cloudos-cli 2.70.1__tar.gz → 2.72.0__tar.gz

{cloudos_cli-2.70.1 → cloudos_cli-2.72.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.70.1
+Version: 2.72.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro

{cloudos_cli-2.70.1 → cloudos_cli-2.72.0}/cloudos_cli/__main__.py

@@ -31,7 +31,6 @@ from cloudos_cli.configure.configure import (
     CLOUDOS_URL
 )
 from cloudos_cli.related_analyses.related_analyses import related_analyses
-from cloudos_cli.delete.results import delete_job_results
 
 
 # GLOBAL VARS
@@ -727,6 +726,12 @@ def job_status(ctx,
 @click.option('--link',
               help='Link the working directory to an interactive session.',
               is_flag=True)
+@click.option('--delete',
+              help='Delete the results directory of a CloudOS job.',
+              is_flag=True)
+@click.option('-y', '--yes',
+              help='Skip confirmation prompt when deleting results.',
+              is_flag=True)
 @click.option('--session-id',
               help='The specific CloudOS interactive session id. Required when using --link flag.',
               required=False)
@@ -751,6 +756,8 @@ def job_workdir(ctx,
                 workspace_id,
                 job_id,
                 link,
+                delete,
+                yes,
                 session_id,
                 status,
                 verbose,
@@ -886,6 +893,39 @@ def job_workdir(ctx,
     except Exception as e:
         raise ValueError(f"Failed to retrieve working directory for job '{job_id}': {str(e)}")
 
+    # Delete workdir directory if requested
+    if delete:
+        try:
+            # Ask for confirmation unless --yes flag is provided
+            if not yes:
+                confirmation_message = (
+                    "\n⚠️ Deleting intermediate results is permanent and cannot be undone. "
+                    "All associated data will be permanently removed and cannot be recovered. "
+                    "The current job, as well as any other jobs sharing the same working directory, "
+                    "will no longer be resumable. This action will be logged in the audit trail "
+                    "(if auditing is enabled for your organisation), and you will be recorded as "
+                    "the user who performed the deletion. You can skip this confirmation step by "
+                    "providing -y or --yes flag to cloudos job workdir --delete. Please confirm "
+                    "that you want to delete intermediate results of this analysis? [y/n] "
+                )
+                click.secho(confirmation_message, fg='black', bg='yellow')
+                user_input = input().strip().lower()
+                if user_input != 'y':
+                    print('\nDeletion cancelled.')
+                    return
+            # Proceed with deletion
+            job = jb.Job(cloudos_url, apikey, None, workspace_id, None, None, workflow_id=1234, project_id="None",
+                        mainfile=None, importsfile=None, verify=verify_ssl)
+            job.delete_job_results(job_id, "workDirectory", verify=verify_ssl)
+            click.secho('\nIntermediate results directories deleted successfully.', fg='green', bold=True)
+        except BadRequestException as e:
+            raise ValueError(f"Job '{job_id}' not found or not accessible: {str(e)}")
+        except Exception as e:
+            raise ValueError(f"Failed to retrieve intermediate results for job '{job_id}': {str(e)}")
+    else:
+        if yes:
+            click.secho("\n'--yes' flag is ignored when '--delete' is not specified.", fg='yellow', bold=True)
+
 
