + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayData" + } + } + } + } + } + }, + "/generic_assay_meta/fetch": { + "post": { + "tags": ["Generic Assays"], + "summary": "Fetch meta data for generic-assay by ID", + "operationId": "fetchGenericAssayMetaUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "genericAssayMetaFilter", + "description": "List of Molecular Profile ID or List of Stable ID", + "required": true, + "schema": { + "$ref": "#/definitions/GenericAssayMetaFilter" + } + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayMeta" + } + } + } + } + } + }, + "/genes": { + "get": { + "tags": ["Genes"], + "summary": "Get all genes", + "operationId": "getAllGenesUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "alias", + "in": "query", + "description": "Alias of the gene", + "required": false, + "type": "string" + }, + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "keyword", + "in": "query", + "description": "Search keyword that applies to hugo gene symbol of the genes", + "required": false, + "type": "string" + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "cytoband", + "entrezGeneId", + "hugoGeneSymbol", + "length", + "type" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Gene" } + } + } + } + } + }, + "/genes/fetch": { + "post": { + "tags": ["Genes"], + "summary": "Fetch genes by ID", + "operationId": "fetchGenesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "geneIds", + "description": "List of Entrez Gene IDs or Hugo Gene Symbols", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + }, + { + "name": "geneIdType", + "in": "query", + "description": "Type of gene ID", + "required": false, + "type": "string", + "default": "ENTREZ_GENE_ID", + "enum": ["ENTREZ_GENE_ID", "HUGO_GENE_SYMBOL"] + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Gene" } + } + } + } + } + }, + "/genes/{geneId}": { + "get": { + "tags": ["Genes"], + "summary": "Get a gene", + "operationId": "getGeneUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "geneId", + "in": "path", + "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/Gene" } + } + } + } + }, + "/genes/{geneId}/aliases": { + "get": { + "tags": ["Genes"], + "summary": "Get aliases of a gene", + "operationId": "getAliasesOfGeneUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "geneId", + "in": "path", + "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "type": "string" } + } + } + } + } + }, + "/health": { + "get": { + "tags": ["Server running status"], + "summary": "Get the running status of the server", + "operationId": "getServerStatusUsingGET", + "produces": ["application/json"], + "responses": { + "200": { + "description": "OK", + "schema": { + "$ref": "#/definitions/ServerStatusMessage" + } + } + } + } + }, + "/info": { + "get": { + "tags": ["Info"], + "summary": "Get information about the running instance", + "operationId": "getInfoUsingGET", + "produces": ["application/json"], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/Info" } + } + } + } + }, + "/molecular-data/fetch": { + "post": { + "tags": ["Molecular Data"], + "summary": "Fetch molecular data", + "operationId": "fetchMolecularDataInMultipleMolecularProfilesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "molecularDataMultipleStudyFilter", + "description": "List of Molecular Profile ID and Sample ID pairs or List of MolecularProfile IDs and Entrez Gene IDs", + "required": true, + "schema": { + "$ref": "#/definitions/MolecularDataMultipleStudyFilter" + } + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/NumericGeneMolecularData" + } + } + } + } + } + }, + "/molecular-profiles": { + "get": { + "tags": ["Molecular Profiles"], + "summary": "Get all molecular profiles", + "operationId": "getAllMolecularProfilesUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "datatype", + "description", + "molecularAlterationType", + "molecularProfileId", + "name", + "showProfileInAnalysisTab" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/MolecularProfile" + } + } + } + } + } + }, + "/molecular-profiles/fetch": { + "post": { + "tags": ["Molecular Profiles"], + "summary": "Fetch molecular profiles", + "operationId": "fetchMolecularProfilesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "molecularProfileFilter", + "description": "List of Molecular Profile IDs or List of Study IDs", + "required": true, + "schema": { + "$ref": "#/definitions/MolecularProfileFilter" + } + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/MolecularProfile" + } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}": { + "get": { + "tags": ["Molecular Profiles"], + "summary": "Get molecular profile", + "operationId": "getMolecularProfileUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_mutations", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/MolecularProfile" } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/discrete-copy-number": { + "get": { + "tags": ["Discrete Copy Number Alterations"], + "summary": "Get discrete copy number alterations in a molecular profile", + "operationId": "getDiscreteCopyNumbersInMolecularProfileUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "discreteCopyNumberEventType", + "in": "query", + "description": "Type of the copy number event", + "required": false, + "type": "string", + "default": "HOMDEL_AND_AMP", + "enum": [ + "ALL", + "AMP", + "DIPLOID", + "GAIN", + "HETLOSS", + "HOMDEL", + "HOMDEL_AND_AMP" + ] + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_gistic", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sampleListId", + "in": "query", + "description": "Sample List ID e.g. acc_tcga_all", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/DiscreteCopyNumberData" + } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/discrete-copy-number/fetch": { + "post": { + "tags": ["Discrete Copy Number Alterations"], + "summary": "Fetch discrete copy number alterations in a molecular profile by sample ID", + "operationId": "fetchDiscreteCopyNumbersInMolecularProfileUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "name": "discreteCopyNumberEventType", + "in": "query", + "description": "Type of the copy number event", + "required": false, + "type": "string", + "default": "HOMDEL_AND_AMP", + "enum": [ + "ALL", + "AMP", + "DIPLOID", + "GAIN", + "HETLOSS", + "HOMDEL", + "HOMDEL_AND_AMP" + ] + }, + { + "in": "body", + "name": "discreteCopyNumberFilter", + "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", + "required": true, + "schema": { + "$ref": "#/definitions/DiscreteCopyNumberFilter" + } + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_gistic", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/DiscreteCopyNumberData" + } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch": { + "post": { + "tags": ["Gene Panel Data"], + "summary": "Get gene panel data", + "operationId": "getGenePanelDataUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "genePanelDataFilter", + "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", + "required": true, + "schema": { + "$ref": "#/definitions/GenePanelDataFilter" + } + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. nsclc_unito_2016_mutations", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/GenePanelData" } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/molecular-data": { + "get": { + "tags": ["Molecular Data"], + "summary": "Get all molecular data in a molecular profile", + "operationId": "getAllMolecularDataInMolecularProfileUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "entrezGeneId", + "in": "query", + "description": "Entrez