cloudos-cli 2.29.0__tar.gz → 2.30.0__tar.gz

{cloudos_cli-2.29.0 → cloudos_cli-2.30.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.29.0
+Version: 2.30.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -695,8 +695,8 @@ The collected workflows are those that can be found in "WORKSPACE TOOLS" section
 You can import new workflows to your CloudOS workspaces. The only requirements are:
 
 - The workflow is a Nextflow pipeline.
-- The workflow repository is located at GitHub or GitLab (specified by the option `--platform`. Available options: `github`, `gitlab`)
-- If your repository is private, you have access to the repository and you have linked your GitHub or Bitbucket server accounts to CloudOS.
+- The workflow repository is located at GitHub, GitLab or BitBucket Server (specified by the option `--repository-platform`. Available options: `github`, `gitlab` and `bitbucketServer`)
+- If your repository is private, you have access to the repository and to have linked your GitHub, Gitlab or Bitbucket server accounts to CloudOS.
 
 #### Usage of the workflow import command
 
@@ -712,7 +712,7 @@ cloudos workflow import \
     --workspace-id $WORKSPACE_ID \
     --workflow-url $WORKFLOW_URL \
     --workflow-name "new_name_for_the_github_workflow" \
-    --platform github 
+    --repository-platform github
 ```
 
 The expected output will be:
@@ -737,7 +737,7 @@ cloudos workflow import \
     --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" \
-    --platform github
+    --repository-platform github
 ```
 
 > NOTE: please, take into account that importing workflows using cloudos-cli is not yet available in all the CloudOS workspaces. If you try to use this feature in a non-prepared workspace you will get the following error message: `It seems your API key is not authorised. Please check if your workspace has support for importing workflows using cloudos-cli`.

{cloudos_cli-2.29.0 → cloudos_cli-2.30.0}/README.md

@@ -660,8 +660,8 @@ The collected workflows are those that can be found in "WORKSPACE TOOLS" section
 You can import new workflows to your CloudOS workspaces. The only requirements are:
 
 - The workflow is a Nextflow pipeline.
-- The workflow repository is located at GitHub or GitLab (specified by the option `--platform`. Available options: `github`, `gitlab`)
-- If your repository is private, you have access to the repository and you have linked your GitHub or Bitbucket server accounts to CloudOS.
+- The workflow repository is located at GitHub, GitLab or BitBucket Server (specified by the option `--repository-platform`. Available options: `github`, `gitlab` and `bitbucketServer`)
+- If your repository is private, you have access to the repository and to have linked your GitHub, Gitlab or Bitbucket server accounts to CloudOS.
 
 #### Usage of the workflow import command
 
@@ -677,7 +677,7 @@ cloudos workflow import \
     --workspace-id $WORKSPACE_ID \
     --workflow-url $WORKFLOW_URL \
     --workflow-name "new_name_for_the_github_workflow" \
-    --platform github 
+    --repository-platform github
 ```
 
 The expected output will be:
@@ -702,7 +702,7 @@ cloudos workflow import \
     --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" \
-    --platform github
+    --repository-platform github
 ```
 
 > NOTE: please, take into account that importing workflows using cloudos-cli is not yet available in all the CloudOS workspaces. If you try to use this feature in a non-prepared workspace you will get the following error message: `It seems your API key is not authorised. Please check if your workspace has support for importing workflows using cloudos-cli`.

{cloudos_cli-2.29.0 → cloudos_cli-2.30.0}/cloudos_cli/__main__.py

@@ -3,7 +3,7 @@
 import rich_click as click
 import cloudos_cli.jobs.job as jb
 from cloudos_cli.clos import Cloudos
-from cloudos_cli.import_wf.import_wf import ImportGitlab, ImportGithub
+from cloudos_cli.import_wf.import_wf import ImportWorflow
 from cloudos_cli.queue.queue import Queue
 from cloudos_cli.utils.errors import BadRequestException
 import json
@@ -289,7 +289,7 @@ def configure(ctx, profile, make_default):
               '--cromwell-token',
               help=('Specific Cromwell server authentication token. Currently, not necessary ' +
                     'as apikey can be used instead, but maintained for backwards compatibility.'))
-@click.option('--repository-platform',
+@click.option('--repository-platform', type=click.Choice(["github", "gitlab", "bitbucketServer"]),
               help='Name of the repository platform of the workflow. Default=github.',
               default='github')
 @click.option('--execution-platform',
@@ -1250,10 +1250,9 @@ def list_workflows(ctx,
 @click.option('--workspace-id',
               help='The specific CloudOS workspace id.',
               required=True)
-@click.option("--platform", type=click.Choice(["github", "gitlab"]),
-              help=('Repository service where the workflow is located. Valid choices: github, gitlab. ' +
-                    'Default=github'),
-              default="github")
+@click.option('--repository-platform', type=click.Choice(["github", "gitlab", "bitbucketServer"]),
+              help='Name of the repository platform of the workflow. Default=github.',
+              default='github')
 @click.option("--workflow-name", help="The name that the workflow will have in CloudOS.", required=True)
 @click.option("-w", "--workflow-url", help="URL of the workflow repository.", required=True)
 @click.option("-d", "--workflow-docs-link", help="URL to the documentation of the workflow.", default='')
@@ -1276,7 +1275,7 @@ def import_wf(ctx,
               workflow_docs_link,
               cost_limit,
               workflow_description,
-              platform,
+              repository_platform,
               disable_ssl_verification,
               ssl_cert,
               profile):
@@ -1303,15 +1302,14 @@ def import_wf(ctx,
             apikey=apikey,
             cloudos_url=cloudos_url,
             workspace_id=workspace_id,
-            workflow_name=workflow_name
+            workflow_name=workflow_name,
+            repository_platform=repository_platform
         )
     )
 
     verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
-    repo_services = {"gitlab": ImportGitlab, "github": ImportGithub}
-    repo_cls = repo_services[platform]
-    repo_import = repo_cls(cloudos_url=cloudos_url, cloudos_apikey=apikey, workspace_id=workspace_id,
-                             platform=platform, workflow_name=workflow_name, workflow_url=workflow_url,
+    repo_import = ImportWorflow(cloudos_url=cloudos_url, cloudos_apikey=apikey, workspace_id=workspace_id,
+                             platform=repository_platform, workflow_name=workflow_name, workflow_url=workflow_url,
                              workflow_docs_link=workflow_docs_link, cost_limit=cost_limit, workflow_description=workflow_description, verify=verify_ssl)
     workflow_id = repo_import.import_workflow()
     print(f'\tWorkflow {workflow_name} was imported successfully with the ' +
@@ -1865,7 +1863,7 @@ def remove_profile(ctx, profile):
               help=('Max time to wait (in seconds) to job completion. ' +
                     'Default=3600.'),
               default=3600)
-@click.option('--repository-platform',
+@click.option('--repository-platform', type=click.Choice(["github", "gitlab", "bitbucketServer"]),
               help='Name of the repository platform of the workflow. Default=github.',
               default='github')
 @click.option('--execution-platform',

cloudos_cli-2.30.0/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.30.0'

{cloudos_cli-2.29.0 → cloudos_cli-2.30.0}/cloudos_cli/import_wf/__init__.py

@@ -2,7 +2,7 @@
 Functions and classes related to importing workflows into CloudOS.
 """
 
-from .import_wf import WFImport, ImportGitlab, ImportGithub
+from .import_wf import WFImport, ImportWorflow
 
 
 __all__ = ['import_wf']

{cloudos_cli-2.29.0 → cloudos_cli-2.30.0}/cloudos_cli/import_wf/import_wf.py

@@ -3,6 +3,8 @@ from urllib.parse import urlsplit
 from cloudos_cli.utils.errors import BadRequestException, AccountNotLinkedException
 from cloudos_cli.utils.requests import retry_requests_post, retry_requests_get
 import json
+from requests.exceptions import RetryError
+import sys
 
 
 class WFImport(ABC):
@@ -96,44 +98,46 @@ class WFImport(ABC):
         return content["_id"]
 
 
-# There are some duplicated lines here and on the github subclass. I did not put them in the abstract class because we
-# still don't know if the bitbucket data will come the same. If it does, then I will put as much as possible as part
-# of the abstract class
-class ImportGitlab(WFImport):
+class ImportWorflow(WFImport):
     def get_repo(self):
-        get_repo_url = f"{self.cloudos_url}/api/v1/git/gitlab/getPublicRepo"
-        self.repo_name = self.parsed_url.path.split("/")[-1]
-        self.repo_owner = "/".join(self.parsed_url.path.split("/")[1:-1])
+        get_repo_url = f"{self.cloudos_url}/api/v1/git/{self.platform}/getPublicRepo"
+        if self.platform == "bitbucketServer":
+            # platform allows to add paths like /browse, so we need to check if the path ends with it
+            if self.parsed_url.path.endswith("browse"):
+                self.repo_name = self.parsed_url.path.split("/")[-2]
+            else:
+                self.repo_name = self.parsed_url.path.split("/")[-1]
+            self.repo_owner = self.parsed_url.path.split("/")[2]
+        else:
+            self.repo_name = self.parsed_url.path.split("/")[-1]
+            self.repo_owner = "/".join(self.parsed_url.path.split("/")[1:-1])
         self.repo_host = f"{self.parsed_url.scheme}://{self.parsed_url.netloc}"
         get_repo_params = dict(repoName=self.repo_name, repoOwner=self.repo_owner, host=self.repo_host, teamId=self.workspace_id)
-        r = retry_requests_get(get_repo_url, params=get_repo_params, headers=self.headers)
-        if r.status_code == 404:
+        try:
+            r = retry_requests_get(get_repo_url, params=get_repo_params, headers=self.headers)
+        except RetryError as e:
+            # RetryError getting from missing BitBucket Server credentials
             raise AccountNotLinkedException(self.workflow_url)
-        elif r.status_code >= 400:
-            raise BadRequestException(r)
-        r_data = r.json()
-        self.payload["repository"]["repositoryId"] = r_data["id"]
-        self.payload["repository"]["name"] = r_data["name"]
-        self.payload["repository"]["owner"]["id"] = r_data["namespace"]["id"]
-        self.payload["repository"]["owner"]["login"] = r_data["namespace"]["full_path"]
-        self.payload["mainFile"] = self.main_file or self.get_repo_main_file()
 
