Develop

.github/workflows/deploy.yml

@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set environment based on branch
         run: |
@@ -35,7 +35,7 @@ jobs:
           fi
 
       - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
+        uses: aws-actions/configure-aws-credentials@v5
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

.gitignore

@@ -114,3 +114,4 @@ build_deploy.sh
 output.txt
 
 .yarn/
+tasks/

app.js

@@ -38,16 +38,14 @@ const limiter = rateLimiter({
 app.engine('html', require('ejs').renderFile);
 
 const {optionalAuth} = require('./v2.0/helpers/validation/sessionauth');
-const allowedOrigins = env === 'production'
-  ? ['https://data.neotomadb.org', 'https://apps.neotomadb.org']
-  : [ 'http://localhost:5173', 'http://127.0.0.1:5173',
-      'http://localhost:3305', 'http://127.0.0.1:3305'
-    ];
+const allowedOrigins = ['https://data.neotomadb.org', 'https://apps.neotomadb.org'];
+const localhostRe = /^https?:\/\/(localhost|127\.0\.0\.1)(:\d+)?$/;
 
 const corsOptions = {
   origin: function(origin, callback) {
     if (!origin) return callback(null, true); // server-to-server, curl, R package
     if (allowedOrigins.includes(origin)) return callback(null, true);
+    if (env !== 'production' && localhostRe.test(origin)) return callback(null, true);
     return callback(new Error(`CORS: origin ${origin} not allowed`));
   },
   credentials: true,

openapi.yaml

@@ -3125,6 +3125,43 @@ paths:
       tags:
         - Contact metadata
         - v2.0
+  /v2.0/data/contacts/{contactid}/publications:
+    get:
+      description: Returns publications authored by a specific contact.
+      parameters:
+        - $ref: '#/components/parameters/contactidPath'
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  status:
+                    type: string
+                    example: success
+                  data:
+                    type: array
+                    items:
+                      type: object
+                      properties:
+                        publicationid:
+                          type: integer
+                        citation:
+                          type: string
+                        year:
+                          type: integer
+                        doi:
+                          type: string
+                          nullable: true
+                  message:
+                    type: string
+          description: An array of publications associated with the contact.
+      summary: Publications by a contact.
+      tags:
+        - Contact metadata
+        - Publication metadata
+        - v2.0
   /v2.0/data/contacts/{contactid}/sites:
     get:
       description: Returns the set of sites associated with an individual (or individuals).
@@ -3946,6 +3983,111 @@ paths:
       tags:
         - Occurrence metadata
         - v2.0
+  /v2.0/data/aedna/sequences/{datasetid}:
+    get:
+      description: >-
+        Returns aeDNA sequences for a given dataset, grouped by taxon. Includes the taxonomic hierarchy chain, model
+        information, primer name, and publication DOI. Only returns the most recent (non-superseded) model assignments.
+      parameters:
+        - $ref: '#/components/parameters/datasetidPath'
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  status:
+                    type: string
+                    example: success
+                  data:
+                    type: object
+                    properties:
+                      datasetid:
+                        type: integer
+                      sequences:
+                        type: array
+                        items:
+                          type: object
+                          properties:
+                            taxonid:
+                              type: integer
+                            taxonname:
+                              type: string
+                            taxonchain:
+                              type: array
+                              items:
+                                type: string
+                              description: Taxonomic hierarchy from highest rank to the taxon itself.
+                            sequences:
+                              type: array
+                              items:
+                                type: object
+                                properties:
+                                  sequenceid:
+                                    type: integer
+                                  sequence:
+                                    type: string
+                                    description: The DNA sequence string.
+                                  model:
+                                    type: string
+                                    description: The bioinformatics model used for taxonomic assignment (e.g. DADA2).
+                                  primername:
+                                    type: string
+                                    nullable: true
+                                  publicationdoi:
+                                    type: string
+                                    nullable: true
+                  message:
+                    type: string
+          description: aeDNA sequences grouped by taxon for the dataset.
+      summary: aeDNA sequences for a dataset.
+      tags:
+        - aeDNA
+        - v2.0
+  /v2.0/data/aedna/taxa/{taxonid}/sequences:
+    get:
+      description: >-
+        Returns all aeDNA sequences associated with a given taxon. Only returns the most recent (non-superseded) model
+        assignments.
+      parameters:
+        - $ref: '#/components/parameters/taxonidPath'
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  status:
+                    type: string
+                    example: success
+                  data:
+                    type: array
+                    items:
+                      type: object
+                      properties:
+                        sequenceid:
+                          type: integer
+                        sequence:
+                          type: string
+                          description: The DNA sequence string.
+                        model:
+                          type: string
+                          description: The bioinformatics model used for taxonomic assignment.
+                        primername:
+                          type: string
+                          nullable: true
+                        publicationdoi:
+                          type: string
+                          nullable: true
+                  message:
+                    type: string
+          description: An array of aeDNA sequences for the taxon.
+      summary: aeDNA sequences for a taxon.
+      tags:
+        - aeDNA
+        - v2.0
 tags:
   - description: |-
       Endpoints that access tables from Neotoma verbatim. Documentation for the database can be found in 

