cloudos-cli 2.19.0__tar.gz → 2.20.0__tar.gz

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.19.0
+Version: 2.20.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -285,10 +285,10 @@ If everything went well, you should see something like:
 
 ```console
 Executing run...
-	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355
+	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355
 	Your assigned job id is: 62c83a1191fe06013b7ef355
 	Your current job status is: initializing
-	To further check your job status you can either go to https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355 or use the following command:
+	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or use the following command:
     cloudos job status \
         --apikey $MY_API_KEY \
         --cloudos-url https://cloudos.lifebit.ai \
@@ -321,7 +321,7 @@ previous command should have an output similar to:
 
 ```console
 Executing run...
-	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/jobs/62c83a6191fe06013b7ef363
+	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a6191fe06013b7ef363
 	Your assigned job id is: 62c83a6191fe06013b7ef363
 	Please, wait until job completion or max wait time of 3600 seconds is reached.
 	Your current job status is: initializing.
@@ -329,6 +329,24 @@ Executing run...
 	Your job took 420 seconds to complete successfully.
 ```
 
+#### Abort single or multiple jobs from CloudOS
+
+Aborts jobs in the CloudOS workspace that are either running or initialising. It can be used with one or more job IDs provided as a comma separated string using the `--job-ids` parameter.
+
+Example:
+```console
+cloudos job abort \
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --job-ids "680a3cf80e56949775c02f16"
+
+
+Aborting jobs...
+        Job 680a3cf80e56949775c02f16 aborted successfully.
+```
+
+
 #### Executor support
 
 CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
@@ -423,7 +441,7 @@ The expected output should be something similar to:
 Executing status...
 	Your current job status is: completed
 
-	To further check your job status you can either go to https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355 or repeat the command you just used.
+	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or repeat the command you just used.
 ```
 
 #### Get a list of your jobs from a CloudOS workspace

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/README.md

@@ -250,10 +250,10 @@ If everything went well, you should see something like:
 
 ```console
 Executing run...
-	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355
+	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355
 	Your assigned job id is: 62c83a1191fe06013b7ef355
 	Your current job status is: initializing
-	To further check your job status you can either go to https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355 or use the following command:
+	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or use the following command:
     cloudos job status \
         --apikey $MY_API_KEY \
         --cloudos-url https://cloudos.lifebit.ai \
@@ -286,7 +286,7 @@ previous command should have an output similar to:
 
 ```console
 Executing run...
-	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/jobs/62c83a6191fe06013b7ef363
+	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a6191fe06013b7ef363
 	Your assigned job id is: 62c83a6191fe06013b7ef363
 	Please, wait until job completion or max wait time of 3600 seconds is reached.
 	Your current job status is: initializing.
@@ -294,6 +294,24 @@ Executing run...
 	Your job took 420 seconds to complete successfully.
 ```
 
+#### Abort single or multiple jobs from CloudOS
+
+Aborts jobs in the CloudOS workspace that are either running or initialising. It can be used with one or more job IDs provided as a comma separated string using the `--job-ids` parameter.
+
+Example:
+```console
+cloudos job abort \
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --job-ids "680a3cf80e56949775c02f16"
+
+
+Aborting jobs...
+        Job 680a3cf80e56949775c02f16 aborted successfully.
+```
+
+
 #### Executor support
 
 CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
@@ -388,7 +406,7 @@ The expected output should be something similar to:
 Executing status...
 	Your current job status is: completed
 
-	To further check your job status you can either go to https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355 or repeat the command you just used.
+	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or repeat the command you just used.
 ```
 
 #### Get a list of your jobs from a CloudOS workspace

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/cloudos_cli/__main__.py

@@ -24,6 +24,7 @@ HPC_NEXTFLOW_VERSIONS = ['22.10.8']
 AWS_NEXTFLOW_LATEST = '24.04.4'
 AZURE_NEXTFLOW_LATEST = '22.11.1-edge'
 HPC_NEXTFLOW_LATEST = '22.10.8'
+ABORT_JOB_STATES = ['running', 'initializing']
 
 
 def ssl_selector(disable_ssl_verification, ssl_cert):
@@ -68,7 +69,7 @@ def run_cloudos_cli():
 
