MIDRC-901 Add S3 endpoint (#30)

.secrets.baseline

@@ -145,13 +145,31 @@
         "line_number": 64
       }
     ],
+    "docs/local_installation.md": [
+      {
+        "type": "Secret Keyword",
+        "filename": "docs/local_installation.md",
+        "hashed_secret": "08d2e98e6754af941484848930ccbaddfefe13d6",
+        "is_verified": false,
+        "line_number": 94
+      }
+    ],
+    "docs/s3.md": [
+      {
+        "type": "Secret Keyword",
+        "filename": "docs/s3.md",
+        "hashed_secret": "08d2e98e6754af941484848930ccbaddfefe13d6",
+        "is_verified": false,
+        "line_number": 56
+      }
+    ],
     "gen3workflow/config-default.yaml": [
       {
         "type": "Secret Keyword",
         "filename": "gen3workflow/config-default.yaml",
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_verified": false,
-        "line_number": 27
+        "line_number": 32
       }
     ],
     "migrations/versions/e1886270d9d2_create_system_key_table.py": [
@@ -169,7 +187,7 @@
         "filename": "tests/conftest.py",
         "hashed_secret": "0dd78d9147bb410f0cb0199c5037da36594f77d8",
         "is_verified": false,
-        "line_number": 188
+        "line_number": 222
       }
     ],
     "tests/migrations/test_migration_e1886270d9d2.py": [
@@ -180,7 +198,16 @@
         "is_verified": false,
         "line_number": 24
       }
+    ],
+    "tests/test-gen3workflow-config.yaml": [
+      {
+        "type": "Secret Keyword",
+        "filename": "tests/test-gen3workflow-config.yaml",
+        "hashed_secret": "900a7331f7bf83bff0e1b2c77f471b4a5145da0f",
+        "is_verified": false,
+        "line_number": 5
+      }
     ]
   },
-  "generated_at": "2024-11-19T19:43:31Z"
+  "generated_at": "2024-12-12T23:42:54Z"
 }

README.md

@@ -13,3 +13,4 @@ The documentation can be browsed in the [docs](docs) folder, and key documents a
 * [Detailed API Documentation](http://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/gen3-workflow/master/docs/openapi.yaml)
 * [Local installation](docs/local_installation.md)
 * [Authorization](docs/authorization.md)
+* [S3 interaction](docs/s3.md)

docs/local_installation.md

@@ -75,7 +75,8 @@ Try out the API at <http://localhost:8080/_status> or <http://localhost:8080/doc
 
 ## Run Nextflow workflows with Gen3Workflow
 
-Example Nextflow configuration:
+- Hit the `/storage/info` endpoint to get your working directory
+- Configure Nextflow. Example Nextflow configuration:
 ```
 plugins {
 	id 'nf-ga4gh'
@@ -85,15 +86,33 @@ process {
 	container = 'quay.io/nextflow/bash'
 }
 tes {
-	endpoint = 'http://localhost:8080/ga4gh/tes'
+	endpoint = '<Gen3Workflow URL>/ga4gh/tes'
+	oauthToken = "${GEN3_TOKEN}"
 }
+aws {
+	accessKey = "${GEN3_TOKEN}"
+	secretKey = 'N/A'
+	region = 'us-east-1'
+	client {
+		s3PathStyleAccess = true
+		endpoint = '<Gen3Workflow URL>/s3'
+	}
+}
+workDir = '<your working directory>'
 ```
-> `http://localhost:8080` is where Gen3Workflow runs by default when started with `python run.py`.
+> The Gen3Workflow URL should be set to `http://localhost:8080` in this case; this is where the service runs by default when started with `python run.py`.
+
+- Run a workflow:
 
-Run a workflow:
+When setting your token manually:
 ```
+export GEN3_TOKEN=<your token>
 nextflow run hello
 ```
+Or, with the [Gen3 Python SDK](https://github.com/uc-cdis/gen3sdk-python) configured with an API key:
+```
+gen3 run nextflow run hello
+```
 
 ## AWS access