Fix/rosettafold (#96)

.github/workflows/rosettafold-master.yaml

@@ -0,0 +1,29 @@
+name: rosettafold-master
+run-name: rosettafold-master
+
+# Build and push nolabs image using GitHub Cache API
+# Only if relevant files were changed
+
+on: workflow_dispatch
+
+jobs:
+  build:
+    permissions:
+      contents: read
+      packages: write
+
+    uses: ./.github/workflows/build-docker.yaml
+    with:
+      microservice_name: "rosettafold"
+
+  push:
+    if: github.repository == 'BasedLabs/NoLabs'
+    needs: build
+
+    permissions:
+      contents: read
+      packages: write
+
+    uses: ./.github/workflows/push-docker.yaml
+    with:
+      microservice_name: "rosettafold"

.github/workflows/rosettafold-pr.yaml

@@ -0,0 +1,22 @@
+name: rosettafold-pr
+run-name: rosettafold-pr
+
+# Build and push nolabs image using GitHub Cache API
+# Only if relevant files were changed
+
+on:
+  pull_request:
+    branches:
+      - master
+    paths:
+      - 'microservices/rosettafold/**'
+
+jobs:
+  build:
+    permissions:
+      contents: read
+      packages: write
+
+    uses: ./.github/workflows/build-docker.yaml
+    with:
+      microservice_name: "rosettafold"

README.md

@@ -314,7 +314,7 @@ Model: [RoseTTAFold](https://github.com/RosettaCommons/RoseTTAFold)
 docker compose up rosettafold
 ```
 
-Swagger UI will be available on http://localhost:5738/docs
+Swagger UI will be available on http://localhost:5737/docs
 
 or
 [Install as python package](microservices/rosettafold/client/README.md)

compose.yaml

@@ -117,6 +117,13 @@ services:
       context: microservices/p2rank
       dockerfile: build/Dockerfile
     command: --host=0.0.0.0 --port=5731
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: 1
+              capabilities: [ gpu ]
   msa_light:
     image: 'ghcr.io/basedlabs/msa-light:1.0.0'
     network_mode: host
@@ -142,7 +149,7 @@ services:
       - TAVILY_API_KEY=${TAVILY_API_KEY}
     command: --host=0.0.0.0 --port=5738
   rosettafold:
-    image: 'ghcr.io/basedlabs/rosettafold:1.0.0'
+    image: 'ghcr.io/basedlabs/rosettafold:1.0.1'
     network_mode: host
     build:
       context: microservices/rosettafold
@@ -151,14 +158,28 @@ services:
       - /media/jt/Local Disk/RoseTTAFold/bfd:/RoseTTAFold/bfd
       - /media/jt/Local Disk/RoseTTAFold/pdb100_2021Mar03:/RoseTTAFold/pdb100_2021Mar03
       - /media/jt/Local Disk/RoseTTAFold/UniRef30_2020_06:/RoseTTAFold/UniRef30_2020_06
-    command: --host=0.0.0.0 --port=5738
+    command: --host=0.0.0.0 --port=5737
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: 1
+              capabilities: [ gpu ]
   reinvent:
     image: 'ghcr.io/basedlabs/reinvent:1.0.1'
     network_mode: host
     build:
       context: microservices/reinvent
       dockerfile: build/Dockerfile
     command: --host=0.0.0.0 --port=5790
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: 1
+              capabilities: [ gpu ]
   blast_query:
     image: 'ghcr.io/basedlabs/blast_query:1.0.0'
     network_mode: host
@@ -167,7 +188,7 @@ services:
       dockerfile: build/Dockerfile
     command: --host=0.0.0.0 --port=5740 --workers=1
   nolabs:
-    image: 'ghcr.io/basedlabs/nolabs:2.1.7'
+    image: 'ghcr.io/basedlabs/nolabs:2.1.8'
     network_mode: host
     build:
       context: .

microservices/rosettafold/microservice/services.py

@@ -84,7 +84,10 @@ async def _run_rosettafold(self, fasta: bytes, a3m: bytes) -> RunRosettaFoldResp
             msa_file.write_bytes(a3m)
             script = f'./run_RF2_msa.sh {msa_file.full_path} {os.path.join(models_dir.full_path, 'model')}'
         else:
-            self._root.add_file(self._fasta_file_name).write_bytes(fasta)
+            sequence = fasta.decode()
+            if '>' not in sequence:
+                sequence = f'>sequence\n{sequence}'
+            self._root.add_file(self._fasta_file_name).write_bytes(sequence.encode())
             runner = self._root.files.first_or_default(lambda o: o.name == 'run_RF2.sh')
             script = f'CPU={cpu_count} MEM={gb} ./{runner.name} {self._fasta_file_name} -o {self._fasta_name}'
 

nolabs/application/use_cases/folding/use_cases.py

@@ -5,6 +5,7 @@
     'GetJobStatusFeature'
 ]
 
+import tempfile
 from typing import List, Tuple, Optional
 from uuid import UUID
 
@@ -220,11 +221,13 @@ def request_factory(self, job_id: JobId, sequence: str, folding_backend: Folding
             return (response.pdb_content, [])
 
         if folding_backend == FoldingBackendEnum.rosettafold:
-            response = self._rosettafold.run_folding_run_folding_post(
-                job_id=job_id.value,
-                fasta=sequence,
-                _request_timeout=(1000.0, 1000.0)
-            )
-            return (response.pdb_content.anyof_schema_1_validator, response.errors)
+            with tempfile.NamedTemporaryFile(mode="w+t", delete=False) as temp_file:
+                temp_file.write(sequence)
+                temp_file.close()
+                response = self._rosettafold.run_folding_run_folding_post(
+                    fasta=temp_file.name,
+                    _request_timeout=(1000.0, 1000.0)
+                )
+                return (response.pdb_content.anyof_schema_1_validator, response.errors)
 
         raise NoLabsException(ErrorCodes.folding_method_unknown, [str(folding_backend)])

nolabs/infrastructure/appsettings.dev.json

@@ -22,7 +22,7 @@
     "microservice": "http://127.0.0.1:5733"
   },
   "rosettafold": {
-    "microservice": "http://127.0.0.1:5736"
+    "microservice": "http://127.0.0.1:5737"
   },
   "solubility": {
     "microservice": "http://127.0.0.1:5786"

nolabs/infrastructure/appsettings.local.json

@@ -22,7 +22,7 @@
     "microservice": "http://127.0.0.1:5733"
   },
   "rosettafold": {
-    "microservice": "http://127.0.0.1:5736"
+    "microservice": "http://127.0.0.1:5737"
   },
   "solubility": {
     "microservice": "http://127.0.0.1:5786"