Tcr db

.gitignore

@@ -3,11 +3,15 @@ ui/dist
 api/build
 keycloak/keycloak-db
 
-.env
+**/.env
+**/.venv
 ui/.env
 ui/.DS_Store
 api/src/cql/Code Book-Table 1.csv
 api/src/cql/Data-Table 1.csv
 zzz.tmp.csv
 
-api/src/funnel/inputs
+api/src/funnel/inputs
+neo4j
+nginx/certs
+minio

.gitmodules

@@ -2,6 +2,3 @@
 	path = api/src/neo4jgraphql
 	url = https://gitlab.com/CHILDdb/neo4jgraphql
 	branch = imic
-[submodule "imic_docs"]
-	path = imic_docs
-	url = https://github.com/mdpham/imic_docs.git

Dockerfile

@@ -9,26 +9,26 @@ WORKDIR /usr/src/app
 COPY package.json .
 COPY package-lock.json .
 COPY .npmrc .
-RUN GITLAB_AUTH_TOKEN=${GITLAB_AUTH_TOKEN} npm install --force graphql-ws
+# RUN GITLAB_AUTH_TOKEN=${GITLAB_AUTH_TOKEN} npm install --force graphql-ws
 RUN GITLAB_AUTH_TOKEN=${GITLAB_AUTH_TOKEN} npm i --force
-RUN GITLAB_AUTH_TOKEN=${GITLAB_AUTH_TOKEN} npm --force ci
+# RUN GITLAB_AUTH_TOKEN=${GITLAB_AUTH_TOKEN} npm --force ci
 
 COPY . .
 ENV NODE_ENV production
 RUN npm run build:ui
 
-WORKDIR /usr/src/app/imic_docs
-RUN npm install --force
-RUN npm run clean
-RUN npm run build
+# WORKDIR /usr/src/app/imic_docs
+# RUN npm install --force
+# RUN npm run clean
+# RUN npm run build
 
 
 
 
 FROM nginx:alpine
 WORKDIR /usr/src/app
 COPY --from=build-deps /usr/src/app/ui/dist ./dist
-COPY --from=build-deps /usr/src/app/imic_docs/public ./docs
+# COPY --from=build-deps /usr/src/app/imic_docs/public ./docs
 
 # RUN sed -i 's/https/http/' /etc/apk/repositories
 # RUN apk add bash

api/src/graphql/graphqlServer.ts

@@ -114,9 +114,9 @@ export const createApolloServer = async () => {
           if (!allowedWithoutTOS.includes(queryName))
           throw new Error(`Access denied. User [${email} / ${sub}] has not accepted the TOS. Please accept the TOS to gain access.`)
         }
-      } else {
-        throw new Error(`Access denied. Keycloak auth token required to access graphql. Please login with keycloak.`)
-      }
+      } //else {
+        //throw new Error(`Access denied. Keycloak auth token required to access graphql. Please login with keycloak.`)
+      //}
 
 
       return {

api/src/graphql/resolvers/curatedAnnotation.ts

@@ -0,0 +1,78 @@
+import { listBucketObjects, makePresignedURL } from '../../minio/minio'
+import papa from 'papaparse'
+import { ApolloError } from 'apollo-server'
+import zlib from 'zlib'
+
+
+export const resolvers = {
+  Query: {
+    countEpitopeSpecies: async (_parent, _args, { driver }) => {
+      const session = driver.session()
+      const epitopeSpeciesList = await session.run("MATCH (a:AnnotationVariable) RETURN DISTINCT a.epitopeSpecies AS e")
+      const annotationVariables = await session.run("MATCH (a:AnnotationVariable) RETURN a")
+      const results = []
+
+      const epitopeSpeciesCount = {}
+      epitopeSpeciesList.records.map((species) => {
+        epitopeSpeciesCount[species.get('e')] = 0
+      })
+
+      annotationVariables.records.forEach((variable) => {
+        const species = variable.get('a').properties['epitopeSpecies']
+        epitopeSpeciesCount[species]++
+      })
+
+      Object.keys(epitopeSpeciesCount).forEach((key) => {
+        results.push({ "epitopeSpecies": key, "count": epitopeSpeciesCount[key] })
+      })
+
+      return results
+    }
+  },
+  Mutation: {
+    createCuratedAnnotationFromRawDataset: async (parent, { name, description, rawDatasetID }, { driver, ogm, minioClient }) => {
+      try {
+        // Create model and add a curated dataset node to db
+        const CuratedAnnotationModel = ogm.model("CuratedAnnotation")
+        const bucketName = `raw-dataset-${rawDatasetID}`
+
+        const curatedAnnotationInput = {name, description, generatedByRawDataset: {connect: {where: {node: {rawDatasetID}}}}}
+        const { curatedAnnotations: [curatedAnnotation] } = await CuratedAnnotationModel.create({ input: [curatedAnnotationInput],  })
+        const { curatedAnnotationID } = curatedAnnotation
+
+        const session = driver.session()
+
+        // const bucketObjects = (await listBucketObjects(minioClient, bucketName)).map(({ name }) => name)
+        // // console.log(bucketObjects)
+        // const presignedURL = await makePresignedURL(minioClient, bucketName, bucketObjects.slice(-1)[0])
+        // // console.log(presignedURL)
+
+        // original api with datavariables containing chr,start,end,datavalue
+        const createCuratedAnnotationFromRawDataset = await session.run(
+          `CALL apoc.periodic.iterate(\'CALL apoc.load.csv($presignedURL, {sep: \"TAB\"}) YIELD list\', \'MATCH (b:CuratedAnnotation {curatedAnnotationID: $curatedAnnotationID}) CREATE (a:AnnotationVariable {annotationVariableID: apoc.create.uuid(), locus: list[0], cdr3b: list[1], trbv: list[2], trbj: list[3], mhc: list[4], mhcClass: list[5], epitope: list[6], epitopeGene: list[7], epitopeSpecies: list[8], reference: list[9] }), (b)-[:HAS_ANNOTATION_VARIABLE]->(a) RETURN a\', { batchSize:10000, iterateList: true, parallel:true, params:{curatedAnnotationID: $curatedAnnotationID, presignedURL: $presignedURL}})`,
+          {curatedAnnotationID: curatedAnnotationID, presignedURL: 'file:///VDJdb_MinimalScoreConfidence3_VersionII.tsv'}
+        )
+        // const createCuratedDatasetFromRawDataset = await session.run(
+        //   `CALL apoc.periodic.iterate(
+        //     \'CALL apoc.load.csv($presignedURL, {sep: \" \", compression: \"GZIP\", header: false}) YIELD list\',
+        //     \'MATCH (b:CuratedDataset {curatedDatasetID: $curatedDatasetID})
+        //     CREATE (a:DataVariable {dataVariableID: apoc.create.uuid()}),
+        //       (c:DataVariableField {name: \"chromosome\", value: toFloat(apoc.text.replace(list[0],\"chr\",\"\")) }),
+        //       (d:DataVariableField {name: \"start\", value: toInteger(list[1])}),
+        //       (e:DataVariableField {name: \"end\", value: toInteger(list[2])}),
+        //       (f:DataVariableField {name: \"datavalue\", value: toFloat(list[3])}),
+        //       (a)-[:HAS_FIELD]->(c), (a)-[:HAS_FIELD]->(d), (a)-[:HAS_FIELD]->(e), (a)-[:HAS_FIELD]->(f), (b)-[:HAS_DATA_VARIABLE]->(a)
+        //     RETURN a\',
+        //     {batchSize:10000, iterateList:true, parallel:true, params:{curatedDatasetID: $curatedDatasetID, presignedURL: $presignedURL}}
+        //   )`,
+        //   {curatedDatasetID: curatedDatasetID, presignedURL: presignedURL}
+        // )
+
+        return curatedAnnotation
+      } catch (error) {
+        console.log(error)
+        throw new ApolloError('curatedAnnotationFromRawDataset', error )
+      }
+    }
+  },
+}