Gene ID e.g. 1", + "required": true, + "type": "integer", + "format": "int32" + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sampleListId", + "in": "query", + "description": "Sample List ID e.g. acc_tcga_all", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/NumericGeneMolecularData" + } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/molecular-data/fetch": { + "post": { + "tags": ["Molecular Data"], + "summary": "Fetch molecular data in a molecular profile", + "operationId": "fetchAllMolecularDataInMolecularProfileUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "molecularDataFilter", + "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", + "required": true, + "schema": { + "$ref": "#/definitions/MolecularDataFilter" + } + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/NumericGeneMolecularData" + } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/mutations": { + "get": { + "tags": ["Mutations"], + "summary": "Get mutations in a molecular profile by Sample List ID", + "operationId": "getMutationsInMolecularProfileBySampleListIdUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "entrezGeneId", + "in": "query", + "description": "Entrez Gene ID", + "required": false, + "type": "integer", + "format": "int32" + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_mutations", + "required": true, + "type": "string" + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sampleListId", + "in": "query", + "description": "Sample List ID e.g. acc_tcga_all", + "required": true, + "type": "string" + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "aminoAcidChange", + "center", + "endPosition", + "entrezGeneId", + "keyword", + "mutationStatus", + "mutationType", + "ncbiBuild", + "normalAltCount", + "normalRefCount", + "proteinChange", + "proteinPosEnd", + "proteinPosStart", + "referenceAllele", + "refseqMrnaId", + "startPosition", + "tumorAltCount", + "tumorRefCount", + "validationStatus", + "variantAllele", + "variantType" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Mutation" } + } + } + } + } + }, + "/molecular-profiles/{molecularProfileId}/mutations/fetch": { + "post": { + "tags": ["Mutations"], + "summary": "Fetch mutations in a molecular profile", + "operationId": "fetchMutationsInMolecularProfileUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID e.g. acc_tcga_mutations", + "required": true, + "type": "string" + }, + { + "in": "body", + "name": "mutationFilter", + "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", + "required": true, + "schema": { "$ref": "#/definitions/MutationFilter" } + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "aminoAcidChange", + "center", + "endPosition", + "entrezGeneId", + "keyword", + "mutationStatus", + "mutationType", + "ncbiBuild", + "normalAltCount", + "normalRefCount", + "proteinChange", + "proteinPosEnd", + "proteinPosStart", + "referenceAllele", + "refseqMrnaId", + "startPosition", + "tumorAltCount", + "tumorRefCount", + "validationStatus", + "variantAllele", + "variantType" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Mutation" } + } + } + } + } + }, + "/mutations/fetch": { + "post": { + "tags": ["Mutations"], + "summary": "Fetch mutations in multiple molecular profiles by sample IDs", + "operationId": "fetchMutationsInMultipleMolecularProfilesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "in": "body", + "name": "mutationMultipleStudyFilter", + "description": "List of Molecular Profile IDs or List of Molecular Profile ID / Sample ID pairs, and List of Entrez Gene IDs", + "required": true, + "schema": { + "$ref": "#/definitions/MutationMultipleStudyFilter" + } + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "aminoAcidChange", + "center", + "endPosition", + "entrezGeneId", + "keyword", + "mutationStatus", + "mutationType", + "ncbiBuild", + "normalAltCount", + "normalRefCount", + "proteinChange", + "proteinPosEnd", + "proteinPosStart", + "referenceAllele", + "refseqMrnaId", + "startPosition", + "tumorAltCount", + "tumorRefCount", + "validationStatus", + "variantAllele", + "variantType" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Mutation" } + } + } + } + } + }, + "/patients": { + "get": { + "tags": ["Patients"], + "summary": "Get all patients", + "operationId": "getAllPatientsUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "keyword", + "in": "query", + "description": "Search keyword that applies to ID of the patients", + "required": false, + "type": "string" + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["patientId"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Patient" } + } + } + } + } + }, + "/patients/fetch": { + "post": { + "tags": ["Patients"], + "summary": "fetchPatients", + "operationId": "fetchPatientsUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "patientFilter", + "description": "List of patient identifiers", + "required": true, + "schema": { "$ref": "#/definitions/PatientFilter" } + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Patient" } + } + } + } + } + }, + "/sample-lists": { + "get": { + "tags": ["Sample Lists"], + "summary": "Get all sample lists", + "operationId": "getAllSampleListsUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "category", + "description", + "name", + "sampleListId", + "studyId" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/SampleList" } + } + } + } + } + }, + "/sample-lists/fetch": { + "post": { + "tags": ["Sample Lists"], + "summary": "Fetch sample lists by ID", + "operationId": "fetchSampleListsUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "in": "body", + "name": "sampleListIds", + "description": "List of sample list IDs", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/SampleList" } + } + } + } + } + }, + "/sample-lists/{sampleListId}": { + "get": { + "tags": ["Sample Lists"], + "summary": "Get sample list", + "operationId": "getSampleListUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "sampleListId", + "in": "path", + "description": "Sample List ID e.g. acc_tcga_all", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/SampleList" } + } + } + } + }, + "/sample-lists/{sampleListId}/sample-ids": { + "get": { + "tags": ["Sample Lists"], + "summary": "Get all sample IDs in a sample list", + "operationId": "getAllSampleIdsInSampleListUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "sampleListId", + "in": "path", + "description": "Sample List ID e.g. acc_tcga_all", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "type": "string" } + } + } + } + } + }, + "/samples": { + "get": { + "tags": ["Samples"], + "summary": "Get all samples matching keyword", + "operationId": "getSamplesByKeywordUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "keyword", + "in": "query", + "description": "Search keyword that applies to the study ID", + "required": false, + "type": "string" + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["sampleId", "sampleType"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Sample" } + } + } + } + } + }, + "/samples/fetch": { + "post": { + "tags": ["Samples"], + "summary": "Fetch samples by ID", + "operationId": "fetchSamplesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "in": "body", + "name": "sampleFilter", + "description": "List of sample identifiers", + "required": true, + "schema": { "$ref": "#/definitions/SampleFilter" } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Sample" } + } + } + } + } + }, + "/studies": { + "get": { + "tags": ["Studies"], + "summary": "Get