Merge pull request #134 from tsheils/development

updating swagger file and api

.travis.yml

@@ -14,5 +14,5 @@ install:
   - npm install
 
 script:
-  -  nx run ramp:lint
-  - ng run-many --all --target=test -- --no-watch --no-progress --browsers=ChromeHeadlessCI
+  - ng run-many --all --target=lint
+  - ng run-many --all --target=test --no-watch --no-progress --browsers=ChromeHeadlessCI

apps/ramp-server/plumber.R

@@ -40,7 +40,7 @@ cors <- function(req, res) {
 ######
 #* Return source version information
 #* @serializer unboxedJSON
-#* @get /api/source_versions
+#* @get /api/source-versions
 function() {
   version_info <- RaMP::getCurrentRaMPSourceDBVersions(db = rampDB)
 
@@ -53,7 +53,7 @@ function() {
 ######
 #* Return database version id
 #* @serializer unboxedJSON
-#* @get /api/ramp_db_version
+#* @get /api/ramp-db-version
 function() {
   version <- RaMP::getCurrentRaMPVersion(db = rampDB)
 
@@ -66,7 +66,7 @@ function() {
 ######
 #* Return current database file url
 #* @serializer unboxedJSON
-#* @get /api/current_db_file_url
+#* @get /api/current-db-file-url
 function() {
   versionInfo <- RaMP::getCurrentRaMPVersion(db = rampDB, justVersion = FALSE)
   dbURL <- unlist(versionInfo$db_sql_url)
@@ -95,7 +95,7 @@ function() {
 ####
 #* Return counts on entities and their associations
 #* @serializer unboxedJSON
-#* @get /api/entity_counts
+#* @get /api/entity-counts
 function() {
   entity_counts <- RaMP::getEntityCountsFromSourceDBs(db = rampDB)
 
@@ -109,7 +109,7 @@ function() {
 #* Return analyte source intersects
 #* @param analytetype specifies type of analyte intersects to return, 'metabolites' or 'genes'
 #* @param query_scope specifies 'global' or 'mapped-to-pathway'
-#* @get /api/analyte_intersects
+#* @get /api/analyte-intersects
 function(analytetype, query_scope = 'global') {
   response <- ""
   if(!missing(analytetype)) {
@@ -209,11 +209,11 @@ function(pathway, analyte_type="both", names_or_ids="names", match="fuzzy", max_
 #####
 #* Return ontologies from list of metabolites
 #* @param metabolite
-#* @param NameOrIds one of “name” or “ids”, default “ids"
+#* @param namesOrIds one of “name” or “ids”, default “ids"
 #* @post /api/ontologies-from-metabolites
-function(metabolite, NameOrIds= "ids") {
+function(metabolite, namesOrIds= "ids") {
     ontologies_df <-
-        RaMP::getOntoFromMeta(db = rampDB, analytes = metabolite, NameOrIds = NameOrIds)
+        RaMP::getOntoFromMeta(db = rampDB, analytes = metabolite, NameOrIds = namesOrIds)
     if(is.null(ontologies_df)){
         ontologies_df<-data.frame()
     }
@@ -328,7 +328,7 @@ function(analyte) {
     analytes_df <- RaMP::rampFastCata(
       db = rampDB,
       analytes = analyte,
-      NameOrIds = "ids"
+      namesOrIds = "ids"
     )
   },
     error = function(cond) {
@@ -339,7 +339,7 @@ function(analyte) {
   #    analytes_df_names <- tryCatch({
   #        analytes_df <- RaMP::rampFastCata(
   #            analytes = analytes,
-  #            NameOrIds = "names"
+  #            namesOrIds = "names"
   #        )
   #    },
   #        error = function(cond) {
@@ -574,15 +574,15 @@ function(metabolites = '', file = '', biospecimen = '', background = "database")
 #' @param humanProtein
 #' @param includeTransportRxns
 #' @param rxnDirs
-#' @post /api/reactions_from_analytes
+#' @post /api/reactions-from-analytes
 #' @serializer json list(digits = 6)
 function(
     analytes,
     namesOrIds,
-    onlyHumanMets,
-    humanProtein,
-    includeTransportRxns,
-    rxnDirs
+    onlyHumanMets = false,
+    humanProtein = true,
+    includeTransportRxns = true,
+    rxnDirs = 'UN'
 ) {
 
