Merge pull request #3 from pughlab/form-generator-schema-refactor

Form generator schema refactor

api/src/graphql/resolvers/form.ts

@@ -105,6 +105,36 @@ export const resolvers = {
         throw new ApolloError('value');
       }
     }
-  })
+  }),
+  Mutation: {
+    findOrCreatePatient: async (_obj, args, { driver }) => {
+      const { patient_id, program_id, study } = args
+      const session = driver.session()
+
+      try {
+        let command = study 
+          ? "MATCH (p:Patient { patient_id: $patient_id, program_id: $program_id, study: $study }) RETURN p"
+          : "MATCH (p:Patient { patient_id: $patient_id, program_id: $program_id }) RETURN p"
+        const result = await session.run(command, study ? { patient_id, program_id, study } : { patient_id, program_id })
+
+        if (result.records.length > 0 ) {
+          return result.records[0].get('p').properties
+        }
+
+        command = study
+          ? "CREATE (p:Patient { patient_id: $patient_id, program_id: $program_id, study: $study }) return p"
+          : "CREATE (p:Patient { patient_id: $patient_id, program_id: $program_id }) return p"
+        const createPatient = await session.run(
+          command,
+          study ? { patient_id, program_id, study } : { patient_id, program_id }
+        )
 
+        return createPatient.records[0].get(0).properties
+      } catch (error) {
+        throw new Error(`Could not find or create Patient. Caused by ${error}`)
+      } finally {
+        session.close()
+      }
+    }
+  }
 };

api/src/graphql/resolvers/keycloak.ts

@@ -32,31 +32,31 @@ export const resolvers = {
         throw new ApolloError('mutation.me error')
       }
     },
-    assignKeycloakUserToSubmitter: async (obj, { submitterID }, { driver, kauth }, resolveInfo) => {
+    assignKeycloakUserToSubmission: async (_obj, { submissionID }, { driver, kauth }) => {
+      const session = driver.session()
       try {
-        const { sub: keycloakUserID, email, name, ...kcAuth } = kauth.accessToken.content
+        const { sub: keycloakUserID, email, name }  = kauth.accessToken.content
         const keycloakUser = { keycloakUserID, email, name }
 
-        const session = driver.session()
         const existingUser = await session.run(
           'MATCH (a:KeycloakUser {keycloakUserID: $keycloakUserID}) RETURN a',
           { keycloakUserID }
         )
-        // console.log('match result', existingUser)
-        if (existingUser.records.length) {
-          const createConnectionToSubmitter = await session.run(
-            'MATCH (s:Submitter {uuid: $submitterID}), (k:KeycloakUser {keycloakUserID: $keycloakUserID}) MERGE (s)-[:SUBMITTED_BY]->(k) RETURN s, k',
-            { submitterID, keycloakUserID }
+
+        if (existingUser.records.length > 0) {
+          await session.run(
+            "MATCH (s:Submission {submission_id: $submissionID}), (k:KeycloakUser {keycloakUserID: $keycloakUserID}) MERGE (s)-[:SUBMITTED_BY]->(k) RETURN s, k",
+            { submissionID, keycloakUserID }
           )
-      
+
           return keycloakUser
         } else {
-          // console.log('existing user props', existingUser.records[0].get(0).properties)
-          throw new ApolloError('mutation.missing user error')
+          throw new ApolloError('Error: The user does not exist')
         }
-
       } catch (error) {
-        throw new ApolloError('mutation.me error')
+        throw new Error(`Could not assign the user data to the submission. Caused by: ${error}`)
+      } finally {
+        session.close()
       }
     }
   },