all studies", + "operationId": "getAllStudiesUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "keyword", + "in": "query", + "description": "Search keyword that applies to name and cancer type of the studies", + "required": false, + "type": "string" + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "cancerTypeId", + "citation", + "description", + "groups", + "importDate", + "name", + "pmid", + "publicStudy", + "status", + "studyId" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/CancerStudy" } + } + } + } + } + }, + "/studies/fetch": { + "post": { + "tags": ["Studies"], + "summary": "Fetch studies by IDs", + "operationId": "fetchStudiesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "in": "body", + "name": "studyIds", + "description": "List of Study IDs", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/CancerStudy" } + } + } + } + } + }, + "/studies/tags/fetch": { + "post": { + "tags": ["Studies"], + "summary": "Get the study tags by IDs", + "operationId": "getTagsForMultipleStudiesUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "studyIds", + "description": "List of Study IDs", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/CancerStudyTags" } + } + } + } + } + }, + "/studies/{studyId}": { + "get": { + "tags": ["Studies"], + "summary": "Get a study", + "operationId": "getStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/CancerStudy" } + } + } + } + }, + "/studies/{studyId}/clinical-attributes": { + "get": { + "tags": ["Clinical Attributes"], + "summary": "Get all clinical attributes in the specified study", + "operationId": "getAllClinicalAttributesInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "clinicalAttributeId", + "datatype", + "description", + "displayName", + "patientAttribute", + "priority", + "studyId" + ] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/ClinicalAttribute" + } + } + } + } + } + }, + "/studies/{studyId}/clinical-attributes/{clinicalAttributeId}": { + "get": { + "tags": ["Clinical Attributes"], + "summary": "Get specified clinical attribute", + "operationId": "getClinicalAttributeInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "clinicalAttributeId", + "in": "path", + "description": "Clinical Attribute ID e.g. CANCER_TYPE", + "required": true, + "type": "string" + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/ClinicalAttribute" } + } + } + } + }, + "/studies/{studyId}/clinical-data": { + "get": { + "tags": ["Clinical Data"], + "summary": "Get all clinical data in a study", + "operationId": "getAllClinicalDataInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "attributeId", + "in": "query", + "description": "Attribute ID e.g. CANCER_TYPE", + "required": false, + "type": "string" + }, + { + "name": "clinicalDataType", + "in": "query", + "description": "Type of the clinical data", + "required": false, + "type": "string", + "default": "SAMPLE", + "enum": ["PATIENT", "SAMPLE"] + }, + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["clinicalAttributeId", "value"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalData" } + } + } + } + } + }, + "/studies/{studyId}/clinical-data/fetch": { + "post": { + "tags": ["Clinical Data"], + "summary": "Fetch clinical data by patient IDs or sample IDs (specific study)", + "operationId": "fetchAllClinicalDataInStudyUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "clinicalDataSingleStudyFilter", + "description": "List of patient or sample IDs and attribute IDs", + "required": true, + "schema": { + "$ref": "#/definitions/ClinicalDataSingleStudyFilter" + } + }, + { + "name": "clinicalDataType", + "in": "query", + "description": "Type of the clinical data", + "required": false, + "type": "string", + "default": "SAMPLE", + "enum": ["PATIENT", "SAMPLE"] + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalData" } + } + } + } + } + }, + "/studies/{studyId}/molecular-profiles": { + "get": { + "tags": ["Molecular Profiles"], + "summary": "Get all molecular profiles in a study", + "operationId": "getAllMolecularProfilesInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "datatype", + "description", + "molecularAlterationType", + "molecularProfileId", + "name", + "showProfileInAnalysisTab" + ] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/MolecularProfile" + } + } + } + } + } + }, + "/studies/{studyId}/patients": { + "get": { + "tags": ["Patients"], + "summary": "Get all patients in a study", + "operationId": "getAllPatientsInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["patientId"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Patient" } + } + } + } + } + }, + "/studies/{studyId}/patients/{patientId}": { + "get": { + "tags": ["Patients"], + "summary": "Get a patient in a study", + "operationId": "getPatientInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "patientId", + "in": "path", + "description": "Patient ID e.g. TCGA-OR-A5J2", + "required": true, + "type": "string" + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/Patient" } + } + } + } + }, + "/studies/{studyId}/patients/{patientId}/clinical-data": { + "get": { + "tags": ["Clinical Data"], + "summary": "Get all clinical data of a patient in a study", + "operationId": "getAllClinicalDataOfPatientInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "attributeId", + "in": "query", + "description": "Attribute ID e.g. AGE", + "required": false, + "type": "string" + }, + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "patientId", + "in": "path", + "description": "Patient ID e.g. TCGA-OR-A5J2", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["clinicalAttributeId", "value"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalData" } + } + } + } + } + }, + "/studies/{studyId}/patients/{patientId}/samples": { + "get": { + "tags": ["Samples"], + "summary": "Get all samples of a patient in a study", + "operationId": "getAllSamplesOfPatientInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "patientId", + "in": "path", + "description": "Patient ID e.g. TCGA-OR-A5J2", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["sampleId", "sampleType"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Sample" } + } + } + } + } + }, + "/studies/{studyId}/sample-lists": { + "get": { + "tags": ["Sample Lists"], + "summary": "Get all sample lists in a study", + "operationId": "getAllSampleListsInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "category", + "description", + "name", + "sampleListId", + "studyId" + ] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/SampleList" } + } + } + } + } + }, + "/studies/{studyId}/samples": { + "get": { + "tags": ["Samples"], + "summary": "Get all samples in a study", + "operationId": "getAllSamplesInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["sampleId", "sampleType"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/Sample" } + } + } + } + } + }, + "/studies/{studyId}/samples/{sampleId}": { + "get": { + "tags": ["Samples"], + "summary": "Get a sample in a study", + "operationId": "getSampleInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "sampleId", + "in": "path", + "description": "Sample ID e.g. TCGA-OR-A5J2-01", + "required": true, + "type": "string" + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "$ref": "#/definitions/Sample" } + } + } + } + }, + "/studies/{studyId}/samples/{sampleId}/clinical-data": { + "get": { + "tags": ["Clinical Data"], + "summary": "Get all clinical data of a sample in a