   result = getReactionsForAnalytes(
@@ -601,7 +601,7 @@ function(
   return(
     list(
       data = result,
-      function_call = paste0("RaMP::getReactionsForAnalytes(db=RaMPDB, analytes=c(",analyteStr,"), namesOrIDs='ids', onlyHumanMets=",onlyHumanMets,", humanProtein=",humanProtein,", includeTransportRxns=",includeTransportRxns,", rxnDirs=c(",rxnDirs,")")
+      function_call = paste0("RaMP::getReactionsForAnalytes(db=RaMPDB, analytes=c(",analyteStr,"), namesOrIds='ids', onlyHumanMets=",onlyHumanMets,", humanProtein=",humanProtein,", includeTransportRxns=",includeTransportRxns,", rxnDirs=c(",rxnDirs,")")
     )
   )
 }
@@ -612,13 +612,14 @@ function(
 #' @param analytes
 #' @param multiRxnParticipantCount
 #' @param humanProtein
-#' @post /api/reaction_classes_from_analytes
+#' @param concatResults
+#' @post /api/reaction-classes-from-analytes
 #' @serializer json list(digits = 6)
 function(
     analytes,
-    multiRxnParticipantCount,
+    multiRxnParticipantCount = 1,
     humanProtein,
-    concatResults
+    concatResults = true
 ) {
   result = getReactionClassesForAnalytes(db=rampDB, analytes=analytes, multiRxnParticipantCount = multiRxnParticipantCount, humanProtein=humanProtein, concatResults=concatResults)
 
@@ -639,7 +640,7 @@ function(
 #' this method can be used to return proteins on some subset of reaction ids to find related proteins.
 #'
 #' @param reactionList Rhea reactions ids, such as rhea:38747
-#' @post /api/get_reaction_participants
+#' @post /api/get-reaction-participants
 #' @serializer json list(digits = 6)
 function(
   reactionList
@@ -663,7 +664,7 @@ function(
 #' this method can be used to return general reaction info on some subset of reaction ids of interest.
 #'
 #' @param reactionList list of reaction ids
-#' @post /api/get_reaction_details
+#' @post /api/get-reaction-details
 #' @serializer json list(digits = 6)
 function(
     reactionList

apps/ramp-server/ramp_openapi_with_extensions.yml

@@ -248,7 +248,7 @@ paths:
                   type: array
                   items:
                     type: string
-                NameOrIds:
+                namesOrIds:
                   type: string
                   enum: ['name', 'ids']
                   required: false
@@ -260,7 +260,7 @@ paths:
                     'hmdb:HMDB0000148',
                     'ensembl:ENSG00000141510',
                   ]
-                NameOrIds: 'ids'
+                namesOrIds: 'ids'
   /api/metabolites-from-ontologies:
     post:
       summary: Return metabolites from ontology
@@ -397,7 +397,7 @@ paths:
                   type: array
                   items:
                     type: string
-                NameOrIds:
+                namesOrIds:
                   type: string
                   enum: ['name', 'ids']
                   required: false

