cloudos-cli 2.91.0__tar.gz → 2.92.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/PKG-INFO +28 -30
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/README.md +27 -29
- cloudos_cli-2.92.0/cloudos_cli/_version.py +1 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/procurement/cli.py +7 -10
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/procurement/images.py +7 -9
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli.egg-info/PKG-INFO +28 -30
- cloudos_cli-2.91.0/cloudos_cli/_version.py +0 -1
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/LICENSE +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/__main__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/bash/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/bash/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/clos.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/configure/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/configure/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/configure/configure.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/constants.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/cost/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/cost/cost.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/cromwell/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/cromwell/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/datasets/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/datasets/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/datasets/datasets.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/import_wf/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/import_wf/import_wf.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/interactive_session/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/interactive_session/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/interactive_session/interactive_session.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/jobs/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/jobs/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/jobs/job.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/link/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/link/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/link/link.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/logging/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/logging/logger.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/procurement/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/projects/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/projects/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/queue/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/queue/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/queue/queue.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/related_analyses/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/related_analyses/related_analyses.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/array_job.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/cli_helpers.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/cloud.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/details.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/errors.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/last_wf.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/nextflow_version.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/requests.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/utils/resources.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/workflows/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/workflows/cli.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli.egg-info/SOURCES.txt +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli.egg-info/dependency_links.txt +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli.egg-info/entry_points.txt +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli.egg-info/requires.txt +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli.egg-info/top_level.txt +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/setup.cfg +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/setup.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/functions_for_pytest.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_cli_project_create.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_cost/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_cost/test_job_cost.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_details.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_error_messages.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_interactive_session/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_interactive_session/test_create_session.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_interactive_session/test_list_sessions.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_logging/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_logging/test_logger.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_nextflow_version.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_related_analyses/__init__.py +0 -0
- {cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_related_analyses/test_related_analyses.py +0 -0
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Metadata-Version: 2.4
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Name: cloudos_cli
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Version: 2.
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Version: 2.92.0
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Summary: Python package for interacting with the Lifebit Platform
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Home-page: https://github.com/lifebit-ai/cloudos-cli
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Author: David Piñeyro
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```bash
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cloudos job list --help
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```
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```console Usage: cloudos job list [OPTIONS]
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Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
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```console Usage: cloudos job list [OPTIONS]
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Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
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╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ * --apikey -k TEXT Your Lifebit Platform API key [required] │
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│ * --cloudos-url -c TEXT The Lifebit Platform url you are trying to access to. │
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### Configure Default Profile
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To facilitate the reuse of required parameters, you can create profiles.
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To facilitate the reuse of required parameters, you can create profiles.
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To generate a profile called `default`, use the following command:
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When configuring a profile, you can specify:
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- **Platform URL**: The Lifebit Platform instance URL
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- **Project Name**: Default project for commands
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- **Execution Platform**: `aws` (default) or `azure` - determines default instance types and available features
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- **Repository Platform**: Version control system (github, gitlab, etc.)
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The expected output is a formatted table showing:
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```console
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Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
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Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
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┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
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┃ ┃ ┃ ┃ ┃ ┃ ┃ ┃ Compute ┃ ┃
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┃ ┃ Instance ┃ ┃ Life-cycle ┃ ┃ Compute ┃ Instance ┃ storage ┃ ┃
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┃ ┃ ┃ ┃ ┃ ┃ ┃ ┃ Compute ┃ ┃
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Total related analyses found: 15
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Related Analyses
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Related Analyses
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┃ Status ┃ Name ┃ Owner ┃ ID ┃ Submit time ┃ Run time ┃ Total Cost ┃
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```
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You can get a list of all interactive sessions in your workspace by running `cloudos interactive-session list`. The command can produce three different output formats that can be selected using the `--output-format` option:
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+
Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder.
|
|
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|
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An example of such command is:
|
|
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2739
|
|
|
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2740
|
```
|
|
2741
|
-
cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
|
|
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|
+
cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
|
|
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|
```
|
|
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|
|
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|
|
|
@@ -2789,7 +2789,7 @@ Create new organizational folders within your projects to maintain structured da
|
|
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> New folders can be created within the `Data` dataset and its subfolders.
|
|
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2790
|
|
|
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2791
|
```bash
|
|
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|
-
cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
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|
+
cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
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2793
|
```
|
|
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2794
|
|
|
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|
#### Remove Files or Folders
|
|
@@ -2797,14 +2797,14 @@ cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
|
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|
Remove unnecessary files or empty folders from your File Explorer. Note that this removes files from Lifebit Platform but not from underlying cloud storage.