 @run_cloudos_cli.group()
 def job():
-    """CloudOS job functionality: run and check jobs in CloudOS."""
+    """CloudOS job functionality: run, check and abort jobs in CloudOS."""
     print(job.__doc__ + '\n')
 
 
@@ -466,7 +467,7 @@ def run(apikey,
                       docker_login=docker_login,
                       verify=verify_ssl)
     print(f'\tYour assigned job id is: {j_id}\n')
-    j_url = f'{cloudos_url}/app/jobs/{j_id}'
+    j_url = f'{cloudos_url}/app/advanced-analytics/analyses/{j_id}'
     if wait_completion:
         print('\tPlease, wait until job completion (max wait time of ' +
               f'{wait_time} seconds).\n')
@@ -752,7 +753,7 @@ def job_status(apikey,
     j_status = cl.get_job_status(job_id, verify_ssl)
     j_status_h = json.loads(j_status.content)["status"]
     print(f'\tYour current job status is: {j_status_h}\n')
-    j_url = f'{cloudos_url}/app/jobs/{job_id}'
+    j_url = f'{cloudos_url}/app/advanced-analytics/analyses/{job_id}'
     print(f'\tTo further check your job status you can either go to {j_url} ' +
           'or repeat the command you just used.')
 
@@ -859,6 +860,73 @@ def list_jobs(apikey,
     print(f'\tJob list saved to {outfile}')
 
 
+@job.command('abort')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--job-ids',
+              help=('One or more job ids to abort. If more than ' +
+                    'one is provided, they must be provided as ' +
+                    'a comma separated list of ids. E.g. id1,id2,id3'),
+              required=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def abort_jobs(apikey,
+              cloudos_url,
+              workspace_id,
+              job_ids,
+              verbose,
+              disable_ssl_verification,
+              ssl_cert):
+    """Abort all specified jobs from a CloudOS workspace."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    print('Aborting jobs...')
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, None)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print('\tSearching for jobs in the following workspace: ' +
+              f'{workspace_id}')
+    # check if the user provided an empty job list
+    jobs = job_ids.replace(' ', '')
+    if not jobs:
+        raise ValueError('No job IDs provided. Please specify at least one job ID to abort.')
+    jobs = jobs.split(',')
+
+    for job in jobs:
+        try:
+            j_status = cl.get_job_status(job, verify_ssl)
+        except Exception as e:
+            print(f"[WARNING] Failed to get status for job {job}, please make sure it exists in the workspace: {e}")
+            continue
+        j_status_content = json.loads(j_status.content)
+        # check if job id is valid & is in working state (initial, running)
+        if j_status_content['status'] not in ABORT_JOB_STATES:
+            print(f"[WARNING] Job {job} is not in a state that can be aborted and is ignored. Current status: {j_status_content['status']}")
+        else:
+            cl.abort_job(job, workspace_id, verify_ssl)
+            print(f"\tJob '{job}' aborted successfully.")
+
+
 @workflow.command('list')
 @click.option('-k',
               '--apikey',

cloudos_cli-2.20.0/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.20.0'

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/cloudos_cli/clos.py

@@ -7,7 +7,7 @@ import time
 import json
 from dataclasses import dataclass
 from cloudos_cli.utils.errors import BadRequestException
-from cloudos_cli.utils.requests import retry_requests_get, retry_requests_post
+from cloudos_cli.utils.requests import retry_requests_get, retry_requests_post, retry_requests_put
 import pandas as pd
 