libs/features/ramp/ramp-api/src/assets/data/ramp_openapi_with_extensions.yml

@@ -248,7 +248,7 @@ paths:
                   type: array
                   items:
                     type: string
-                NameOrIds:
+                namesOrIds:
                   type: string
                   enum: ['name', 'ids']
                   required: false
@@ -260,7 +260,7 @@ paths:
                     'hmdb:HMDB0000148',
                     'ensembl:ENSG00000141510',
                   ]
-                NameOrIds: 'ids'
+                namesOrIds: 'ids'
   /api/metabolites-from-ontologies:
     post:
       summary: Return metabolites from ontology
@@ -393,11 +393,11 @@ paths:
             schema:
               type: object
               properties:
-                analyte:
+                analytes:
                   type: array
                   items:
                     type: string
-                NameOrIds:
+                namesOrIds:
                   type: string
                   enum: ['name', 'ids']
                   required: false
@@ -409,6 +409,97 @@ paths:
                     'hmdb:HMDB0000148',
                     'ensembl:ENSG00000141510',
                   ]
+  /api/reactions-from-analytes:
+    post:
+      summary: Return reactions from a given list of analytes
+      responses:
+        '200':
+          description: OK
+        '500':
+          description: Internal Server Error
+      requestBody:
+        description: Retrieve reactions from a list of analytes. IDs should be prepended by ID source (e.g. **hmdb**:C00412).
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                analytes:
+                  type: array
+                  items:
+                    type: string
+                namesOrIds:
+                  type: string
+                  enum: ['name', 'ids']
+                  required: false
+                multiRxnParticipantCount:
+                  type: number
+                  required: false
+                humanProtein:
+                  type: boolean
+                  required: false
+                concatResults:
+                  type: boolean
+                  required: false
+              example:
+                analytes:
+                  [
+                    'hmdb:HMDB0000033',
+                    'hmdb:HMDB0000052',
+                    'hmdb:HMDB0000094',
+                    'hmdb:HMDBP00789',
+                    'hmdb:HMDBP00283',
+                    'hmdb:HMDBP00284'
+                  ]
+
+  /api/reaction-classes-from-analytes:
+    post:
+      summary: Return reaction classes from a given list of analytes
+      responses:
+        '200':
+          description: OK
+        '500':
+          description: Internal Server Error
+      requestBody:
+        description: Retrieve reaction classes from a list of analytes. IDs should be prepended by ID source (e.g. **hmdb**:C00412).
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                analytes:
+                  type: array
+                  items:
+                    type: string
+                namesOrIds:
+                  type: string
+                  enum: ['name', 'ids']
+                  required: false
+                onlyHumanMets:
+                  type: boolean
+                  required: false
+                humanProtein:
+                  type: boolean
+                  required: false
+                includeTransportRxns:
+                  type: boolean
+                  required: false
+                rxnDirs:
+                  type: string
+                  enum: ['UN']
+                  required: false
+              example:
+                analytes:
+                  [
+                    'hmdb:HMDB0000033',
+                    'hmdb:HMDB0000052',
+                    'hmdb:HMDB0000094',
+                    'hmdb:HMDBP00789',
+                    'hmdb:HMDBP00283',
+                    'hmdb:HMDBP00284'
+                  ]
   /api/combined-fisher-test:
     post:
       summary: Return combined Fisher's test results from given list of analytes query results

libs/stores/ramp-store/src/lib/+state/ramp.service.ts

@@ -59,7 +59,7 @@ export class RampService {
 
   fetchSourceVersions(): Observable<SourceVersion[]> {
     return this.http
-      .get<{ data: SourceVersion[] }>(`${this.url}source_versions`) // ,{responseType: 'text'})
+      .get<{ data: SourceVersion[] }>(`${this.url}source-versions`) // ,{responseType: 'text'})
       .pipe(
         map((response) => response.data),
         catchError(this.handleError('fetchSourceVersions', [])),
@@ -68,7 +68,7 @@ export class RampService {
 
   fetchEntityCounts() {
     return this.http
-      .get<{ data: {[p: string]: string}[] }>(`${this.url}entity_counts`) // ,{responseType: 'text'})
+      .get<{ data: {[p: string]: string}[] }>(`${this.url}entity-counts`) // ,{responseType: 'text'})
       .pipe(
         map((response: { data: {[p: string]: string}[] }) =>
           response.data.map((obj: {[p: string]: string}) => new EntityCount(obj)),
@@ -92,7 +92,7 @@ export class RampService {
 
   fetchDatabaseUrl() {
     return this.http
-      .get<{ data: string }>(`${this.url}current_db_file_url`)
+      .get<{ data: string }>(`${this.url}current-db-file-url`)
       .pipe(
         map((response:{data:string}) => response.data),
       //  catchError(this.handleError('fetchAnalyteIntersects', [])),
@@ -110,7 +110,7 @@ export class RampService {
   fetchAnalyteIntersects(param: string) {
     return this.http
       .get<{ data: { id: string; sets: string[]; size: number }[]; }>(
-        `${this.url}analyte_intersects?analytetype=${param}&query_scope=global`,
+        `${this.url}analyte-intersects?analytetype=${param}&query_scope=global`,
       )
       .pipe(
         map((response: {data: { id: string; sets: string[]; size: number }[]}) => response.data),