api/src/graphql/typeDefinitions/annotationVariable.graphql

@@ -0,0 +1,20 @@
+type AnnotationVariable {
+    annotationVariableID: ID! @id
+    locus: String
+    cdr3b: String
+    trbv: String
+    trbj: String
+    mhc: String
+    mhcClass: String
+    epitope: String
+    epitopeGene: String
+    epitopeSpecies: String
+    reference: String
+    # Define fields you want to search over here, transformation script must map to this shape
+
+    # currentDefinition: DataVariableDefinition! @relationship(type: "HAS_DEFINITION", direction: OUT, properties: "HasDefinition")
+    # currentDefinition: DataVariableDefinition! @relationship(type: "HAS_DEFINITION", direction: OUT)
+    # previousDefinitions: [DataVariableDefinition!]! @relationship(type: "HAS_DEFINITION", direction: OUT)
+
+    # fields: [DataVariableField!]! @relationship(type: "HAS_FIELD", direction: OUT)
+}

api/src/graphql/typeDefinitions/curatedAnnotation.graphql

@@ -0,0 +1,62 @@
+# type Subject {
+#     subjectID: ID! @id
+#     childID: ID!
+# }
+
+
+
+# type DataVariableDefinition {
+#     dataVariable: DataVariable! @relationship(type: "HAS_DEFINITION", direction: IN)
+#     dataVariableDefinitionID: ID! @id
+#     label: String!
+# }
+
+# type DataVariableSample {
+#     dataVariableSampleID: ID! @id
+#     # value: JSON
+#     currentValueState: DataVariableSampleState! @relationship(type: "HAS_DEFINITION", direction: IN)
+#     previousValueStates: [DataVariableSampleState!]! @relationship(type: "HAS_DEFINITION", direction: IN)
+# }
+
+# # For time versioning
+# type DataVariableSampleState {
+#     value: JSON
+# }
+
+type CuratedAnnotation {
+    curatedAnnotationID: ID! @id
+    # createdAt: DateTime! @timestamp(operations: [CREATE])
+    # updatedAt: DateTime! @timestamp(operations: [UPDATE])
+    name: String!
+    description: String!
+    annotationVariables: [AnnotationVariable!]! @relationship(type: "HAS_ANNOTATION_VARIABLE", direction: OUT)
+
+    generatedByRawDataset: RawDataset! @relationship(type: "GENERATED_CURATED_ANNOTATION", direction: IN)
+}
+
+type EpitopeSpeciesCount {
+    epitopeSpecies: String!
+    count: Int!
+}
+
+type Mutation {
+    createCuratedAnnotationFromRawDataset(
+        name: String!
+        description: String!
+        rawDatasetID: ID!
+    ): CuratedAnnotation!
+}
+
+type Query {
+    countEpitopeSpecies: [EpitopeSpeciesCount]!
+}
+
+# extend type CuratedAnnotation @auth(
+#   rules: [{
+#       isAuthenticated: true,
+#       where: {AND: [
+#         {allowedStudies: "$jwt.resource_access.pibu-app.roles"},
+#         {allowedSites: "$jwt.resource_access.pibu-app.roles"},
+#         ]}
+#     }]
+# )