compose.yml

@@ -19,7 +19,6 @@ x-api: &api
     npm_config_cache: /app/.npm
     NEO4J_PORT: 7687
   env_file: *authfile
-  command: "npm start"
 
 services:
 
@@ -37,6 +36,7 @@ services:
       - "4000:4000"
     profiles:
       - prod
+    command: "npm start"
 
   api-dev:
     <<: *api
@@ -50,9 +50,11 @@ services:
       - "4000"
     ports:
       - "4000:4000"
+      - "9229:9229"
     profiles:
       - api-standalone
       - dev
+    command: "npm run debug"
   
   server-install:
     <<: *api

package.json

@@ -5,7 +5,8 @@
   "main": "server/index.js",
   "type": "module",
   "scripts": {
-    "start": "nodemon --watch './server'"
+    "start": "nodemon --watch './server'",
+    "debug": "nodemon --inspect=0.0.0.0 --watch './server'"
   },
   "license": "AGPL-version-3.0",
   "private": false,
@@ -27,19 +28,20 @@
   },
   "contributors": [],
   "dependencies": {
-    "@apollo/server": "^4.10.0",
-    "@graphql-tools/graphql-file-loader": "^8.0.1",
-    "@graphql-tools/load": "^8.0.1",
-    "@neo4j/graphql": "^5.4.4",
-    "express": "^4.18.2",
-    "graphql": "^16.8.1",
+    "@apollo/server": "^4.11.3",
+    "@graphql-tools/graphql-file-loader": "^8.0.14",
+    "@graphql-tools/load": "^8.0.14",
+    "@neo4j/graphql": "^5.11.5",
+    "@neo4j/graphql-ogm": "^5.11.5",
+    "express": "^4.21.2",
+    "graphql": "^16.10.0",
     "graphql-tag": "^2.12.6",
-    "neo4j-driver": "^5.18.0",
-    "nodemon": "^3.0.3"
+    "neo4j-driver": "^5.28.1",
+    "nodemon": "^3.1.9"
   },
   "devDependencies": {
-    "@graphql-eslint/eslint-plugin": "^3.20.1",
-    "@graphql-tools/mock": "^9.0.1",
-    "@graphql-tools/schema": "^10.0.2"
+    "@graphql-eslint/eslint-plugin": "^4.3.0",
+    "@graphql-tools/mock": "^9.0.17",
+    "@graphql-tools/schema": "^10.0.18"
   }
 }

server/resolvers.js

@@ -3,7 +3,7 @@ import { resolvers as documentsResolver } from './resolvers/documents.js'
 
 const resolvers = [
     guideClassLabelResolver,
-    documentsResolver
+    documentsResolver,
 ]
 
 export default resolvers
\ No newline at end of file

server/schema.js

@@ -13,6 +13,10 @@ import { typeDefs as genericSequenceDefs } from './schema/generic_sequence.js'
 import { typeDefs as groupDefs } from './schema/guide_group.js'
 import { typeDefs as clusterDefs } from './schema/cluster.js'
 import { typeDefs as isoformDefs } from './schema/isoform.js'
+import { typeDefs as modificationMappingDefs } from './schema/modification_mapping.js'
+import { typeDefs as trackDefs } from './schema/track.js'
+import { typeDefs as alignmentDefs } from './schema/alignment.js'
+import { typeDefs as alignedModificationsDefs } from './schema/aligned_modifications.js'
 import { typeDefs as entryDefs } from './schema/table_entry.js'
 import { typeDefs as documentsDefs } from './schema/documents.js'
 
@@ -36,6 +40,10 @@ const typeDefs = [
     groupDefs,
     clusterDefs,
     isoformDefs,
+    modificationMappingDefs,
+    alignedModificationsDefs,
+    trackDefs,
+    alignmentDefs,
     documentsDefs,
     schemaDef
 ]

server/schema/aligned_modifications.js

+import { gql } from 'graphql-tag'
+
+export const typeDefs = gql`
+"""
+A group of aligned modifications
+"""
+type AlignedModifications {
+    "The group id"
+    id: ID!
+
+    "The guides that are part of group"
+    modifications: [Modification!]! @relationship(type: "IS_PART_OF", direction: IN)
+}
+`
\ No newline at end of file