|
|
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2798
|
|
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> [!NOTE]
|
|
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|
-
> Files and folders can be removed in the `Data` datasets and its subfolders.
|
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|
+
> Files and folders can be removed in the `Data` datasets and its subfolders.
|
|
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2801
|
|
|
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2802
|
```bash
|
|
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2803
|
cloudos datasets rm <path> --profile my_profile
|
|
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2804
|
```
|
|
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2805
|
> [!NOTE]
|
|
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|
> If a file was uploaded by the user, in order to be removed you must use `--force` and that will permanently remove the file. If the file is "linked" (e.g a s3 folder or file), removing it using `cloudos datasets rm` will not remove it from the the s3 bucket.
|
|
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|
-
|
|
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|
+
|
|
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2808
|
---
|
|
2809
2809
|
|
|
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2810
|
### Link
|
|
@@ -2926,7 +2926,7 @@ To list images for a specific procurement, use the following command:
|
|
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|
|
|
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|
```bash
|
|
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|
cloudos procurement images ls \
|
|
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|
-
-- profile procurement_profile
|
|
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|
+
-- profile procurement_profile
|
|
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|
--procurement-id "your_procurement_id_here"
|
|
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|
```
|
|
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|
|
@@ -2985,12 +2985,10 @@ cloudos procurement images set --profile procurement_profile --image-type "JobDe
|
|
|
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|
- `--image-type`: The Lifebit Platform resource image type (required). Possible values:
|
|
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|
- `RegularInteractiveSessions`
|
|
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|
- `SparkInteractiveSessions`
|
|
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|
-
- `RStudioInteractiveSessions`
|
|
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|
-
- `JupyterInteractiveSessions`
|
|
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|
- `JobDefault`
|
|
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- `NextflowBatchComputeEnvironment`
|
|
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|
-
- `--provider`: The cloud provider (required). Currently only `aws`
|
|
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|
-
- `--region`: The cloud region (required). Currently only
|
|
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|
+
- `--provider`: The cloud provider (required). Currently only supporting `aws` and `azure`.
|
|
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|
+
- `--region`: The cloud region (required). Currently only supporting aws and azure regions.
|
|
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- `--image-id`: The new image ID value (required)
|
|
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|
- `--image-name`: The new image name value (optional)
|
|
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- `--image-version`: The new image version (required)
|
|
@@ -3023,7 +3021,7 @@ cloudos procurement images reset --profile procurement_profile --image-type "Job
|
|
|
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3021
|
- `--organisation-id`: The organization ID where the change will be applied (required)
|
|
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3022
|
- `--image-type`: The Lifebit Platform resource image type (required). Same values as for `set` command
|
|
3025
3023
|
- `--provider`: The cloud provider (required). Currently only `aws` is supported
|
|
3026
|
-
- `--region`: The cloud region (required). Currently only
|
|
3024
|
+
- `--region`: The cloud region (required). Currently only supporting aws and azure regions.
|
|
3027
3025
|
- `--disable-ssl-verification`: Disable SSL certificate verification
|
|
3028
3026
|
- `--ssl-cert`: Path to your SSL certificate file
|
|
3029
3027
|
- `--profile`: Profile to use from the config file
|
|
@@ -3052,7 +3050,7 @@ Executing status...
|
|
|
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3050
|
Current Cromwell server status is: Stopped
|
|
3053
3051
|
```
|
|
3054
3052
|
|
|
3055
|
-
```bash
|
|
3053
|
+
```bash
|
|
3056
3054
|
# Cromwell start
|
|
3057
3055
|
cloudos cromwell start --profile my_profile
|
|
3058
3056
|
```
|
|
@@ -3278,8 +3276,8 @@ responses>=0.21.0
|
|
|
3278
3276
|
mock>=3.0.5
|
|
3279
3277
|
```
|
|
3280
3278
|
|
|
3281
|
-
Command to run tests from the `cloudos-cli` main folder:
|
|
3279
|
+
Command to run tests from the `cloudos-cli` main folder:
|
|
3282
3280
|
|
|
3283
3281
|
```
|
|
3284
3282
|
python -m pytest -s -v
|
|
3285
|
-
```
|
|
3283
|
+
```
|
|
@@ -196,10 +196,10 @@ This will tell you the implemented commands. Each implemented command has its ow
|
|
|
196
196
|
```bash
|
|
197
197
|
cloudos job list --help
|
|
198
198
|
```
|
|
199
|
-
```console Usage: cloudos job list [OPTIONS]
|
|
200
|
-
|
|
201
|
-
Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
|
|
202
|
-
|
|
199
|
+
```console Usage: cloudos job list [OPTIONS]
|
|
200
|
+
|
|
201
|
+
Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
|
|
202
|
+
|
|
203
203
|
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────╮
|
|
204
204
|
│ * --apikey -k TEXT Your Lifebit Platform API key [required] │
|
|
205
205
|
│ * --cloudos-url -c TEXT The Lifebit Platform url you are trying to access to. │
|
|
@@ -264,7 +264,7 @@ $HOME
|
|
|
264
264
|
|
|
265
265
|
### Configure Default Profile
|
|
266
266
|
|
|
267
|
-
To facilitate the reuse of required parameters, you can create profiles.
