cloudos-cli 2.21.0__tar.gz → 2.22.0__tar.gz

{cloudos_cli-2.21.0/cloudos_cli.egg-info → cloudos_cli-2.22.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.21.0
+Version: 2.22.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -8,13 +8,13 @@ Author-email: david.pineyro@lifebit.ai
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: POSIX :: Linux
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Requires-Python: >=3.7
+Requires-Python: >=3.9
 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: numpy>=1.26.4
 Requires-Dist: requests>=2.26.0
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
@@ -41,12 +41,12 @@ Python package for interacting with CloudOS
 
 ## Requirements
 
-The package requires Python >= 3.7 and the following python packages:
+The package requires Python >= 3.9 and the following python packages:
 
 ```
 click>=8.0.1
 pandas>=1.3.4
-numpy==1.26.4
+numpy>=1.26.4
 requests>=2.26.0
 rich_click>=1.8.2
 ```
@@ -399,6 +399,56 @@ Executing run...
 	Your job took 420 seconds to complete successfully.
 ```
 
+#### Send a bash job to CloudOS (sequential sample processing)
+
+A bash job can be sent to CloudOS using the command `bash` and the subcommand `job`. In this case, the `--workflow-name` must be a bash job already
+present in the platform. Bash jobs are identified by bash icon (unlike Nextflow jobs, which are identified with Nextflow icon).
+
+```bash
+WORKFLOW_NAME="ubuntu"  # This should be a bash workflow
+cloudos bash job \
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --project-name "$PROJECT_NAME" \
+    --workflow-name $WORKFLOW_NAME \
+    --parameter -test_variable=value \
+    --parameter --flag=activate \
+    --parameter send="yes" \
+    --job-name $JOB_NAME \
+    --command "echo 'send' > new_file.txt" \
+    --resumable
+```
+The `--command` parameter is required and will setup the command for the parameters to run.
+
+Each `--parameter` can have a different prefix, either '--', '-', or '', depending on the use case. These can be used as many times as needed.
+
+> [!NOTE]
+> At the moment only string values are allowed to the `--parameter` options, adding a filepath at the moment does not upload/download the file. This feature will be available in a future implementation.
+
+If everything went well, you should see something like:
+
+```console
+CloudOS bash functionality.
+
+        Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/682622d09f305de717327334
+        Your assigned job id is: 682622d09f305de717327334
+
+        Your current job status is: initializing
+        To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/682622d09f305de717327334 or use the following command:
+        cloudos job status \
+                --apikey $MY_API_KEY \
+                --cloudos-url https://cloudos.lifebit.ai \
+                --job-id 682622d09f305de717327334
+```
+
+As you can see, the current status is `initializing`. This will change
+while the job progresses. To check the status, just apply the suggested
+command.
+
+Other options like `--wait-completion` are also available and work in the same way as for the `cloudos job run` command.
+Check `cloudos bash job --help` for more details.
+
 #### 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.

cloudos_cli-2.21.0/PKG-INFO → cloudos_cli-2.22.0/README.md

@@ -1,38 +1,3 @@
-Metadata-Version: 2.4
-Name: cloudos_cli
-Version: 2.21.0
-Summary: Python package for interacting with CloudOS
-Home-page: https://github.com/lifebit-ai/cloudos-cli
-Author: David Piñeyro
-Author-email: david.pineyro@lifebit.ai
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: POSIX :: Linux
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-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
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: mock; extra == "test"
-Requires-Dist: responses; extra == "test"
-Requires-Dist: requests_mock; extra == "test"
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license-file
-Dynamic: provides-extra
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
-
 # cloudos-cli
 
 [![CI_tests](https://github.com/lifebit-ai/cloudos-cli/actions/workflows/ci.yml/badge.svg)](https://github.com/lifebit-ai/cloudos-cli/actions/workflows/ci.yml)
@@ -41,12 +6,12 @@ Python package for interacting with CloudOS
 
 ## Requirements
 
-The package requires Python >= 3.7 and the following python packages:
+The package requires Python >= 3.9 and the following python packages:
 
 ```
 click>=8.0.1
 pandas>=1.3.4
-numpy==1.26.4
+numpy>=1.26.4
 requests>=2.26.0
 rich_click>=1.8.2
 ```
@@ -399,6 +364,56 @@ Executing run...
 	Your job took 420 seconds to complete successfully.
 ```
 
+#### Send a bash job to CloudOS (sequential sample processing)
+
+A bash job can be sent to CloudOS using the command `bash` and the subcommand `job`. In this case, the `--workflow-name` must be a bash job already
+present in the platform. Bash jobs are identified by bash icon (unlike Nextflow jobs, which are identified with Nextflow icon).
+
+```bash
+WORKFLOW_NAME="ubuntu"  # This should be a bash workflow
+cloudos bash job \
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --project-name "$PROJECT_NAME" \
+    --workflow-name $WORKFLOW_NAME \
+    --parameter -test_variable=value \
+    --parameter --flag=activate \
+    --parameter send="yes" \
+    --job-name $JOB_NAME \
+    --command "echo 'send' > new_file.txt" \
+    --resumable
+```
+The `--command` parameter is required and will setup the command for the parameters to run.
+
+Each `--parameter` can have a different prefix, either '--', '-', or '', depending on the use case. These can be used as many times as needed.
+
+> [!NOTE]
+> At the moment only string values are allowed to the `--parameter` options, adding a filepath at the moment does not upload/download the file. This feature will be available in a future implementation.
+
+If everything went well, you should see something like:
+
+```console
+CloudOS bash functionality.
+
+        Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/682622d09f305de717327334
+        Your assigned job id is: 682622d09f305de717327334
+
+        Your current job status is: initializing
+        To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/682622d09f305de717327334 or use the following command:
+        cloudos job status \
+                --apikey $MY_API_KEY \
+                --cloudos-url https://cloudos.lifebit.ai \
+                --job-id 682622d09f305de717327334
+```
+
+As you can see, the current status is `initializing`. This will change
+while the job progresses. To check the status, just apply the suggested
+command.
+
+Other options like `--wait-completion` are also available and work in the same way as for the `cloudos job run` command.
+Check `cloudos bash job --help` for more details.
+
 #### 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.