server/schema/alignment.js

+import { gql } from 'graphql-tag'
+
+export const typeDefs = gql`
+
+type Alignment {
+
+    "The alignment id"
+    id: ID!
+
+    "The name of the alignment (Optional)"
+    name: String
+
+    "The description of the alignment (Optional)"
+    description: String
+    
+    "The sequences that are part of alignment"
+    sequences: [Sequence!]!
+
+    "A track is a sequence of something (including sequences)"
+    tracks: [Track!]! @relationship(type: "ALIGN_WITH", direction: IN)
+
+    "The type of alignment, either GUIDE or TARGET"
+    type: AlignType
+}
+
+
+enum AlignType {
+
+    "Alignment is about guides"
+    GUIDE
+
+    "Alignment is about targets"
+    TARGET
+
+    "Alignment is about something else"
+    OTHER
+}
+`
\ No newline at end of file

server/schema/chromosome.js

@@ -14,6 +14,9 @@ type Chromosome implements Sequence @node(labels: ["Sequence", "Chromosome"]) {
   "ALternative chromosome names"
   altnames: [String!]
   
+  "Fasta id if any"
+  fasta_id: String
+  
   """The chromosome description (i.e. the comment part in fasta file)"""
   description: String
 
@@ -49,5 +52,8 @@ type Chromosome implements Sequence @node(labels: ["Sequence", "Chromosome"]) {
 
   "The type of GraphQL object"
   graphql_type: GraphQLType!
+
+  "Tracks the sequence is part of"
+  tracks: [Track!]! @relationship(type: "HAS_REFERENCE", direction: IN)
 }
 `
\ No newline at end of file

server/schema/generic_sequence.js

@@ -16,6 +16,9 @@ type GenericSequence implements Sequence @node(labels: ["Sequence", "GenericSequ
   
   """The sequence description (i.e. the comment part in fasta file)"""
   description: String
+  
+  "Fasta id if any"
+  fasta_id: String
 
   """The type of the sequence (DNA or RNA)"""
   type: SequenceType!
@@ -52,5 +55,8 @@ type GenericSequence implements Sequence @node(labels: ["Sequence", "GenericSequ
 
   "The parent sequence if any"
   parent: Sequence @relationship(type: "HAS_FEATURE", direction: IN, properties: "HasFeature")
+
+  "Tracks the sequence is part of"
+  tracks: [Track!]! @relationship(type: "HAS_REFERENCE", direction: IN)
 }
 `

server/schema/guide.js

@@ -13,6 +13,9 @@ type Guide implements Sequence @node(labels: ["Sequence", "Guide"]) {
 
   "Alternative guide names"
   altnames: [String!]
+  
+  "Fasta id if any"
+  fasta_id: String
 
   "Guide description"
   description: String
@@ -58,7 +61,7 @@ type Guide implements Sequence @node(labels: ["Sequence", "Guide"]) {
 
   "The type of GraphQL object"
   graphql_type: GraphQLType!
-
+  
   """The modifications guided by the guide"""
   modifications: [Modification!]! @relationship(type: "GUIDE", direction: OUT)
 
@@ -76,6 +79,9 @@ type Guide implements Sequence @node(labels: ["Sequence", "Guide"]) {
 
   "Table entries associated to the guide"
   entries: [TableEntry!]! @relationship(type: "IS_PART_OF", direction: OUT, aggregate: false) @selectable(onRead: true, onAggregate: false)
+
+  "Tracks the sequence is part of"
+  tracks: [Track!]! @relationship(type: "HAS_REFERENCE", direction: IN)
 }
 
 """
@@ -91,6 +97,9 @@ enum GuideClass {
   "ScaRNA"
   ScaRNA
 
+  "Protein"
+  PROT
+
   "Other"
   Other
 }

server/schema/modification.js

@@ -39,11 +39,15 @@ type Modification {
     "Short label of modification type formatted with markdown syntax"
     type_short_label: String
 
-    "Interactions that cause the modification"
+    "Interactions that position the modification"
     interactions: [Interaction!]! @relationship(type: "CAUSE", direction: IN)
 
     "Table entries associated to the modification"
     entries: [TableEntry!]! @relationship(type: "IS_PART_OF", direction: OUT, aggregate: false) @selectable(onRead: true, onAggregate: false)
+
+    "Aligned Modification Group"
+    align_groups: [AlignedModifications!]! @relationship(type: "IS_PART_OF", direction: OUT)
+
 }
 
 """

server/schema/modification_mapping.js

+import { gql } from 'graphql-tag'
+
+export const typeDefs = gql`
+type ModificationMapping @relationshipProperties {
+    
+    "The position corrected for the alignement"
+    position: Int!
+
+}
+`

server/schema/sequence.js

@@ -14,6 +14,9 @@ interface Sequence {
   "ALternative sequence names"
   altnames: [String!]
   