 @job.command('logs')
 @click.option('-k',
@@ -1198,8 +1238,11 @@ def job_results(ctx,
                     return
             if verbose:
                 print(f'\nDeleting {len(results)} result directories from CloudOS...')
-            delete_job_results(cloudos_url, apikey, job_id, workspace_id, verify_ssl)
-            print('Results directories deleted successfully.')
+            # Proceed with deletion
+            job = jb.Job(cloudos_url, apikey, None, workspace_id, None, None, workflow_id=1234, project_id="None",
+                        mainfile=None, importsfile=None, verify=verify_ssl)
+            job.delete_job_results(job_id, "analysisResults", verify=verify_ssl)
+            click.secho('\nResults directories deleted successfully.', fg='green', bold=True)
         else:
             if yes:
                 click.secho("\n'--yes' flag is ignored when '--delete' is not specified.", fg='yellow', bold=True)
@@ -1288,7 +1331,7 @@ def job_details(ctx,
             raise ValueError(f"Job '{job_id}' not found or not accessible: {str(e)}")
     except Exception as e:
         raise ValueError(f"Failed to retrieve details for job '{job_id}': {str(e)}")
-    create_job_details(json.loads(j_details.content), job_id, output_format, output_basename, parameters)
+    create_job_details(json.loads(j_details.content), job_id, output_format, output_basename, parameters, cloudos_url)
 
 
 @job.command('list')

cloudos_cli-2.72.0/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.72.0'

{cloudos_cli-2.70.1 → cloudos_cli-2.72.0}/cloudos_cli/jobs/job.py

@@ -1428,14 +1428,16 @@ class Job(Cloudos):
         else:
             return parent_job_id
 
-    def delete_job_results(self, folder_id, verify=True):
+    def delete_job_results(self, job_id, mode, verify=True):
         """Delete job results folder.
 
         Parameters
         ----------
-        folder_id : str
-            The ID of the folder to delete (typically a job results folder).
-        verify : [bool | str], optional
+        job_id : str
+            The CloudOS job ID whose results folder is to be deleted.
+        mode : str
+            The mode to use for deletion (e.g., "analysisResults" or "workDirectory").
+        verify : [bool|string]
             Whether to use SSL verification or not. Alternatively, if
             a string is passed, it will be interpreted as the path to
             the SSL certificate file. Default is True.
@@ -1452,11 +1454,14 @@ class Job(Cloudos):
         ValueError
             If the folder ID is invalid or the folder does not exist.
         """
+        if mode not in ["analysisResults", "workDirectory"]:
+            raise ValueError(f"Invalid mode '{mode}'. Supported modes are 'analysisResults' and 'workDirectory'.")
+
         headers = {
             "Content-type": "application/json",
             "apikey": self.apikey
         }
-        url = f"{self.cloudos_url}/api/v1/folders/{folder_id}?teamId={self.workspace_id}"
+        url = f"{self.cloudos_url}/api/v1/jobs/{job_id}/data?properties[]={mode}&teamId={self.workspace_id}"
         response = retry_requests_delete(url, headers=headers, verify=verify)
 
         # Handle specific status codes according to API specification
@@ -1464,13 +1469,20 @@ class Job(Cloudos):
             # NoContent - successful deletion
             return {"message": "Results deleted successfully", "status": "deleted"}
         elif response.status_code == 400:
-            raise ValueError("Operation not permitted: Your workspace does not have the option to delete results folders enabled. Please consult with the organisation owner to enable this feature.")
+            raise ValueError(f"Operation not permitted: Your workspace does not have the option to delete {'results' if mode == 'analysisResults' else 'intermediate'} folders enabled. Please consult with the organisation owner to enable this feature.")
         elif response.status_code == 401:
             raise ValueError("Unauthorized: Invalid or missing API key.")
         elif response.status_code == 403:
             raise ValueError("Forbidden: You don't have permission to delete this folder.")
         elif response.status_code == 404:
-            raise ValueError(f"{json.loads(response.content)['message']}")
+            if response.content:
+                try:
+                    error_message = json.loads(response.content).get('message', f"Job with ID '{job_id}' not found or data does not exist.")
+                except (json.JSONDecodeError, KeyError):
+                    error_message = f"Job with ID '{job_id}' not found or data does not exist."
+            else:
+                error_message = f"Job with ID '{job_id}' not found or data does not exist."
+            raise ValueError(error_message)
         elif response.status_code == 409:
             raise ValueError("Conflict: The folder cannot be deleted due to a conflict (e.g., folder is not empty or has dependencies).")
         elif response.status_code == 500:
@@ -1481,4 +1493,4 @@ class Job(Cloudos):
         # For any other successful response, parse content if available
         if response.content:
             return json.loads(response.content)
-        return {"message": "Results deleted successfully"}
+        return {"message": f"'{mode}' deleted successfully"}