study", + "operationId": "getAllClinicalDataOfSampleInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "attributeId", + "in": "query", + "description": "Attribute ID e.g. CANCER_TYPE", + "required": false, + "type": "string" + }, + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 10000000, + "maximum": 10000000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sampleId", + "in": "path", + "description": "Sample ID e.g. TCGA-OR-A5J2-01", + "required": true, + "type": "string" + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": ["clinicalAttributeId", "value"] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalData" } + } + } + } + } + }, + "/studies/{studyId}/samples/{sampleId}/copy-number-segments": { + "get": { + "tags": ["Copy Number Segments"], + "summary": "Get copy number segments in a sample in a study", + "operationId": "getCopyNumberSegmentsInSampleInStudyUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "chromosome", + "in": "query", + "description": "Chromosome", + "required": false, + "type": "string" + }, + { + "name": "direction", + "in": "query", + "description": "Direction of the sort", + "required": false, + "type": "string", + "default": "ASC", + "enum": ["ASC", "DESC"] + }, + { + "name": "pageNumber", + "in": "query", + "description": "Page number of the result list", + "required": false, + "type": "integer", + "default": 0, + "minimum": 0, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "pageSize", + "in": "query", + "description": "Page size of the result list", + "required": false, + "type": "integer", + "default": 20000, + "maximum": 20000, + "exclusiveMaximum": false, + "minimum": 1, + "exclusiveMinimum": false, + "format": "int32" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "enum": ["DETAILED", "ID", "META", "SUMMARY"] + }, + { + "name": "sampleId", + "in": "path", + "description": "Sample ID e.g. TCGA-OR-A5J2-01", + "required": true, + "type": "string" + }, + { + "name": "sortBy", + "in": "query", + "description": "Name of the property that the result list is sorted by", + "required": false, + "type": "string", + "enum": [ + "chromosome", + "end", + "numberOfProbes", + "segmentMean", + "start" + ] + }, + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { "$ref": "#/definitions/CopyNumberSeg" } + } + } + } + } + }, + "/studies/{studyId}/tags": { + "get": { + "tags": ["Studies"], + "summary": "Get the tags of a study", + "operationId": "getTagsUsingGET", + "produces": ["application/json"], + "parameters": [ + { + "name": "studyId", + "in": "path", + "description": "Study ID e.g. acc_tcga", + "required": true, + "type": "string" + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "type": "object" } + } + } + } + }, + "/treatments/display-patient": { + "post": { + "tags": ["Treatments"], + "summary": "Should patient level treatments be displayed", + "operationId": "getContainsTreatmentDataUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "studyIds", + "description": "List of Study IDs", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + }, + { + "name": "tier", + "in": "query", + "description": "tier", + "required": false, + "type": "string", + "default": "Agent", + "enum": ["Agent", "AgentClass", "AgentTarget"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "type": "boolean" } + } + } + } + }, + "/treatments/display-sample": { + "post": { + "tags": ["Treatments"], + "summary": "Should sample level treatments be displayed", + "operationId": "getContainsSampleTreatmentDataUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "studyIds", + "description": "List of Study IDs", + "required": true, + "schema": { + "type": "array", + "items": { "type": "string" } + } + }, + { + "name": "tier", + "in": "query", + "description": "tier", + "required": false, + "type": "string", + "default": "Agent", + "enum": ["Agent", "AgentClass", "AgentTarget"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { "type": "boolean" } + } + } + } + }, + "/treatments/patient": { + "post": { + "tags": ["Treatments"], + "summary": "Get all patient level treatments", + "operationId": "getAllPatientTreatmentsUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "studyViewFilter", + "description": "Study view filter", + "required": true, + "schema": { "$ref": "#/definitions/StudyViewFilter" } + }, + { + "name": "tier", + "in": "query", + "description": "tier", + "required": false, + "type": "string", + "default": "Agent", + "enum": ["Agent", "AgentClass", "AgentTarget"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/PatientTreatmentRow" + } + } + } + } + } + }, + "/treatments/sample": { + "post": { + "tags": ["Treatments"], + "summary": "Get all sample level treatments", + "operationId": "getAllSampleTreatmentsUsingPOST", + "consumes": ["application/json"], + "produces": ["application/json"], + "parameters": [ + { + "in": "body", + "name": "studyViewFilter", + "description": "Study view filter", + "required": true, + "schema": { "$ref": "#/definitions/StudyViewFilter" } + }, + { + "name": "tier", + "in": "query", + "description": "tier", + "required": false, + "type": "string", + "default": "Agent", + "enum": ["Agent", "AgentClass", "AgentTarget"] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/SampleTreatmentRow" + } + } + } + } + } + } + }, + "definitions": { + "AlleleSpecificCopyNumber": { + "type": "object", + "properties": { + "ascnIntegerCopyNumber": { + "type": "integer", + "format": "int32" + }, + "ascnMethod": { "type": "string" }, + "ccfExpectedCopies": { "type": "number", "format": "float" }, + "ccfExpectedCopiesUpper": { + "type": "number", + "format": "float" + }, + "clonal": { "type": "string" }, + "expectedAltCopies": { "type": "integer", "format": "int32" }, + "minorCopyNumber": { "type": "integer", "format": "int32" }, + "totalCopyNumber": { "type": "integer", "format": "int32" } + }, + "title": "AlleleSpecificCopyNumber" + }, + "AlterationFilter": { + "type": "object", + "properties": { + "copyNumberAlterationEventTypes": { + "type": "object", + "additionalProperties": { "type": "boolean" } + }, + "includeDriver": { "type": "boolean" }, + "includeGermline": { "type": "boolean" }, + "includeSomatic": { "type": "boolean" }, + "includeUnknownOncogenicity": { "type": "boolean" }, + "includeUnknownStatus": { "type": "boolean" }, + "includeUnknownTier": { "type": "boolean" }, + "includeVUS": { "type": "boolean" }, + "mutationEventTypes": { + "type": "object", + "additionalProperties": { "type": "boolean" } + }, + "structuralVariants": { "type": "boolean" }, + "tiersBooleanMap": { + "type": "object", + "additionalProperties": { "type": "boolean" } + } + }, + "title": "AlterationFilter" + }, + "AndedPatientTreatmentFilters": { + "type": "object", + "properties": { + "filters": { + "type": "array", + "items": { + "$ref": "#/definitions/OredPatientTreatmentFilters" + } + } + }, + "title": "AndedPatientTreatmentFilters" + }, + "AndedSampleTreatmentFilters": { + "type": "object", + "properties": { + "filters": { + "type": "array", + "items": { + "$ref": "#/definitions/OredSampleTreatmentFilters" + } + } + }, + "title": "AndedSampleTreatmentFilters" + }, + "CancerStudy": { + "type": "object", + "required": ["studyId"], + "properties": { + "allSampleCount": { "type": "integer", "format": "int32" }, + "cancerType": { "$ref": "#/definitions/TypeOfCancer" }, + "cancerTypeId": { "type": "string" }, + "citation": { "type": "string" }, + "cnaSampleCount": { "type": "integer", "format": "int32" }, + "completeSampleCount": { "type": "integer", "format": "int32" }, + "description": { "type": "string" }, + "groups": { "type": "string" }, + "importDate": { + "type": "string", + "example": "yyyy-MM-dd