 # GLOBAL VARS
@@ -87,7 +87,7 @@ class Cloudos:
         : dict
             A dict with three elements collected from the job status: 'name', 'id', 'status'.
         """
-        j_url = f'{self.cloudos_url}/app/jobs/{job_id}'
+        j_url = f'{self.cloudos_url}/app/advanced-analytics/analyses/{job_id}'
         elapsed = 0
         j_status_h_old = ''
         # make sure user doesn't surpass the wait time
@@ -757,3 +757,31 @@ class Cloudos:
         if r.status_code >= 400:
             raise BadRequestException(r)
         return json.loads(r.content)
+
+    def abort_job(self, job, workspace_id, verify=True):
+        """Abort a job.
+
+        Parameters
+        ----------
+        job : string
+            The CloudOS job id of the job to abort.
+        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.
+
+        Returns
+        -------
+        r : requests.models.Response
+            The server response
+        """
+        cloudos_url = self.cloudos_url
+        apikey = self.apikey
+        headers = {
+            "Content-type": "application/json",
+            "apikey": apikey
+        }
+        r = retry_requests_put("{}/api/v1/jobs/{}/abort?teamId={}".format(cloudos_url, job, workspace_id), headers=headers, verify=verify)
+        if r.status_code >= 400:
+            raise BadRequestException(r)
+        return r

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/cloudos_cli/jobs/job.py

@@ -544,5 +544,5 @@ class Job(Cloudos):
             raise BadRequestException(r)
         j_id = json.loads(r.content)["_id"]
         print('\tJob successfully launched to CloudOS, please check the ' +
-              f'following link: {cloudos_url}/app/jobs/{j_id}')
+              f'following link: {cloudos_url}/app/advanced-analytics/analyses/{j_id}')
         return j_id

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/cloudos_cli/utils/requests.py

@@ -73,3 +73,37 @@ def retry_requests_post(url, total=5, status_forcelist=[429, 500, 502, 503, 504]
     # Make a request using the session object
     response = session.post(url, **kwargs)
     return response
+
+
+def retry_requests_put(url, total=5, status_forcelist=[429, 500, 502, 503, 504], **kwargs):
+    """Wrap normal requests put with an error strategy.
+
+    Parameters
+    ----------
+    url : string
+        The request URL
+    total : int
+        Total number of retries
+    status_forcelist : list
+        A list of ints with the status codes to trigger the retries
+
+    Return
+    ------
+    response : requests.Response
+        The Response object returned by the API server
+    """
+    retry_strategy = Retry(
+        total=total,
+        status_forcelist=status_forcelist
+    )
+    # Create an HTTP adapter with the retry strategy and mount it to session
+    adapter = HTTPAdapter(max_retries=retry_strategy)
+
+    # Create a new session object
+    session = requests.Session()
+    session.mount('http://', adapter)
+    session.mount('https://', adapter)
+
+    # Make a request using the session object
+    response = session.put(url, **kwargs)
+    return response

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.19.0
+Version: 2.20.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -285,10 +285,10 @@ If everything went well, you should see something like:
 
 ```console
 Executing run...
-	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355
+	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355
 	Your assigned job id is: 62c83a1191fe06013b7ef355
 	Your current job status is: initializing
-	To further check your job status you can either go to https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355 or use the following command:
+	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or use the following command:
     cloudos job status \
         --apikey $MY_API_KEY \
         --cloudos-url https://cloudos.lifebit.ai \
@@ -321,7 +321,7 @@ previous command should have an output similar to:
 
 ```console
 Executing run...
-	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/jobs/62c83a6191fe06013b7ef363
+	Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a6191fe06013b7ef363
 	Your assigned job id is: 62c83a6191fe06013b7ef363
 	Please, wait until job completion or max wait time of 3600 seconds is reached.
 	Your current job status is: initializing.
@@ -329,6 +329,24 @@ Executing run...
 	Your job took 420 seconds to complete successfully.
 ```
 
+#### Abort single or multiple jobs from CloudOS
+
+Aborts jobs in the CloudOS workspace that are either running or initialising. It can be used with one or more job IDs provided as a comma separated string using the `--job-ids` parameter.
+
+Example:
+```console
+cloudos job abort \
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --job-ids "680a3cf80e56949775c02f16"
+
+
+Aborting jobs...
+        Job 680a3cf80e56949775c02f16 aborted successfully.
+```
+
+
 #### Executor support
 
 CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
@@ -423,7 +441,7 @@ The expected output should be something similar to:
 Executing status...
 	Your current job status is: completed
 
-	To further check your job status you can either go to https://cloudos.lifebit.ai/app/jobs/62c83a1191fe06013b7ef355 or repeat the command you just used.
+	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or repeat the command you just used.
 ```
 