openapi/paths/v20/data.yml

@@ -113,6 +113,43 @@
     tags:
       - Contact metadata
       - v2.0
+/v2.0/data/contacts/{contactid}/publications:
+  get:
+    description: Returns publications authored by a specific contact.
+    parameters:
+      - $ref: '#/components/parameters/contactidPath'
+    responses:
+      '200':
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                status:
+                  type: string
+                  example: success
+                data:
+                  type: array
+                  items:
+                    type: object
+                    properties:
+                      publicationid:
+                        type: integer
+                      citation:
+                        type: string
+                      year:
+                        type: integer
+                      doi:
+                        type: string
+                        nullable: true
+                message:
+                  type: string
+        description: An array of publications associated with the contact.
+    summary: Publications by a contact.
+    tags:
+      - Contact metadata
+      - Publication metadata
+      - v2.0
 /v2.0/data/contacts/{contactid}/sites:
   get:
     description: Returns the set of sites associated with an individual (or individuals).
@@ -949,3 +986,104 @@
     tags:
       - Occurrence metadata
       - v2.0
+/v2.0/data/aedna/sequences/{datasetid}:
+  get:
+    description: Returns aeDNA sequences for a given dataset, grouped by taxon. Includes the taxonomic hierarchy chain, model information, primer name, and publication DOI. Only returns the most recent (non-superseded) model assignments.
+    parameters:
+      - $ref: '#/components/parameters/datasetidPath'
+    responses:
+      '200':
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                status:
+                  type: string
+                  example: success
+                data:
+                  type: object
+                  properties:
+                    datasetid:
+                      type: integer
+                    sequences:
+                      type: array
+                      items:
+                        type: object
+                        properties:
+                          taxonid:
+                            type: integer
+                          taxonname:
+                            type: string
+                          taxonchain:
+                            type: array
+                            items:
+                              type: string
+                            description: Taxonomic hierarchy from highest rank to the taxon itself.
+                          sequences:
+                            type: array
+                            items:
+                              type: object
+                              properties:
+                                sequenceid:
+                                  type: integer
+                                sequence:
+                                  type: string
+                                  description: The DNA sequence string.
+                                model:
+                                  type: string
+                                  description: The bioinformatics model used for taxonomic assignment (e.g. DADA2).
+                                primername:
+                                  type: string
+                                  nullable: true
+                                publicationdoi:
+                                  type: string
+                                  nullable: true
+                message:
+                  type: string
+        description: aeDNA sequences grouped by taxon for the dataset.
+    summary: aeDNA sequences for a dataset.
+    tags:
+      - aeDNA
+      - v2.0
+/v2.0/data/aedna/taxa/{taxonid}/sequences:
+  get:
+    description: Returns all aeDNA sequences associated with a given taxon. Only returns the most recent (non-superseded) model assignments.
+    parameters:
+      - $ref: '#/components/parameters/taxonidPath'
+    responses:
+      '200':
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                status:
+                  type: string
+                  example: success
+                data:
+                  type: array
+                  items:
+                    type: object
+                    properties:
+                      sequenceid:
+                        type: integer
+                      sequence:
+                        type: string
+                        description: The DNA sequence string.
+                      model:
+                        type: string
+                        description: The bioinformatics model used for taxonomic assignment.
+                      primername:
+                        type: string
+                        nullable: true
+                      publicationdoi:
+                        type: string
+                        nullable: true
+                message:
+                  type: string
+        description: An array of aeDNA sequences for the taxon.
+    summary: aeDNA sequences for a taxon.
+    tags:
+      - aeDNA
+      - v2.0