|
|
267
|
+
To facilitate the reuse of required parameters, you can create profiles.
|
|
268
268
|
|
|
269
269
|
To generate a profile called `default`, use the following command:
|
|
270
270
|
|
|
@@ -286,7 +286,7 @@ The same prompts will appear, including the execution platform (aws or azure). I
|
|
|
286
286
|
|
|
287
287
|
When configuring a profile, you can specify:
|
|
288
288
|
- **API Key**: Your Lifebit Platform API credentials
|
|
289
|
-
- **Platform URL**: The Lifebit Platform instance URL
|
|
289
|
+
- **Platform URL**: The Lifebit Platform instance URL
|
|
290
290
|
- **Project Name**: Default project for commands
|
|
291
291
|
- **Execution Platform**: `aws` (default) or `azure` - determines default instance types and available features
|
|
292
292
|
- **Repository Platform**: Version control system (github, gitlab, etc.)
|
|
@@ -1279,7 +1279,7 @@ cloudos job cost --profile my_profile --job-id 62c83a1191fe06013b7ef355
|
|
|
1279
1279
|
The expected output is a formatted table showing:
|
|
1280
1280
|
|
|
1281
1281
|
```console
|
|
1282
|
-
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
|
1282
|
+
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
|
1283
1283
|
┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
|
|
1284
1284
|
┃ ┃ ┃ ┃ ┃ ┃ ┃ ┃ Compute ┃ ┃
|
|
1285
1285
|
┃ ┃ Instance ┃ ┃ Life-cycle ┃ ┃ Compute ┃ Instance ┃ storage ┃ ┃
|
|
@@ -1308,7 +1308,7 @@ On page 1/2: n = next, p = prev, q = quit
|
|
|
1308
1308
|
|
|
1309
1309
|
By pressing 'n', it will show the next page or the last if it is the case.
|
|
1310
1310
|
|
|
1311
|
-
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
|
1311
|
+
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
|
1312
1312
|
┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
|
|
1313
1313
|
┃ ┃ ┃ ┃ ┃ ┃ ┃ ┃ Compute ┃ ┃
|
|
1314
1314
|
┃ ┃ Instance ┃ ┃ Life-cycle ┃ ┃ Compute ┃ Instance ┃ storage ┃ ┃
|
|
@@ -1427,7 +1427,7 @@ The expected output is a formatted table showing:
|
|
|
1427
1427
|
```console
|
|
1428
1428
|
Total related analyses found: 15
|
|
1429
1429
|
|
|
1430
|
-
Related Analyses
|
|
1430
|
+
Related Analyses
|
|
1431
1431
|
┏━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━┓
|
|
1432
1432
|
┃ Status ┃ Name ┃ Owner ┃ ID ┃ Submit time ┃ Run time ┃ Total Cost ┃
|
|
1433
1433
|
┡━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━┩
|
|
@@ -1909,7 +1909,7 @@ Example Python Script:
|
|
|
1909
1909
|
#!/usr/bin/python3
|
|
1910
1910
|
print("Hello world")
|
|
1911
1911
|
```
|
|
1912
|
-
|
|
1912
|
+
|
|
1913
1913
|
2. Or use an interpreter command in the executable field
|
|
1914
1914
|
|
|
1915
1915
|
If your script doesn’t have a shebang line, you can execute it by explicitly specifying the interpreter in the executable command:
|
|
@@ -1986,7 +1986,7 @@ Interactive sessions allow you to work within the platform using different virtu
|
|
|
1986
1986
|
|
|
1987
1987
|
You can get a list of all interactive sessions in your workspace by running `cloudos interactive-session list`. The command can produce three different output formats that can be selected using the `--output-format` option:
|
|
1988
1988
|
|
|
1989
|
-
- **stdout** (default): Displays a table directly in the terminal with interactive pagination
|
|
1989
|
+
- **stdout** (default): Displays a table directly in the terminal with interactive pagination
|
|
1990
1990
|
- **csv**: Saves session data to a CSV file with a minimum predefined set of columns by default, or all available columns using the `--all-fields` parameter
|
|
1991
1991
|
- **json**: Saves complete session information to a JSON file with all available fields
|
|
1992
1992
|
|
|
@@ -2001,7 +2001,7 @@ cloudos interactive-session list --profile my_profile --output-format stdout