{cloudos_cli-2.70.1 → cloudos_cli-2.72.0}/cloudos_cli/utils/details.py

@@ -73,7 +73,7 @@ def get_path(param, param_kind_map, execution_platform, storage_provider, mode="
     return value
 
 
-def create_job_details(j_details_h, job_id, output_format, output_basename, parameters):
+def create_job_details(j_details_h, job_id, output_format, output_basename, parameters, cloudos_url="https://cloudos.lifebit.ai"):
     """
     Creates formatted job details output from job data in multiple formats.
 
@@ -113,6 +113,8 @@ def create_job_details(j_details_h, job_id, output_format, output_basename, para
         Whether to create a separate configuration file containing job parameters.
         If True and parameters exist, creates a '.config' file with Nextflow-style
         parameter formatting.
+    cloudos_url : str, optional
+        The base URL of the CloudOS instance. Defaults to "https://cloudos.lifebit.ai".
 
     Returns
     -------
@@ -293,6 +295,11 @@ def create_job_details(j_details_h, job_id, output_format, output_basename, para
         for key, value in job_details_json.items():
             if key == "Parameters":
                 table.add_row(key, "\n".join(value.split(";")))
+            elif key == "ID":
+                # Add hyperlink to job ID
+                job_url = f"{cloudos_url}/app/advanced-analytics/analyses/{value}"
+                job_id_with_link = f"[link={job_url}]{value}[/link]"
+                table.add_row(key, job_id_with_link)
             else:
                 table.add_row(key, str(value))
 

{cloudos_cli-2.70.1 → cloudos_cli-2.72.0}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.70.1
+Version: 2.72.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro

{cloudos_cli-2.70.1 → cloudos_cli-2.72.0}/cloudos_cli.egg-info/SOURCES.txt

@@ -17,8 +17,6 @@ cloudos_cli/cost/__init__.py
 cloudos_cli/cost/cost.py
 cloudos_cli/datasets/__init__.py
 cloudos_cli/datasets/datasets.py
-cloudos_cli/delete/__init__.py
-cloudos_cli/delete/results.py
 cloudos_cli/import_wf/__init__.py
 cloudos_cli/import_wf/import_wf.py
 cloudos_cli/jobs/__init__.py

cloudos_cli-2.70.1/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.70.1'

cloudos_cli-2.70.1/cloudos_cli/delete/__init__.py

@@ -1,8 +0,0 @@
-"""
-Functions and classes related to delete (results & workdir).
-"""
-
-from .results import delete_job_results
-
-
-__all__ = ['results']

cloudos_cli-2.70.1/cloudos_cli/delete/results.py

@@ -1,24 +0,0 @@
-import click
-import cloudos_cli.jobs.job as jb
-
-
-def delete_job_results(cloudos_url, apikey, j_id, workspace_id, verify=True):
-    job = jb.Job(cloudos_url, apikey, None, workspace_id, None, None, workflow_id=1234, project_id="None",
-                 mainfile=None, importsfile=None, verify=verify)
-
-    # Get job results directory
-    try:
-        j_results_dir = job.get_field_from_jobs_endpoint(j_id, field='analysisResults', verify=verify)
-    except Exception as e:
-        if "Field 'analysisResults' not found in endpoint 'jobs'" in str(e):
-            click.secho("Selected job does not have 'Results' information.", fg="yellow", bold=True)
-            return
-        else:
-            raise e
-
-    # Get folder ID
-    folder_id = j_results_dir.get('folderId')
-    if not folder_id:
-        raise ValueError("The job does not have a results directory associated.")
-
-    job.delete_job_results(folder_id, verify=verify)