HH:mm:ss" + }, + "massSpectrometrySampleCount": { + "type": "integer", + "format": "int32" + }, + "methylationHm27SampleCount": { + "type": "integer", + "format": "int32" + }, + "miRnaSampleCount": { "type": "integer", "format": "int32" }, + "mrnaMicroarraySampleCount": { + "type": "integer", + "format": "int32" + }, + "mrnaRnaSeqSampleCount": { + "type": "integer", + "format": "int32" + }, + "mrnaRnaSeqV2SampleCount": { + "type": "integer", + "format": "int32" + }, + "name": { "type": "string" }, + "pmid": { "type": "string" }, + "publicStudy": { "type": "boolean" }, + "readPermission": { "type": "boolean" }, + "referenceGenome": { "type": "string" }, + "rppaSampleCount": { "type": "integer", "format": "int32" }, + "sequencedSampleCount": { + "type": "integer", + "format": "int32" + }, + "status": { "type": "integer", "format": "int32" }, + "studyId": { "type": "string" }, + "treatmentCount": { "type": "integer", "format": "int32" } + }, + "title": "CancerStudy" + }, + "CancerStudyTags": { + "type": "object", + "properties": { + "cancerStudyId": { "type": "integer", "format": "int32" }, + "studyId": { "type": "string" }, + "tags": { "type": "string" } + }, + "title": "CancerStudyTags" + }, + "ClinicalAttribute": { + "type": "object", + "required": [ + "clinicalAttributeId", + "displayName", + "patientAttribute", + "studyId" + ], + "properties": { + "clinicalAttributeId": { "type": "string" }, + "datatype": { "type": "string" }, + "description": { "type": "string" }, + "displayName": { "type": "string" }, + "patientAttribute": { "type": "boolean" }, + "priority": { "type": "string" }, + "studyId": { "type": "string" } + }, + "title": "ClinicalAttribute" + }, + "ClinicalData": { + "type": "object", + "required": ["clinicalAttributeId", "patientId", "studyId"], + "properties": { + "clinicalAttribute": { + "$ref": "#/definitions/ClinicalAttribute" + }, + "clinicalAttributeId": { "type": "string" }, + "patientAttribute": { "type": "boolean" }, + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" }, + "value": { "type": "string" } + }, + "title": "ClinicalData" + }, + "ClinicalDataFilter": { + "type": "object", + "properties": { + "attributeId": { "type": "string" }, + "values": { + "type": "array", + "items": { "$ref": "#/definitions/DataFilterValue" } + } + }, + "title": "ClinicalDataFilter" + }, + "ClinicalDataIdentifier": { + "type": "object", + "properties": { + "entityId": { "type": "string" }, + "studyId": { "type": "string" } + }, + "title": "ClinicalDataIdentifier" + }, + "ClinicalDataMultiStudyFilter": { + "type": "object", + "properties": { + "attributeIds": { + "type": "array", + "items": { "type": "string" } + }, + "identifiers": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalDataIdentifier" } + } + }, + "title": "ClinicalDataMultiStudyFilter" + }, + "ClinicalDataSingleStudyFilter": { + "type": "object", + "properties": { + "attributeIds": { + "type": "array", + "items": { "type": "string" } + }, + "ids": { "type": "array", "items": { "type": "string" } } + }, + "title": "ClinicalDataSingleStudyFilter" + }, + "ClinicalEventSample": { + "type": "object", + "properties": { + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "studyId": { "type": "string" }, + "timeTaken": { "type": "integer", "format": "int32" } + }, + "title": "ClinicalEventSample" + }, + "CopyNumberSeg": { + "type": "object", + "required": [ + "chromosome", + "end", + "numberOfProbes", + "patientId", + "sampleId", + "segmentMean", + "start", + "studyId" + ], + "properties": { + "chromosome": { "type": "string" }, + "end": { "type": "integer", "format": "int32" }, + "numberOfProbes": { "type": "integer", "format": "int32" }, + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "segmentMean": { "type": "number" }, + "start": { "type": "integer", "format": "int32" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" } + }, + "title": "CopyNumberSeg" + }, + "DataFilter": { + "type": "object", + "properties": { + "values": { + "type": "array", + "items": { "$ref": "#/definitions/DataFilterValue" } + } + }, + "title": "DataFilter" + }, + "DataFilterValue": { + "type": "object", + "properties": { + "end": { "type": "number" }, + "start": { "type": "number" }, + "value": { "type": "string" } + }, + "title": "DataFilterValue" + }, + "DiscreteCopyNumberData": { + "type": "object", + "required": [ + "alteration", + "entrezGeneId", + "molecularProfileId", + "patientId", + "sampleId", + "studyId" + ], + "properties": { + "alteration": { "type": "integer", "format": "int32" }, + "driverFilter": { "type": "string" }, + "driverFilterAnnotation": { "type": "string" }, + "driverTiersFilter": { "type": "string" }, + "driverTiersFilterAnnotation": { "type": "string" }, + "entrezGeneId": { "type": "integer", "format": "int32" }, + "gene": { "$ref": "#/definitions/Gene" }, + "molecularProfileId": { "type": "string" }, + "namespaceColumns": { + "type": "object", + "additionalProperties": { "type": "object" } + }, + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" } + }, + "title": "DiscreteCopyNumberData" + }, + "DiscreteCopyNumberFilter": { + "type": "object", + "properties": { + "entrezGeneIds": { + "type": "array", + "items": { "type": "integer", "format": "int32" } + }, + "sampleIds": { "type": "array", "items": { "type": "string" } }, + "sampleListId": { "type": "string" } + }, + "title": "DiscreteCopyNumberFilter" + }, + "Gene": { + "type": "object", + "required": ["entrezGeneId", "geneticEntityId", "hugoGeneSymbol"], + "properties": { + "entrezGeneId": { "type": "integer", "format": "int32" }, + "geneticEntityId": { "type": "integer", "format": "int32" }, + "hugoGeneSymbol": { "type": "string" }, + "type": { "type": "string" } + }, + "title": "Gene" + }, + "GeneFilter": { + "type": "object", + "properties": { + "geneQueries": { + "type": "array", + "items": { + "type": "array", + "items": { "$ref": "#/definitions/GeneFilterQuery" } + } + }, + "molecularProfileIds": { + "type": "array", + "uniqueItems": true, + "items": { "type": "string" } + } + }, + "title": "GeneFilter" + }, + "GeneFilterQuery": { + "type": "object", + "properties": { + "alterations": { + "type": "array", + "items": { + "type": "string", + "enum": ["AMP", "DIPLOID", "GAIN", "HETLOSS", "HOMDEL"] + } + }, + "entrezGeneId": { "type": "integer", "format": "int32" }, + "hugoGeneSymbol": { "type": "string" }, + "includeDriver": { "type": "boolean" }, + "includeGermline": { "type": "boolean" }, + "includeSomatic": { "type": "boolean" }, + "includeUnknownOncogenicity": { "type": "boolean" }, + "includeUnknownStatus": { "type": "boolean" }, + "includeUnknownTier": { "type": "boolean" }, + "includeVUS": { "type": "boolean" }, + "tiersBooleanMap": { + "type": "object", + "additionalProperties": { "type": "boolean" } + } + }, + "title": "GeneFilterQuery" + }, + "GenePanel": { + "type": "object", + "required": ["genePanelId"], + "properties": { + "description": { "type": "string" }, + "genePanelId": { "type": "string" }, + "genes": { + "type": "array", + "items": { "$ref": "#/definitions/GenePanelToGene" } + } + }, + "title": "GenePanel" + }, + "GenePanelData": { + "type": "object", + "required": [ + "molecularProfileId", + "patientId", + "profiled", + "sampleId", + "studyId" + ], + "properties": { + "genePanelId": { "type": "string" }, + "molecularProfileId": { "type": "string" }, + "patientId": { "type": "string" }, + "profiled": { "type": "boolean" }, + "sampleId": { "type": "string" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" } + }, + "title": "GenePanelData" + }, + "GenePanelDataFilter": { + "type": "object", + "properties": { + "sampleIds": { "type": "array", "items": { "type": "string" } }, + "sampleListId": { "type": "string" } + }, + "title": "GenePanelDataFilter" + }, + "GenePanelDataMultipleStudyFilter": { + "type": "object", + "properties": { + "molecularProfileIds": { + "type": "array", + "items": { "type": "string" } + }, + "sampleMolecularIdentifiers": { + "type": "array", + "items": { + "$ref": "#/definitions/SampleMolecularIdentifier" + } + } + }, + "title": "GenePanelDataMultipleStudyFilter" + }, + "GenePanelToGene": { + "type": "object", + "required": ["entrezGeneId", "hugoGeneSymbol"], + "properties": { + "entrezGeneId": { "type": "integer", "format": "int32" }, + "hugoGeneSymbol": { "type": "string" } + }, + "title": "GenePanelToGene" + }, + "GenericAssayData": { + "type": "object", + "required": [ + "genericAssayStableId", + "molecularProfileId", + "patientId", + "sampleId", + "studyId", + "value" + ], + "properties": { + "genericAssayStableId": { "type": "string" }, + "molecularProfileId": { "type": "string" }, + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "stableId": { "type": "string" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" }, + "value": { "type": "string" } + }, + "title": "GenericAssayData" + }, + "GenericAssayDataFilter": { + "type": "object", + "properties": { + "profileType": { "type": "string" }, + "stableId": { "type": "string" }, + "values": { + "type": "array", + "items": { "$ref": "#/definitions/DataFilterValue" } + } + }, + "title": "GenericAssayDataFilter" + }, + "GenericAssayDataMultipleStudyFilter": { + "type": "object", + "properties": { + "genericAssayStableIds": { + "type": "array", + "items": { "type": "string" } + }, + "molecularProfileIds": { + "type": "array", + "items": { "type": "string" } + }, + "sampleMolecularIdentifiers": { + "type": "array", + "items": { + "$ref": "#/definitions/SampleMolecularIdentifier" + } + } + }, + "title": "GenericAssayDataMultipleStudyFilter" + }, + "GenericAssayFilter": { + "type": "object", + "properties": { + "genericAssayStableIds": { + "type": "array", + "items": { "type": "string" } + }, + "sampleIds": { "type": "array", "items": { "type": "string" } }, + "sampleListId": { "type": "string" } + }, + "title": "GenericAssayFilter" + }, + "GenericAssayMeta": { + "type": "object", + "properties": { + "entityType": { "type": "string" }, + "genericEntityMetaProperties": { + "type": "object", + "additionalProperties": { "type": "string" } + }, + "stableId": { "type": "string" } + }, + "title": "GenericAssayMeta" + }, + "GenericAssayMetaFilter": { + "type": "object", + "properties": { + "genericAssayStableIds": { + "type": "array", + "items": { "type": "string" } + }, + "molecularProfileIds": { + "type": "array", + "items": { "type": "string" } + } + }, + "title": "GenericAssayMetaFilter" + }, + "GenomicDataFilter": { + "type": "object", + "properties": { + "hugoGeneSymbol": { "type": "string" }, + "profileType": { "type": "string" }, + "values": { + "type": "array", + "items": { "$ref": "#/definitions/DataFilterValue" } + } + }, + "title": "GenomicDataFilter" + }, + "Info": { + "type": "object", + "required": [ + "dbVersion", + "geneTableVersion", + "gitBranch", + "gitCommitId", + "gitCommitIdAbbrev", + "gitCommitIdDescribe", + "gitCommitIdDescribeShort", + "gitCommitMessageFull", + "gitCommitMessageShort", + "gitCommitMessageUserEmail", + "gitCommitMessageUserName", + "gitDirty", + "portalVersion" + ], + "properties": { + "dbVersion": { "type": "string" }, + "geneTableVersion": { "type": "string" }, + "gitBranch": { "type": "string" }, + "gitCommitId": { "type": "string" }, + "gitCommitIdAbbrev": { "type": "string" }, + "gitCommitIdDescribe": { "type": "string" }, + "gitCommitIdDescribeShort": { "type": "string" }, + "gitCommitMessageFull": { "type": "string" }, + "gitCommitMessageShort": { "type": "string" }, + "gitCommitMessageUserEmail": { "type": "string" }, + "gitCommitMessageUserName": { "type": "string" }, + "gitDirty": { "type": "boolean" }, + "portalVersion": { "type": "string" } + }, + "title": "Info" + }, + "MolecularDataFilter": { + "type": "object", + "properties": { + "entrezGeneIds": { + "type": "array", + "items": { "type": "integer", "format": "int32" } + }, + "sampleIds": { "type": "array", "items": { "type": "string" } }, + "sampleListId": { "type": "string" } + }, + "title": "MolecularDataFilter" + }, + "MolecularDataMultipleStudyFilter": { + "type": "object", + "properties": { + "entrezGeneIds": { + "type": "array", + "items": { "type": "integer", "format": "int32" } + }, + "molecularProfileIds": { + "type": "array", + "items": { "type": "string" } + }, + "sampleMolecularIdentifiers": { + "type": "array", + "items": { + "$ref": "#/definitions/SampleMolecularIdentifier" + } + } + }, + "title": "MolecularDataMultipleStudyFilter" + }, + "MolecularProfile": { + "type": "object", + "required": ["molecularProfileId", "patientLevel", "studyId"], + "properties": { + "datatype": { "type": "string" }, + "description": { "type": "string" }, + "genericAssayType": { "type": "string" }, + "molecularAlterationType": { + "type": "string", + "enum": [ + "COPY_NUMBER_ALTERATION", + "GENERIC_ASSAY", + "GENESET_SCORE", + "METHYLATION", + "METHYLATION_BINARY", + "MICRO_RNA_EXPRESSION", + "MRNA_EXPRESSION", + "MRNA_EXPRESSION_NORMALS", + "MUTATION_EXTENDED", + "MUTATION_UNCALLED", + "PHOSPHORYLATION", + "PROTEIN_ARRAY_PHOSPHORYLATION", + "PROTEIN_ARRAY_PROTEIN_LEVEL", + "PROTEIN_LEVEL", + "RNA_EXPRESSION", + "STRUCTURAL_VARIANT" + ] + }, + "molecularProfileId": { "type": "string" }, + "name": { "type": "string" }, + "patientLevel": { "type": "boolean" }, + "pivotThreshold": { "type": "number", "format": "float" }, + "showProfileInAnalysisTab": { "type": "boolean" }, + "sortOrder": { "type": "string" }, + "study": { "$ref": "#/definitions/CancerStudy" }, + "studyId": { "type": "string" } + }, + "title": "MolecularProfile" + }, + "MolecularProfileFilter": { + "type": "object", + "properties": { + "molecularProfileIds": { + "type": "array", + "uniqueItems": true, + "items": { "type": "string" } + }, + "studyIds": { "type": "array", "items": { "type": "string" } } + }, + "title": "MolecularProfileFilter" + }, + "Mutation": { + "type": "object", + "required": [ + "entrezGeneId", + "molecularProfileId", + "patientId", + "sampleId", + "studyId" + ], + "properties": { + "alleleSpecificCopyNumber": { + "$ref": "#/definitions/AlleleSpecificCopyNumber" + }, + "aminoAcidChange": { "type": "string" }, + "center": { "type": "string" }, + "chr": { "type": "string" }, + "driverFilter": { "type": "string" }, + "driverFilterAnnotation": { "type": "string" }, + "driverTiersFilter": { "type": "string" }, + "driverTiersFilterAnnotation": { "type": "string" }, + "endPosition": { "type": "integer", "format": "int64" }, + "entrezGeneId": { "type": "integer", "format": "int32" }, + "gene": { "$ref": "#/definitions/Gene" }, + "keyword": { "type": "string" }, + "molecularProfileId": { "type": "string" }, + "mutationStatus": { "type": "string" }, + "mutationType": { "type": "string" }, + "namespaceColumns": { + "type": "object", + "additionalProperties": { "type": "object" } + }, + "ncbiBuild": { "type": "string" }, + "normalAltCount": { "type": "integer", "format": "int32" }, + "normalRefCount": { "type": "integer", "format": "int32" }, + "patientId": { "type": "string" }, + "proteinChange": { "type": "string" }, + "proteinPosEnd": { "type": "integer", "format": "int32" }, + "proteinPosStart": { "type": "integer", "format": "int32" }, + "referenceAllele": { "type": "string" }, + "refseqMrnaId": { "type": "string" }, + "sampleId": { "type": "string" }, + "startPosition": { "type": "integer", "format": "int64" }, + "studyId": { "type": "string" }, + "tumorAltCount": { "type": "integer", "format": "int32" }, + "tumorRefCount": { "type": "integer", "format": "int32" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" }, + "validationStatus": { "type": "string" }, + "variantAllele": { "type": "string" }, + "variantType": { "type": "string" } + }, + "title": "Mutation" + }, + "MutationFilter": { + "type": "object", + "properties": { + "entrezGeneIds": { + "type": "array", + "items": { "type": "integer", "format": "int32" } + }, + "sampleIds": { "type": "array", "items": { "type": "string" } }, + "sampleListId": { "type": "string" } + }, + "title": "MutationFilter" + }, + "MutationMultipleStudyFilter": { + "type": "object", + "properties": { + "entrezGeneIds": { + "type": "array", + "items": { "type": "integer", "format": "int32" } + }, + "molecularProfileIds": { + "type": "array", + "items": { "type": "string" } + }, + "sampleMolecularIdentifiers": { + "type": "array", + "items": { + "$ref": "#/definitions/SampleMolecularIdentifier" + } + } + }, + "title": "MutationMultipleStudyFilter" + }, + "NumericGeneMolecularData": { + "type": "object", + "required": [ + "entrezGeneId", + "molecularProfileId", + "patientId", + "sampleId", + "studyId", + "value" + ], + "properties": { + "entrezGeneId": { "type": "integer", "format": "int32" }, + "gene": { "$ref": "#/definitions/Gene" }, + "molecularProfileId": { "type": "string" }, + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" }, + "value": { "type": "number" } + }, + "title": "NumericGeneMolecularData" + }, + "OredPatientTreatmentFilters": { + "type": "object", + "properties": { + "filters": { + "type": "array", + "items": { "$ref": "#/definitions/PatientTreatmentFilter" } + } + }, + "title": "OredPatientTreatmentFilters" + }, + "OredSampleTreatmentFilters": { + "type": "object", + "properties": { + "filters": { + "type": "array", + "items": { "$ref": "#/definitions/SampleTreatmentFilter" } + } + }, + "title": "OredSampleTreatmentFilters" + }, + "Patient": { + "type": "object", + "required": ["patientId", "studyId"], + "properties": { + "cancerStudy": { "$ref": "#/definitions/CancerStudy" }, + "patientId": { "type": "string" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" } + }, + "title": "Patient" + }, + "PatientFilter": { + "type": "object", + "properties": { + "patientIdentifiers": { + "type": "array", + "items": { "$ref": "#/definitions/PatientIdentifier" } + }, + "uniquePatientKeys": { + "type": "array", + "items": { "type": "string" } + } + }, + "title": "PatientFilter" + }, + "PatientIdentifier": { + "type": "object", + "properties": { + "patientId": { "type": "string" }, + "studyId": { "type": "string" } + }, + "title": "PatientIdentifier" + }, + "PatientTreatmentFilter": { + "type": "object", + "properties": { "treatment": { "type": "string" } }, + "title": "PatientTreatmentFilter" + }, + "PatientTreatmentRow": { + "type": "object", + "properties": { + "count": { "type": "integer", "format": "int32" }, + "samples": { + "type": "array", + "uniqueItems": true, + "items": { "$ref": "#/definitions/ClinicalEventSample" } + }, + "treatment": { "type": "string" } + }, + "title": "PatientTreatmentRow" + }, + "Sample": { + "type": "object", + "required": ["patientId", "sampleId", "studyId"], + "properties": { + "copyNumberSegmentPresent": { "type": "boolean" }, + "patientId": { "type": "string" }, + "sampleId": { "type": "string" }, + "sampleType": { + "type": "string", + "enum": [ + "BLOOD_NORMAL", + "METASTATIC", + "PRIMARY_BLOOD_TUMOR", + "PRIMARY_SOLID_TUMOR", + "RECURRENT_BLOOD_TUMOR", + "RECURRENT_SOLID_TUMOR", + "SOLID_NORMAL" + ] + }, + "sequenced": { "type": "boolean" }, + "studyId": { "type": "string" }, + "uniquePatientKey": { "type": "string" }, + "uniqueSampleKey": { "type": "string" } + }, + "title": "Sample" + }, + "SampleFilter": { + "type": "object", + "properties": { + "sampleIdentifiers": { + "type": "array", + "items": { "$ref": "#/definitions/SampleIdentifier" } + }, + "sampleListIds": { + "type": "array", + "items": { "type": "string" } + }, + "uniqueSampleKeys": { + "type": "array", + "items": { "type": "string" } + } + }, + "title": "SampleFilter" + }, + "SampleIdentifier": { + "type": "object", + "properties": { + "sampleId": { "type": "string" }, + "studyId": { "type": "string" } + }, + "title": "SampleIdentifier" + }, + "SampleList": { + "type": "object", + "required": ["sampleListId"], + "properties": { + "category": { "type": "string" }, + "description": { "type": "string" }, + "name": { "type": "string" }, + "sampleCount": { "type": "integer", "format": "int32" }, + "sampleIds": { "type": "array", "items": { "type": "string" } }, + "sampleListId": { "type": "string" }, + "studyId": { "type": "string" } + }, + "title": "SampleList" + }, + "SampleMolecularIdentifier": { + "type": "object", + "properties": { + "molecularProfileId": { "type": "string" }, + "sampleId": { "type": "string" } + }, + "title": "SampleMolecularIdentifier" + }, + "SampleTreatmentFilter": { + "type": "object", + "properties": { + "time": { "type": "string", "enum": ["Post", "Pre"] }, + "treatment": { "type": "string" } + }, + "title": "SampleTreatmentFilter" + }, + "SampleTreatmentRow": { + "type": "object", + "properties": { + "count": { "type": "integer", "format": "int32" }, + "samples": { + "type": "array", + "uniqueItems": true, + "items": { "$ref": "#/definitions/ClinicalEventSample" } + }, + "time": { "type": "string", "enum": ["Post", "Pre"] }, + "treatment": { "type": "string" } + }, + "title": "SampleTreatmentRow" + }, + "ServerStatusMessage": { + "type": "object", + "properties": { "status": { "type": "string" } }, + "title": "ServerStatusMessage" + }, + "StructuralVariantFilterQuery": { + "type": "object", + "properties": { + "gene1Query": { + "$ref": "#/definitions/StructuralVariantGeneSubQuery" + }, + "gene2Query": { + "$ref": "#/definitions/StructuralVariantGeneSubQuery" + }, + "includeDriver": { "type": "boolean" }, + "includeGermline": { "type": "boolean" }, + "includeSomatic": { "type": "boolean" }, + "includeUnknownOncogenicity": { "type": "boolean" }, + "includeUnknownStatus": { "type": "boolean" }, + "includeUnknownTier": { "type": "boolean" }, + "includeVUS": { "type": "boolean" }, + "tiersBooleanMap": { + "type": "object", + "additionalProperties": { "type": "boolean" } + } + }, + "title": "StructuralVariantFilterQuery" + }, + "StructuralVariantGeneSubQuery": { + "type": "object", + "properties": { + "entrezId": { "type": "integer", "format": "int32" }, + "hugoSymbol": { "type": "string" }, + "specialValue": { + "type": "string", + "enum": ["ANY_GENE", "NO_GENE"] + } + }, + "title": "StructuralVariantGeneSubQuery" + }, + "StudyViewFilter": { + "type": "object", + "properties": { + "alterationFilter": { + "$ref": "#/definitions/AlterationFilter" + }, + "caseLists": { + "type": "array", + "items": { "type": "array", "items": { "type": "string" } } + }, + "clinicalDataFilters": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalDataFilter" } + }, + "clinicalEventFilters": { + "type": "array", + "items": { "$ref": "#/definitions/DataFilter" } + }, + "customDataFilters": { + "type": "array", + "items": { "$ref": "#/definitions/ClinicalDataFilter" } + }, + "geneFilters": { + "type": "array", + "items": { "$ref": "#/definitions/GeneFilter" } + }, + "genericAssayDataFilters": { + "type": "array", + "items": { "$ref": "#/definitions/GenericAssayDataFilter" } + }, + "genomicDataFilters": { + "type": "array", + "items": { "$ref": "#/definitions/GenomicDataFilter" } + }, + "genomicProfiles": { + "type": "array", + "items": { "type": "array", "items": { "type": "string" } } + }, + "patientTreatmentFilters": { + "$ref": "#/definitions/AndedPatientTreatmentFilters" + }, + "patientTreatmentGroupFilters": { + "$ref": "#/definitions/AndedPatientTreatmentFilters" + }, + "patientTreatmentTargetFilters": { + "$ref": "#/definitions/AndedPatientTreatmentFilters" + }, + "sampleIdentifiers": { + "type": "array", + "items": { "$ref": "#/definitions/SampleIdentifier" } + }, + "sampleTreatmentFilters": { + "$ref": "#/definitions/AndedSampleTreatmentFilters" + }, + "sampleTreatmentGroupFilters": { + "$ref": "#/definitions/AndedSampleTreatmentFilters" + }, + "sampleTreatmentTargetFilters": { + "$ref": "#/definitions/AndedSampleTreatmentFilters" + }, + "structuralVariantFilters": { + "type": "array", + "items": { + "$ref": "#/definitions/StudyViewStructuralVariantFilter" + } + }, + "studyIds": { "type": "array", "items": { "type": "string" } } + }, + "title": "StudyViewFilter" + }, + "StudyViewStructuralVariantFilter": { + "type": "object", + "properties": { + "molecularProfileIds": { + "type": "array", + "uniqueItems": true, + "items": { "type": "string" } + }, + "structVarQueries": { + "type": "array", + "items": { + "type": "array", + "items": { + "$ref": "#/definitions/StructuralVariantFilterQuery" + } + } + } + }, + "title": "StudyViewStructuralVariantFilter" + }, + "TypeOfCancer": { + "type": "object", + "required": ["cancerTypeId"], + "properties": { + "cancerTypeId": { "type": "string" }, + "dedicatedColor": { "type": "string" }, + "name": { "type": "string" }, + "parent": { "type": "string" }, + "shortName": { "type": "string" } + }, + "title": "TypeOfCancer" + } + } +} diff --git a/src/main/resources/maven.properties b/src/main/resources/maven.properties index 24e2bf7fc5a..97251404b67 100644 --- a/src/main/resources/maven.properties +++ b/src/main/resources/maven.properties @@ -1,4 +1,5 @@ app.version=@maven.build.timestamp@ portal.version=@project.version@ # this is the *expected* DB version (expected by the code). Don't set it manually, it is filled by maven: -db.version=@db.version@ \ No newline at end of file +db.version=@db.version@ +genetable.version=@genetable.version@ \ No newline at end of file diff --git a/src/test/java/org/cbioportal/web/InfoControllerTest.java b/src/test/java/org/cbioportal/web/InfoControllerTest.java index af78e860bb1..270a9ffe632 100644 --- a/src/test/java/org/cbioportal/web/InfoControllerTest.java +++ b/src/test/java/org/cbioportal/web/InfoControllerTest.java @@ -19,7 +19,8 @@ @ContextConfiguration(classes = {InfoController.class, TestConfig.class}) @TestPropertySource(properties = { "portal.version=test_portal_version", - "db.version=test_db_version" + "db.version=test_db_version", + "genetable.version=test_genetable_version" }) public class InfoControllerTest { @@ -35,6 +36,7 @@ public void getInfo() throws Exception { .andExpect(MockMvcResultMatchers.status().isOk()) .andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON)) .andExpect(MockMvcResultMatchers.jsonPath("$.portalVersion").value("test_portal_version")) - .andExpect(MockMvcResultMatchers.jsonPath("$.dbVersion").value("test_db_version")); + .andExpect(MockMvcResultMatchers.jsonPath("$.dbVersion").value("test_db_version")) + .andExpect(MockMvcResultMatchers.jsonPath("$.genetableVersion").value("test_genetable_version")); } } diff --git a/src/test/resources/maven.properties b/src/test/resources/maven.properties index 9ef36016da2..3cd316a83a4 100644 --- a/src/test/resources/maven.properties +++ b/src/test/resources/maven.properties @@ -1,3 +1,4 @@ portal.version=test_portal_version db.version=test_db_version app.version=test_app_version +genetable.version=test_genetable_version diff --git a/test/test_db_version.sh b/test/test_db_version.sh index e370ed930ca..67ade154410 100755 --- a/test/test_db_version.sh +++ b/test/test_db_version.sh @@ -1,30 +1,54 @@ #!/usr/bin/env bash -# halt on error +# Halt on error set -e -# script dir + +# Script directory DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )" -#colors + +# Colors for output RED='\033[0;31m' GREEN='\033[0;32m' YELLOW='\033[1;33m' NC='\033[0m' -echo "Making sure all db versions are the same in cgds.sql, pom.xml and migration.sql" +echo "Checking db and genetable versions in pom.xml, cgds.sql, and migration.sql" + +# Fetch db version from pom.xml +POM_DB_VERSION=$(grep '' ${DIR}/../pom.xml | cut -d'>' -f2 | cut -d'<' -f1) +echo "pom.xml db version is $POM_DB_VERSION" + +# Fetch geneTable version from pom.xml +POM_GENE_TABLE_VERSION=$(grep '' ${DIR}/../pom.xml | cut -d'>' -f2 | cut -d'<' -f1) +echo "pom.xml genetable version is $POM_GENE_TABLE_VERSION" -POM_DB_VERSION=$(grep db.version ${DIR}/../pom.xml | cut -d'>' -f2 | cut -d'<' -f1) -echo pom.xml db version is $POM_DB_VERSION +# Fetch db version from cgds.sql +CGDS_DB_SQL_VERSION=$(grep "INSERT INTO info" ${DIR}/../src/main/resources/db-scripts/cgds.sql | cut -d"'" -f2 | cut -d"'" -f1) +echo "src/main/resources/db-scripts/cgds.sql db version is $CGDS_DB_SQL_VERSION" -CGDS_DB_SQL_VERSION=$(grep 'INSERT INTO info' ${DIR}/../src/main/resources/db-scripts/cgds.sql | cut -d"'" -f2 | cut -d"'" -f1) -echo src/main/resources/db-scripts/cgds.sql db version is $CGDS_DB_SQL_VERSION +# Fetch geneTable version from cgds.sql +CGDS_GENE_TABLE_VERSION=$(grep "INSERT INTO info" ${DIR}/../src/main/resources/db-scripts/cgds.sql | grep "genetable" | cut -d"'" -f4) +echo "src/main/resources/db-scripts/cgds.sql genetable version is $CGDS_GENE_TABLE_VERSION" +# Fetch db version from migration.sql MIGRATION_DB_VERSION=$(grep 'UPDATE `info`' ${DIR}/../src/main/resources/db-scripts/migration.sql | tail -1 | cut -d '"' -f2 | cut -d'"' -f1) -echo src/main/resources/db-scripts/migration.sql db version is $MIGRATION_DB_VERSION +echo "src/main/resources/db-scripts/migration.sql db version is $MIGRATION_DB_VERSION" + +# Fetch geneTable version from migration.sql +MIGRATION_GENE_TABLE_VERSION=$(grep 'UPDATE `info`' ${DIR}/../src/main/resources/db-scripts/migration.sql | tail -1 | cut -d '"' -f4 | cut -d'"' -f1) +echo "src/main/resources/db-scripts/migration.sql genetable version is $MIGRATION_GENE_TABLE_VERSION" + +# Verify db versions match +if [ "$POM_DB_VERSION" == "$CGDS_DB_SQL_VERSION" ] && [ "$CGDS_DB_SQL_VERSION" == "$MIGRATION_DB_VERSION" ]; then + echo -e "${GREEN}db versions match${NC}" +else + echo -e "${RED}db versions mismatch${NC}" + exit 1 +fi -if [ "$POM_DB_VERSION" == "$CGDS_DB_SQL_VERSION" ] && [ "$CGDS_DB_SQL_VERSION" == "$MIGRATION_DB_VERSION" ] -then - echo -e "${GREEN}db versions match${NC}"; - exit 0; +# Verify geneTable versions match +if [ "$POM_GENE_TABLE_VERSION" == "$CGDS_GENE_TABLE_VERSION" ] && [ "$CGDS_GENE_TABLE_VERSION" == "$MIGRATION_GENE_TABLE_VERSION" ]; then + echo -e "${GREEN}genetable versions match${NC}" else - echo -e "${RED}db versions mismatch${NC}"; - exit 1; + echo -e "${RED}genetable versions mismatch${NC}" + exit 1 fi