cloudos-cli 2.18.0__tar.gz → 2.19.1__tar.gz

{cloudos_cli-2.18.0 → cloudos_cli-2.19.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.18.0
+Version: 2.19.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -12,6 +12,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click>=8.0.1
+Requires-Dist: rich-click>=1.8.2
 Requires-Dist: pandas>=1.3.4
 Requires-Dist: numpy==1.26.4
 Requires-Dist: requests>=2.26.0
@@ -26,6 +27,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
@@ -46,6 +48,7 @@ click>=8.0.1
 pandas>=1.3.4
 numpy==1.26.4
 requests>=2.26.0
+rich_click>=1.8.2
 ```
 
 ## Installation
@@ -282,10 +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 \
@@ -318,7 +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.
@@ -420,7 +423,7 @@ 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-2.18.0 → cloudos_cli-2.19.1}/README.md

@@ -13,6 +13,7 @@ click>=8.0.1
 pandas>=1.3.4
 numpy==1.26.4
 requests>=2.26.0
+rich_click>=1.8.2
 ```
 
 ## Installation
@@ -249,10 +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 \
@@ -285,7 +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.
@@ -387,7 +388,7 @@ 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-2.18.0 → cloudos_cli-2.19.1}/cloudos_cli/__main__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-import click
+import rich_click as click
 import cloudos_cli.jobs.job as jb
 from cloudos_cli.clos import Cloudos
 from cloudos_cli.queue.queue import Queue
@@ -18,6 +18,12 @@ JOB_FAILED = 'failed'
 JOB_ABORTED = 'aborted'
 JOB_RUNNING = 'running'
 REQUEST_INTERVAL_CROMWELL = 30
+AWS_NEXTFLOW_VERSIONS = ['22.10.8', '24.04.4']
+AZURE_NEXTFLOW_VERSIONS = ['22.11.1-edge']
+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'
 
 
 def ssl_selector(disable_ssl_verification, ssl_cert):
@@ -126,7 +132,7 @@ def queue():
               help=('Nextflow version to use when executing the workflow in CloudOS. ' +
                     'Please, note that versions above 22.10.8 are only DSL2 compatible. ' +
                     'Default=22.10.8.'),
-              type=click.Choice(['22.10.8', '24.04.4', 'latest']),
+              type=click.Choice(['22.10.8', '24.04.4', '22.11.1-edge', 'latest']),
               default='22.10.8')
 @click.option('--git-commit',
               help=('The exact whole 40 character commit hash to run for ' +
@@ -410,9 +416,26 @@ def run(apikey,
     else:
         docker_login = False
     if nextflow_version == 'latest':
-        nextflow_version = '24.04.4'
-        print('[Message] You have specified Nextflow version \'latest\'. The workflow will use the ' +
+        if execution_platform == 'aws':
+            nextflow_version = AWS_NEXTFLOW_LATEST
+        elif execution_platform == 'azure':
+            nextflow_version = AZURE_NEXTFLOW_LATEST
+        else:
+            nextflow_version = HPC_NEXTFLOW_LATEST
+        print(f'[Message] You have specified Nextflow version \'latest\' for execution platform \'{execution_platform}\'. The workflow will use the ' +
               f'latest version available on CloudOS: {nextflow_version}.')
+    if execution_platform == 'aws':
+        if nextflow_version not in AWS_NEXTFLOW_VERSIONS:
+            print(f'[Message] For execution platform \'aws\', the workflow will use the default \'22.10.8\' version on CloudOS.')
+            nextflow_version = '22.10.8'
+    if execution_platform == 'azure':
+        if nextflow_version not in AZURE_NEXTFLOW_VERSIONS:
+            print(f'[Message] For execution platform \'azure\', the workflow will use the \'22.11.1-edge\' version on CloudOS.')
+            nextflow_version = '22.11.1-edge'
+    if execution_platform == 'hpc':
+        if nextflow_version not in HPC_NEXTFLOW_VERSIONS:
+            print(f'[Message] For execution platform \'hpc\', the workflow will use the \'22.10.8\' version on CloudOS.')
+            nextflow_version = '22.10.8'
     if nextflow_version != '22.10.8':
         print(f'[Warning] You have specified Nextflow version {nextflow_version}. This version requires the pipeline ' +
               'to be written in DSL2 and does not support DSL1.')
@@ -443,7 +466,7 @@ 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')
@@ -729,7 +752,7 @@ 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.')
 

cloudos_cli-2.19.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.19.1'

{cloudos_cli-2.18.0 → cloudos_cli-2.19.1}/cloudos_cli/clos.py

@@ -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

{cloudos_cli-2.18.0 → cloudos_cli-2.19.1}/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-2.18.0 → cloudos_cli-2.19.1}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.18.0
+Version: 2.19.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -12,6 +12,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click>=8.0.1
+Requires-Dist: rich-click>=1.8.2
 Requires-Dist: pandas>=1.3.4
 Requires-Dist: numpy==1.26.4
 Requires-Dist: requests>=2.26.0
@@ -26,6 +27,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
@@ -46,6 +48,7 @@ click>=8.0.1
 pandas>=1.3.4
 numpy==1.26.4
 requests>=2.26.0
+rich_click>=1.8.2
 ```
 
 ## Installation
@@ -282,10 +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 \
@@ -318,7 +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.
@@ -420,7 +423,7 @@ 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-2.18.0 → cloudos_cli-2.19.1}/cloudos_cli.egg-info/requires.txt

@@ -1,4 +1,5 @@
 click>=8.0.1
+rich-click>=1.8.2
 pandas>=1.3.4
 numpy==1.26.4
 requests>=2.26.0

{cloudos_cli-2.18.0 → cloudos_cli-2.19.1}/setup.py

@@ -23,7 +23,7 @@ setuptools.setup(
     entry_points={"console_scripts": [
         "cloudos=cloudos_cli.__main__:run_cloudos_cli"
     ]},
-    install_requires=["click>=8.0.1", "pandas>=1.3.4", "numpy==1.26.4", "requests>=2.26.0"],
+    install_requires=["click>=8.0.1", "rich-click>=1.8.2", "pandas>=1.3.4", "numpy==1.26.4", "requests>=2.26.0"],
     extras_require={
         "test": ["pytest", "mock", "responses", "requests_mock"]
     },

cloudos_cli-2.18.0/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.18.0'