 #### Get a list of your jobs from a CloudOS workspace

{cloudos_cli-2.19.0 → cloudos_cli-2.20.0}/cloudos_cli.egg-info/SOURCES.txt

@@ -21,6 +21,7 @@ cloudos_cli/utils/requests.py
 tests/__init__.py
 tests/functions_for_pytest.py
 tests/test_clos/__init__.py
+tests/test_clos/test_abort_job.py
 tests/test_clos/test_create_cromwell_header.py
 tests/test_clos/test_cromwell_switch.py
 tests/test_clos/test_detect_workflow.py

cloudos_cli-2.20.0/tests/test_clos/test_abort_job.py

@@ -0,0 +1,68 @@
+"""Pytest added for function abort_job"""
+import json
+import mock
+import pytest
+import requests
+import responses
+from cloudos_cli.clos import Cloudos
+from cloudos_cli.utils.errors import BadRequestException
+from tests.functions_for_pytest import load_json_file
+
+APIKEY = 'vnoiweur89u2ongs'
+CLOUDOS_URL = 'http://cloudos.lifebit.ai'
+WORKSPACE_ID = 'lv89ufc838sdig'
+JOB_ID = "616ee9681b866a01d69fa1cd"
+
+
+@mock.patch('cloudos_cli.clos', mock.MagicMock())
+@responses.activate
+def test_abort_job_correct_response():
+    """
+    Test 'abort_job' to work as intended
+    API request is mocked and replicated with json files
+    """
+    header = {
+            "Content-type": "application/json",
+            "apikey": APIKEY
+        }
+    # mock GET method with the .json
+    responses.add(
+            responses.PUT,
+            url=f"{CLOUDOS_URL}/api/v1/jobs/{JOB_ID}/abort?teamId={WORKSPACE_ID}",
+            headers=header,
+            status=200)
+    # start cloudOS service
+    clos = Cloudos(apikey=APIKEY, cromwell_token=None, cloudos_url=CLOUDOS_URL)
+    # get mock response
+    response = clos.abort_job(JOB_ID, WORKSPACE_ID)
+    assert response.status_code == 200
+    assert isinstance(response, requests.models.Response)
+
+
+@mock.patch('cloudos_cli.clos', mock.MagicMock())
+@responses.activate
+def test_abort_job_incorrect_response():
+    """
+    Test 'abort_job' to fail with '400' response
+    """
+    # prepare error message
+    error_message = {"statusCode": 400, "code": "BadRequest",
+                     "message": "Bad Request.", "time": "2025-04-25_17:31:07"}
+    error_json = json.dumps(error_message)
+    header = {
+            "Content-type": "application/json",
+            "apikey": APIKEY
+        }
+    # mock GET method with the .json
+    responses.add(
+            responses.PUT,
+            url=f"{CLOUDOS_URL}/api/v1/jobs/{JOB_ID}/abort?teamId={WORKSPACE_ID}",
+            body=error_json,
+            headers=header,
+            status=400)
+    # raise 400 error
+    with pytest.raises(BadRequestException) as error:
+        # check if it failed
+        clos = Cloudos(apikey=APIKEY, cromwell_token=None, cloudos_url=CLOUDOS_URL)
+        clos.abort_job(JOB_ID, WORKSPACE_ID)
+    assert "Bad Request" in (str(error))

cloudos_cli-2.19.0/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.19.0'