|
|
|
2001
2001
|
The table displays sessions with pagination controls (press `n` for next page, `p` for previous page, or `q` to quit):
|
|
2002
2002
|
|
|
2003
2003
|
```console
|
|
2004
|
-
Interactive Sessions
|
|
2004
|
+
Interactive Sessions
|
|
2005
2005
|
┏━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━┓
|
|
2006
2006
|
┃ Status ┃ Name ┃ Type ┃ ID ┃ Owner ┃
|
|
2007
2007
|
┡━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━┩
|
|
@@ -2611,7 +2611,7 @@ The `datasets ls` command supports different output formats using the `--output-
|
|
|
2611
2611
|
- **`stdout` (default)**: Displays results in the console with Rich formatting
|
|
2612
2612
|
- Without `--details`: Simple list of file/folder names with color coding (blue underlined for folders)
|
|
2613
2613
|
- With `--details`: Rich formatted table with all file information
|
|
2614
|
-
|
|
2614
|
+
|
|
2615
2615
|
- **`csv`**: Saves results to a CSV file
|
|
2616
2616
|
- Without `--details`: CSV with two columns: "Name,Storage Path"
|
|
2617
2617
|
- With `--details`: CSV with columns "Type, Owner, Size, Size (bytes), Last Updated, Virtual Name, Storage Path"
|
|
@@ -2661,7 +2661,7 @@ Any of the `source_path` must be a full path, starting from the `Data` datasets
|
|
|
2661
2661
|
An example of such command is:
|
|
2662
2662
|
|
|
2663
2663
|
```
|
|
2664
|
-
cloudos datasets mv Data/results/my_plot.png Data/plots
|
|
2664
|
+
cloudos datasets mv Data/results/my_plot.png Data/plots
|
|
2665
2665
|
```
|
|
2666
2666
|
|
|
2667
2667
|
#### Rename Files
|
|
@@ -2672,7 +2672,7 @@ Change file and folder names while keeping them in the same location. This helps
|
|
|
2672
2672
|
> Files and folders within the `Data` dataset can be renamed using the following command
|
|
2673
2673
|
|
|
2674
2674
|
```bash
|
|
2675
|
-
cloudos datasets rename <path> <new_name> --profile my_profile
|
|
2675
|
+
cloudos datasets rename <path> <new_name> --profile my_profile
|
|
2676
2676
|
```
|
|
2677
2677
|
where `path` is the full path to the file/folder to be renamed and `new_name` is just the name, no path required, as the file will not be moved.
|
|
2678
2678
|
|
|
@@ -2698,12 +2698,12 @@ or it can happen **across different projects** within the same workspace
|
|
|
2698
2698
|
cloudos datasets cp <source_path> <destination_path> --profile <profile> --destination-project-name <project>
|
|
2699
2699
|
```
|
|
2700
2700
|
|
|
2701
|
-
Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder.
|
|
2701
|
+
Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder.
|
|
2702
2702
|
|
|
2703
2703
|
An example of such command is:
|
|
2704
2704
|
|
|
2705
2705
|
```
|
|
2706
|
-
cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
|
|
2706
|
+
cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
|
|
2707
2707
|
```
|
|
2708
2708
|
|
|
2709
2709
|
|
|
@@ -2754,7 +2754,7 @@ Create new organizational folders within your projects to maintain structured da
|
|
|
2754
2754
|
> New folders can be created within the `Data` dataset and its subfolders.
|
|
2755
2755
|
|
|
2756
2756
|
```bash
|
|
2757
|
-
cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
2757
|
+
cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
2758
2758
|
```
|
|
2759
2759
|
|
|
2760
2760
|
#### Remove Files or Folders
|
|
@@ -2762,14 +2762,14 @@ cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
|
2762
2762
|
Remove unnecessary files or empty folders from your File Explorer. Note that this removes files from Lifebit Platform but not from underlying cloud storage.
|
|
2763
2763
|
|
|
2764
2764
|
> [!NOTE]
|
|
2765
|
-
> Files and folders can be removed in the `Data` datasets and its subfolders.
