Deploy Nextflow and WDL workflows to Seven Bridges platforms

Deploy Nextflow and WDL workflows to Seven Bridges platforms

.github/workflows/tests.yml

@@ -41,6 +41,7 @@ jobs:
         pip install -r test-requirements.txt
         pip install pipx
         pipx install cwltool>=3.0
+        pip uninstall -y pytest-workflow
         pipx ensurepath
     # Need a new shell so that ensurepath takes
     - name: Test with pytest

requirements.txt

@@ -1,4 +1,5 @@
 ruamel.yaml >= 0.16
 sevenbridges-python >= 2.0
+nf-core==2.1
 cwlformat
 packaging

sbpack/noncwl/Readme.md

@@ -0,0 +1,110 @@
+# sbpack_wdl
+Developed to support WDL workflows on Seven Bridges Platform. 
+This command enables users to create and upload WDL workflows
+to the Platform.
+
+### Usage
+```
+$ sbpack_wdl -h
+
+usage: sbpack_wdl [-h] [--profile PROFILE] --appid APPID --entrypoint ENTRYPOINT --workflow-path WORKFLOW_PATH [--sb-package-id SB_PACKAGE_ID] [--womtool-input WOMTOOL_INPUT]
+                  [--sb-inputs SB_INPUTS] [--sb-outputs SB_OUTPUTS] [--sb-doc SB_DOC] [--dump-sb-app] [--no-package] [--womtool-path WOMTOOL_PATH] [--json] [--sb-schema SB_SCHEMA]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --profile PROFILE     SB platform profile as set in the SB API credentials file.
+  --appid APPID         Takes the form {user or division}/{project}/{app_id}.
+  --entrypoint ENTRYPOINT
+                        Relative path to the workflow from the main workflow directory
+  --workflow-path WORKFLOW_PATH
+                        Path to the main workflow directory
+  --sb-package-id SB_PACKAGE_ID
+                        Id of an already uploaded package
+  --womtool-input WOMTOOL_INPUT
+                        Path to inputs .JSON generated by womtool
+  --sb-inputs SB_INPUTS
+                        Path to pre built sb app inputs schema
+  --sb-outputs SB_OUTPUTS
+                        Path to pre build sb app outputs schema
+  --sb-doc SB_DOC       Path to a doc file for sb app. If not provided, README.md will be used if available
+  --dump-sb-app         Dump created sb app to file if true and exit
+  --no-package          Only provide a sb app schema and a git URL for entrypoint
+  --womtool-path WOMTOOL_PATH
+                        Path to womtool-X.jar
+  --json                Dump sb app schema in JSON format (YAML by default)
+  --sb-schema SB_SCHEMA
+                        Do not create new schema, use this schema file. It is sb_wdl_schema in JSON or YAML format.
+```
+
+### Example
+
+```
+$ sbpack_wdl --profile default --workflow-path /path/to/workflow_dir 
+--appid user/project/app --entrypoint workflow.wdl 
+--womtool-path /path/to/womtool-X.jar
+```
+
+# sbpack_nf
+Developed to support Nextflow workflows on Seven Bridges Platform. 
+This command enables users to create and upload Nextflow workflows
+to the Platform.
+
+### Usage
+```
+$ sbpack_nf -h
+
+usage: sbpack_nf [-h] [--profile PROFILE] --appid APPID --entrypoint ENTRYPOINT --workflow-path WORKFLOW_PATH [--sb-package-id SB_PACKAGE_ID] [--sb-inputs SB_INPUTS] [--sb-outputs SB_OUTPUTS]
+                 [--sb-doc SB_DOC] [--dump-sb-app] [--no-package] [--json] [--sb-schema SB_SCHEMA]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --profile PROFILE     SB platform profile as set in the SB API credentials file.
+  --appid APPID         Takes the form {user or division}/{project}/{app_id}.
+  --entrypoint ENTRYPOINT
+                        Relative path to the workflow from the main workflow directory
+  --workflow-path WORKFLOW_PATH
+                        Path to the main workflow directory
+  --sb-package-id SB_PACKAGE_ID
+                        Id of an already uploaded package
+  --sb-inputs SB_INPUTS
+                        Path to pre built sb app inputs schema
+  --sb-outputs SB_OUTPUTS
+                        Path to pre build sb app outputs schema
+  --sb-doc SB_DOC       Path to a doc file for sb app. If not provided, README.md will be used if available
+  --dump-sb-app         Dump created sb app to file if true and exit
+  --no-package          Only provide a sb app schema and a git URL for entrypoint
+  --json                Dump sb app schema in JSON format (YAML by default)
+  --sb-schema SB_SCHEMA
+                        Do not create new schema, use this schema file. It is sb_nextflow_schema in JSON or YAML format.
+```
+### Example
+
+```
+$ sbpack_nf --profile default --workflow-path /path/to/workflow_dir  
+--appid user/project/app --entrypoint main.nf
+```
+
+# sbcopy
+
+Developed to enable deep copying of Nextflow and WDL apps on the SB platform between projects.
+Note: The link between the original, and the new app will not be available. 
+
+### Usage
+
+```
+sbcopy -h
+usage: sbcopy [-h] [--profile PROFILE] --appid APPID --projectid PROJECTID
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --profile PROFILE     SB platform profile as set in the SB API credentials file.
+  --appid APPID         What to copy? Takes the form {user or division}/{project}/{app_id} or {user or division}/{project}/{app_id}/{revision_no}.
+  --projectid PROJECTID
+                        Where to copy? Takes the form {user or division}/{project}
+```
+
+### Example
+
+```
+sbcopy --appid division-name/project-name/app-name --projectid division-name/destination-project-name
+```

sbpack/noncwl/copy.py

@@ -0,0 +1,45 @@
+import argparse
+import logging
+import sbpack.lib as lib
+from sevenbridges.errors import NotFound
+from sbpack.noncwl.utils import install_or_upgrade_app
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+
+def main():
+    # CLI parameters
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--profile", default="default",
+                        help="SB platform profile as set in the SB API "
+                             "credentials file.")
+    parser.add_argument("--appid", required=True,
+                        help="What to copy? Takes the form {user or division}/{project}/{app_id} "
+                             "or {user or division}/{project}/{app_id}/{revision_no}.")
+    parser.add_argument("--projectid", required=True,
+                        help="Where to copy? Takes the form "
+                             "{user or division}/{project}")
+    args = parser.parse_args()
+
+    # Preprocess CLI parameter values
+
+    # Init api
+    api = lib.get_profile(args.profile)
+
+    # Source and destination apps
+    source_app = api.apps.get(args.appid)
+    sb_app_raw = source_app.raw
+    destination_app_id = args.projectid + '/' + args.appid.split('/')[2]
+
+    # Copy the code package
+    source_package = source_app.raw.get('app_content', {}).get('code_package', '')
+    if source_package:
+        new_file = api.files.get(api.files.get(source_package).copy(project=args.projectid))
+        sb_app_raw['app_content']['code_package'] = new_file.id
+
+    install_or_upgrade_app(api,destination_app_id, sb_app_raw)
+
+
+if __name__ == "__main__":
+    main()