-
-class ImportGithub(WFImport):
-    def get_repo(self):
-        get_repo_url = f"{self.cloudos_url}/api/v1/git/github/getPublicRepo"
-        self.repo_name = self.parsed_url.path.split("/")[-1]
-        self.repo_owner = "/".join(self.parsed_url.path.split("/")[1:-1])
-        self.repo_host = f"{self.parsed_url.scheme}://{self.parsed_url.netloc}"
-        get_repo_params = dict(repoName=self.repo_name, repoOwner=self.repo_owner, host=self.repo_host, teamId=self.workspace_id)
-        r = retry_requests_get(get_repo_url, params=get_repo_params, headers=self.headers)
+        # for Github and Gitlab the API gives very general errors on missing credentials
+        # therefore we only have these at the moment
         if r.status_code == 404:
             raise AccountNotLinkedException(self.workflow_url)
         elif r.status_code >= 400:
             raise BadRequestException(r)
+
         r_data = r.json()
-        self.payload["repository"]["repositoryId"] = r_data["id"]
+        if self.platform == "bitbucketServer":
+            self.payload["repository"]["repositoryId"] = r_data["name"]
+        else:
+            self.payload["repository"]["repositoryId"] = r_data["id"]
         self.payload["repository"]["name"] = r_data["name"]
-        self.payload["repository"]["owner"]["id"] = r_data["owner"]["id"]
-        self.payload["repository"]["owner"]["login"] = r_data["owner"]["login"]
+        owner_data = {
+            "bitbucketServer": ("project", "id", "key"),
+            "gitlab": ("namespace", "id", "full_path"),
+            "github": ("owner", "id", "login")
+        }
+        key, id_field, login_field = owner_data[self.platform]
+        self.payload["repository"]["owner"]["id"] = r_data[key][id_field]
+        self.payload["repository"]["owner"]["login"] = r_data[key][login_field]
         self.payload["mainFile"] = self.main_file or self.get_repo_main_file()

{cloudos_cli-2.29.0 → cloudos_cli-2.30.0}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.29.0
+Version: 2.30.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -695,8 +695,8 @@ The collected workflows are those that can be found in "WORKSPACE TOOLS" section
 You can import new workflows to your CloudOS workspaces. The only requirements are:
 
 - The workflow is a Nextflow pipeline.
-- The workflow repository is located at GitHub or GitLab (specified by the option `--platform`. Available options: `github`, `gitlab`)
-- If your repository is private, you have access to the repository and you have linked your GitHub or Bitbucket server accounts to CloudOS.
+- The workflow repository is located at GitHub, GitLab or BitBucket Server (specified by the option `--repository-platform`. Available options: `github`, `gitlab` and `bitbucketServer`)
+- If your repository is private, you have access to the repository and to have linked your GitHub, Gitlab or Bitbucket server accounts to CloudOS.
 
 #### Usage of the workflow import command
 
@@ -712,7 +712,7 @@ cloudos workflow import \
     --workspace-id $WORKSPACE_ID \
     --workflow-url $WORKFLOW_URL \
     --workflow-name "new_name_for_the_github_workflow" \
-    --platform github 
+    --repository-platform github
 ```
 
 The expected output will be:
@@ -737,7 +737,7 @@ cloudos workflow import \
     --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" \
-    --platform github
+    --repository-platform github
 ```
 
 > NOTE: please, take into account that importing workflows using cloudos-cli is not yet available in all the CloudOS workspaces. If you try to use this feature in a non-prepared workspace you will get the following error message: `It seems your API key is not authorised. Please check if your workspace has support for importing workflows using cloudos-cli`.

cloudos_cli-2.29.0/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.29.0'