api/src/graphql/typeDefinitions/form.graphql

@@ -17,18 +17,19 @@
     value : FormValue!
   }
 
-  type Submitter{
-    """
-    
-    """
-    uuid                               : String!
-    form                               : String!
-    formPrimaryIdentifierKeys          : Parser
-    fields                             : [FieldKeyValuePair!]! @relationship(type : "HAS_FIELD_VALUE", direction : OUT)
-    formReferenceKeys                  : [Submitter!]! @relationship(type : "REFERENCE_PRIMARY_KEY", direction : OUT)
-    connectedFormsReferencingSubmitter : [Submitter!]! @relationship(type : "REFERENCE_PRIMARY_KEY", direction : IN)
-
-    submittedByKeycloakUser            : KeycloakUser! @relationship(type : "SUBMITTED_BY", direction : OUT) 
+  type Patient {
+    patient_id: String!
+    program_id: String!
+    study: String
+    submissions: [Submission] @relationship(type: "DATA_FOR", direction: IN)
+  }
+
+  type Submission {
+    submission_id: ID! @id
+    form_id: String!
+    patient: Patient! @relationship(type: "DATA_FOR", direction: OUT)
+    fields: [FieldKeyValuePair!]! @relationship(type: "HAS_VALUE", direction: OUT)
+    submittedBy: KeycloakUser! @relationship(type: "SUBMITTED_BY", direction: OUT)
   }
 
   type FormDraft {
@@ -41,6 +42,7 @@
     patient_id: String!
     secondary_ids: String # Secondary IDs are fields that are unique to a form, but are not part of the patient's data
     data: String
+    createdBy: KeycloakUser @relationship(type: "CREATED_BY", direction: OUT) 
   }
 
   type Form {
@@ -50,14 +52,12 @@
     form_id                       : String
     form_name                     : String
     form_relationship_cardinality : FormValue
-    has_next_question             : Field @relationship(type : "HAS_NEXT_QUESTION", direction : OUT)
-    next_form                     : [Form!]!  @relationship(type : "NEXT_FORM", direction : OUT)
-    primary_key                   : [Field!]! @relationship(type : "HAS_PRIMARY_KEY", direction : OUT)
-    foreign_key                   : [Field!]! @relationship(type : "HAS_FOREIGN_KEY", properties : "reference", direction : OUT)
-    identifier                    : [Field!]! @cypher(statement: """ MATCH (f:Form)-[:HAS_PRIMARY_KEY]->(pk)
-                                                         WHERE NOT ()-[:NEXT_FORM]->(f)
-                                                         RETURN pk 
-                                                     """ )
+    next_form: [Form!]!  @relationship(type : "NEXT_FORM", direction : OUT, properties: "Studies")
+    display_name: Parser
+    fields: [Field!] @relationship(type: "BELONGS_TO", direction: IN, properties: "IsID")
+    has_next_question: [Field] @relationship(type : "HAS_NEXT_QUESTION", direction : OUT)
+    studies: [String]
+    branch_fields: [String]
   }
 
   type Field {
@@ -72,36 +72,52 @@
     regex             : String
     value             : FormValue
     set               : SampleSet
-    required          : Boolean
+    required          : FormValue
     component         : String
     conditionals      : Parser
     placeholder       : String
     filter            : Parser
-    has_next_question : Field @relationship(type : "HAS_NEXT_QUESTION", direction : OUT)
-    foreign_key_to    : [Form!]! @relationship(type : "HAS_FOREIGN_KEY",  direction : IN)
-    primaryFormIdentifiers    : Form @relationship(type : "HAS_PRIMARY_KEY", direction : IN)
+    info: String
+    display_name: Parser
+    studies: [String]
+    has_next_question: Field @relationship(type : "HAS_NEXT_QUESTION", direction : OUT)
+    belongs_to(isID: Boolean): Form! @relationship(type: "BELONGS_TO", direction: OUT)
   }
 
-  interface reference @relationshipProperties {
-    """
-    reference relation holds extra information to inter connection
-    Override: switches any metadata value within the field its connected to 
-    [EX: a reference key might not be required witin the current form but is set to required]
-    
-    relationship_cardinality : holds the how many time the referencekey can be allocated to another submitter
-    EX : Radiation has a relationship cardinality of 1 towards Treatment meaning that per each Treatment generated
-    we can only refernce the primary identifiers once
-    """
-    relationship_cardinality : FormValue
-    override                 : Parser
+  interface IsID @relationshipProperties {
+    isID: Boolean!
+    override: Parser
+  }
+
+  interface Studies @relationshipProperties {
+    studies: [String]
   }
 