+  "Fasta id if any"
+  fasta_id: String
+
   """The sequence description (i.e. the comment part in fasta file)"""
   description: String
 
@@ -44,12 +47,12 @@ interface Sequence {
   "The reference genome the sequence comes from"
   genome: Genome @declareRelationship
 
-  #"The other genome in which the sequence exists"
-  #genomes: [Genome!] @declareRelationship
-
   "The features associated with the sequence"
   features: [Sequence!]! @declareRelationship
 
+  "Tracks the sequence is part of"
+  tracks: [Track!]! @declareRelationship
+
   "The type of GraphQL object"
   graphql_type: GraphQLType!
 }

server/schema/target.js

@@ -13,6 +13,9 @@ type Target implements Sequence @node(labels: ["Sequence", "Target"]) {
 
   "ALternative guide names"
   altnames: [String!]
+  
+  "Fasta id if any"
+  fasta_id: String
 
   "Family (e.g. 16S, 18S, U2, ...)"
   family: String
@@ -62,6 +65,9 @@ type Target implements Sequence @node(labels: ["Sequence", "Target"]) {
   "The type of GraphQL object"
   graphql_type: GraphQLType!
 
+  "True if current sequence is a reference sequence"
+  is_ref: Boolean!
+  
   "The target is a feature from parent"
   parent: Sequence @relationship(type: "HAS_FEATURE", direction: IN, properties: "HasFeature")
 
@@ -74,5 +80,7 @@ type Target implements Sequence @node(labels: ["Sequence", "Target"]) {
   "Table entries associated to the guide"
   entries: [TableEntry!]! @relationship(type: "IS_PART_OF", direction: OUT, aggregate: false) @selectable(onRead: true, onAggregate: false)
 
+  "Tracks the sequence is part of"
+  tracks: [Track!]! @relationship(type: "HAS_REFERENCE", direction: IN)
 }
 `
\ No newline at end of file

server/schema/track.js

+import { gql } from 'graphql-tag'
+
+export const typeDefs = gql`
+
+interface Track {
+    "The track ID"
+    id: ID!
+
+    "The track name"
+    name: String
+
+    "The track short name"
+    shortname: String
+
+    "The sequence"
+    content: String !
+
+    "The sequence the track is associated to"
+    ref: Sequence! @declareRelationship
+
+    "The alignment the track is part of"
+    alignment: Alignment @declareRelationship
+
+    "Other tracks associated/coupled/grouped with the current track"
+    links: [Track!]!
+}
+
+
+"""
+Tracks encoding the RNA sequence adjusted to alignment by including some aditional '-' and correcting the modification position
+"""
+type SequenceTrack implements Track {
+    
+    "The track ID"
+    id: ID!
+    
+    "The track name"
+    name: String
+
+    "The track short name"
+    shortname: String
+
+    "The sequence"
+    content: String !
+
+    "The sequence the track is associated to"
+    ref: Sequence! @relationship(type: "HAS_REFERENCE", direction: OUT)
+    
+    "The alignment the track is part of"
+    alignment: Alignment @relationship(type: "ALIGN_WITH", direction: OUT)
+
+    "Other tracks associated/coupled/grouped with the current track"
+    links: [Track!]!
+
+    "The modifications which position are adjusted to current Alignement"
+    aligned_modifications: [Modification!]! @relationship(type: "HAS_ALIGNED_MODIFICATION", direction: OUT, properties: "ModificationMapping")
+}
+
+"""
+Tracks encoding the structure of the RNA sequence with parenthesis and dots chars
+"""
+type StructureTrack implements Track {
+    
+    "The track ID"
+    id: ID!
+
+    "The track name"
+    name: String
+
+    "The track short name"
+    shortname: String
+
+    "The sequence"
+    content: String !
+
+    "The sequence the track is associated to"
+    ref: Sequence! @relationship(type: "HAS_REFERENCE", direction: OUT)
+
+    "The alignment the track is part of"
+    alignment: Alignment @relationship(type: "ALIGN_WITH", direction: OUT)
+    
+    "Other tracks associated with the current track"
+    links: [Track!]!
+}
+`