adding support for docs

lifebit-ai · Apr 11, 2024 · 5d3413e · 5d3413e
1 parent 79a651e
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Showing 6 changed files with 32 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 ## lifebit-ai/cloudos-cli: changelog
 
+## v2.10.0 (2024-04-11)
+
+- Adds the new parameter `--workflow-docs-link` to add a documentation link to the imported workflow.
+
 ## v2.9.0 (2024-04-09)
 
 - Adds `workflow import` command, allowing user to import Nextflow workflows to CloudOS.

diff --git a/README.md b/README.md
@@ -601,6 +601,20 @@ Executing workflow import...
 	Workflow test_import_github_3 was imported successfully with the following ID: 6616a8cb454b09bbb3d9dc20
 ```
 
+Optionally, you can add a link to your workflow documentation by providing the URL using the parameter `--workflow-docs-link`. E.g.:
+
+```bash
+cloudos workflow import \
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --workflow-url $WORKFLOW_URL \
+    --workflow-name "new_name_for_the_github_workflow" \
+    --workflow-docs-link "https://github.com/lifebit-ai/DeepVariant/blob/master/README.md" \
+    --repository-project-id $REPOSITORY_PROJECT_ID \
+    --repository-id $REPOSITORY_ID
+```
+
 To import bitbucket server workflows, `--repository-id` parameter is not required:
 
 ```bash

diff --git a/cloudos/__main__.py b/cloudos/__main__.py
@@ -799,6 +799,9 @@ def list_workflows(apikey,
 @click.option('--workflow-name',
               help="The name that the workflow will have in CloudOS",
               required=True)
+@click.option('--workflow-docs-link',
+              help="Workflow documentation URL.",
+              default='')
 @click.option('--repository-project-id',
               type=int,
               help="The ID of your repository project",
@@ -818,6 +821,7 @@ def import_workflows(apikey,
                      workflow_url,
                      workflow_name,
                      repository_project_id,
+                     workflow_docs_link,
                      repository_id,
                      disable_ssl_verification,
                      ssl_cert):
@@ -830,6 +834,7 @@ def import_workflows(apikey,
                                      workflow_url,
                                      workflow_name,
                                      repository_project_id,
+                                     workflow_docs_link,
                                      repository_id,
                                      verify=verify_ssl)
     print(f'\tWorkflow {workflow_name} was imported successfully with the ' +

diff --git a/cloudos/_version.py b/cloudos/_version.py
@@ -1 +1 @@
-__version__ = '2.9.0'
+__version__ = '2.10.0'
diff --git a/cloudos/clos.py b/cloudos/clos.py
@@ -534,7 +534,8 @@ def process_project_list(r, all_fields=False):
         return df
 
     def workflow_import(self, workspace_id, workflow_url, workflow_name,
-                        repository_project_id, repository_id=None, verify=True):
+                        repository_project_id, workflow_docs_link='',
+                        repository_id=None, verify=True):
         """Imports workflows to CloudOS.
 
         Parameters
@@ -547,6 +548,8 @@ def workflow_import(self, workspace_id, workflow_url, workflow_name,
             A name for the imported pipeline in CloudOS.
         repository_project_id : int
             The repository project ID.
+        workflow_docs_link : string
+            Link to the documentation URL.
         repository_id : int
             The repository ID. Only required for GitHub repositories.
         verify: [bool|string]
@@ -596,7 +599,7 @@ def workflow_import(self, workspace_id, workflow_url, workflow_name,
             "mainFile": "main.nf",
             "defaultContainer": None,
             "processes": [],
-            "docsLink": "",
+            "docsLink": workflow_docs_link,
             "team": workspace_id
         }
         r = retry_requests_post("{}/api/v1/workflows?teamId={}".format(self.cloudos_url,

diff --git a/tests/test_clos/test_workflow_import.py b/tests/test_clos/test_workflow_import.py
@@ -12,6 +12,7 @@
 WORKSPACE_ID = 'lv89ufc838sdig'
 WORKFLOW_URL = 'https://github.com/lifebit-ai/repo'
 WORKFLOW_NAME = 'test-repo'
+WORKFLOW_DOCS_LINK = ''
 REPOSITORY_PROJECT_ID = 1234
 REPOSITORY_ID = 567
 
@@ -38,6 +39,7 @@ def test_workflow_import_correct():
                                        WORKFLOW_URL,
                                        WORKFLOW_NAME,
                                        REPOSITORY_PROJECT_ID,
+                                       WORKFLOW_DOCS_LINK,
                                        REPOSITORY_ID)
     # check the response
     assert isinstance(workflow_id, str)
@@ -70,5 +72,6 @@ def test_workflow_import_incorrect():
                              WORKFLOW_URL,
                              WORKFLOW_NAME,
                              REPOSITORY_PROJECT_ID,
+                             WORKFLOW_DOCS_LINK,
                              REPOSITORY_ID)
     assert "Server returned status 400." in (str(error))