 
   type Query {
 
-    PopulateForm(id : String!) : [Field]
+    GetFormFields(id: String!, study: String) : [Field]
     @cypher( statement: """ 
-    MATCH (:Form {form_id : $id})-[:HAS_NEXT_QUESTION*]->(f:Field) RETURN f
+    MATCH (:Form {form_id : $id})-[:HAS_NEXT_QUESTION*]->(f:Field)
+    WHERE single(x in f.studies WHERE x = $study)
+    RETURN f
     """)
+    GetRootForm(study: String!): Form @cypher(statement: """
+    MATCH (f:Form)
+    WHERE NOT ()-[:NEXT_FORM]->(f)
+    AND single(x IN f.studies WHERE x = $study)
+    RETURN f
+    """)
+    GetPatientID: [Field!]! @cypher(statement:"""
+    MATCH (f:Form)
+    WHERE NOT ()-[:NEXT_FORM]->(f)
+    WITH f
+    MATCH (n:Field)-[r:BELONGS_TO]->(f)
+    WHERE r.isID = true
+    RETURN n
+    """)
+  }
 
+  type Mutation {
+    findOrCreatePatient(patient_id: String!, program_id: String!, study: String): Patient
   }

api/src/graphql/typeDefinitions/keycloak.graphql

@@ -8,5 +8,6 @@ type KeycloakUser @exclude {
 
 type Mutation {
     me: KeycloakUser @auth
-    assignKeycloakUserToSubmitter(submitterID: ID!): KeycloakUser @auth
+    assignKeycloakUserToSubmission(submissionID: ID!): KeycloakUser @auth
+    assignKeycloakUserToDraft(draftID: ID!): KeycloakUser @auth
 }

ui/src/components/Portal.tsx

@@ -1,4 +1,4 @@
-import React, { useState } from "react";
+import React, { useState, createContext } from "react";
 import { Sticky, Menu, Divider, Label, Popup, Header, Icon } from 'semantic-ui-react'
 import useKeycloakMeMutation from '../hooks/useKeycloakMeMutation'
 import dayjs from 'dayjs'
@@ -13,6 +13,10 @@ import PortalNavBarIntro, {HOME_MENU_ELEMENT_ID} from './intros/PortalNavBarIntr
 import FormFactory  from './layout/FormFactory';
 import PatientSearchForm from './layout/PatientSearchForm'
 
+export const PatientIdentifierContext = createContext({})
+export const ActiveSubmissionContext = createContext({})
+export const PatientFoundContext = createContext({})
+
 const DocsLink = () => {
   return (
   <>
@@ -36,7 +40,9 @@ export default function Portal () {
   const {navigate, location, isActivePathElement} = useRouter()
   const [meMutationState] = useKeycloakMeMutation()
 
-  const [patientIdentifier, setPatientIdentifier] = useState({submitter_donor_id: '', program_id: ''})
+  const [patientIdentifier, setPatientIdentifier] = useState({submitter_donor_id: '', program_id: '', study: ''})
+  const [activeSubmission, setActiveSubmission] = useState({})
+  const [patientFound, setPatientFound] = useState(false)
 
   const routes = [
     {path: '/', icon: 'info circle', introID: HOME_MENU_ELEMENT_ID},
@@ -71,12 +77,17 @@ export default function Portal () {
     </Sticky>
 
     <Divider horizontal />
-    <div style={{padding: '1em'}}>
-      <PatientSearchForm patientIdentifier={patientIdentifier} setPatientIdentifier={setPatientIdentifier}/>
-      <Divider horizontal />
-
-      <FormFactory patientIdentifier={patientIdentifier} setPatientIdentifier={setPatientIdentifier}/>
-    </div>
+      <PatientIdentifierContext.Provider value={{patientIdentifier, setPatientIdentifier }}>
+        <ActiveSubmissionContext.Provider value={{activeSubmission, setActiveSubmission}}>
+          <PatientFoundContext.Provider value={{patientFound, setPatientFound}}>
+            <div style={{padding: '1em'}}>
+              <PatientSearchForm />
+              <Divider horizontal />
+              <FormFactory />
+            </div>
+          </PatientFoundContext.Provider>
+        </ActiveSubmissionContext.Provider>
+      </PatientIdentifierContext.Provider>
     </>
   )
 }