|
|
2765
|
+
> Files and folders can be removed in the `Data` datasets and its subfolders.
|
|
2766
2766
|
|
|
2767
2767
|
```bash
|
|
2768
2768
|
cloudos datasets rm <path> --profile my_profile
|
|
2769
2769
|
```
|
|
2770
2770
|
> [!NOTE]
|
|
2771
2771
|
> If a file was uploaded by the user, in order to be removed you must use `--force` and that will permanently remove the file. If the file is "linked" (e.g a s3 folder or file), removing it using `cloudos datasets rm` will not remove it from the the s3 bucket.
|
|
2772
|
-
|
|
2772
|
+
|
|
2773
2773
|
---
|
|
2774
2774
|
|
|
2775
2775
|
### Link
|
|
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Current Cromwell server status is: Stopped
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```bash
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Command to run tests from the `cloudos-cli` main folder:
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```
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__version__ = '2.92.0'
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"""CLI commands for Lifebit Platform procurement management."""
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import rich_click as click
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import json
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The image type. Possible values are:
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The cloud provider. Currently only supporting 'aws' and 'azure'.
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The region. Currently only supporting aws regions.
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The region. Currently only supporting aws and azure regions.
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imageId
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The new value for image Id. Required.
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imageName
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The cloud provider. Currently only supporting 'aws' and 'azure'.
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The region. Currently only supporting aws regions.
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"""
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headers = {
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Metadata-Version: 2.4
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Name: cloudos_cli
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Version: 2.
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Version: 2.92.0
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Summary: Python package for interacting with the Lifebit Platform
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Home-page: https://github.com/lifebit-ai/cloudos-cli
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Author: David Piñeyro
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@@ -231,10 +231,10 @@ This will tell you the implemented commands. Each implemented command has its ow
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```bash
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cloudos job list --help
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```
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```console Usage: cloudos job list [OPTIONS]
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Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
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```console Usage: cloudos job list [OPTIONS]
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Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
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╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ * --apikey -k TEXT Your Lifebit Platform API key [required] │
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│ * --cloudos-url -c TEXT The Lifebit Platform url you are trying to access to. │
|
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@@ -299,7 +299,7 @@ $HOME
|
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### Configure Default Profile
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To facilitate the reuse of required parameters, you can create profiles.
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To facilitate the reuse of required parameters, you can create profiles.
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To generate a profile called `default`, use the following command:
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@@ -321,7 +321,7 @@ The same prompts will appear, including the execution platform (aws or azure). I
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When configuring a profile, you can specify:
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- **API Key**: Your Lifebit Platform API credentials
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|
-
- **Platform URL**: The Lifebit Platform instance URL
|
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+
- **Platform URL**: The Lifebit Platform instance URL
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- **Project Name**: Default project for commands
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- **Execution Platform**: `aws` (default) or `azure` - determines default instance types and available features
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- **Repository Platform**: Version control system (github, gitlab, etc.)
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|
@@ -1314,7 +1314,7 @@ cloudos job cost --profile my_profile --job-id 62c83a1191fe06013b7ef355
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The expected output is a formatted table showing:
|
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|
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```console
|
|
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-
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
|
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+
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
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┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
|
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┃ ┃ ┃ ┃ ┃ ┃ ┃ ┃ Compute ┃ ┃
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┃ ┃ Instance ┃ ┃ Life-cycle ┃ ┃ Compute ┃ Instance ┃ storage ┃ ┃
|
|
@@ -1343,7 +1343,7 @@ On page 1/2: n = next, p = prev, q = quit
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By pressing 'n', it will show the next page or the last if it is the case.
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-
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
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+
Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
|
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1347
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┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
|
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┃ ┃ ┃ ┃ ┃ ┃ ┃ ┃ Compute ┃ ┃
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┃ ┃ Instance ┃ ┃ Life-cycle ┃ ┃ Compute ┃ Instance ┃ storage ┃ ┃
|
|
@@ -1462,7 +1462,7 @@ The expected output is a formatted table showing:
|
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```console
|
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Total related analyses found: 15
|
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-
Related Analyses
|
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|
+
Related Analyses
|
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┏━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━┓
|
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┃ Status ┃ Name ┃ Owner ┃ ID ┃ Submit time ┃ Run time ┃ Total Cost ┃
|
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┡━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━┩
|
|
@@ -1944,7 +1944,7 @@ Example Python Script:
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#!/usr/bin/python3
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print("Hello world")
|
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```
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2. Or use an interpreter command in the executable field
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If your script doesn’t have a shebang line, you can execute it by explicitly specifying the interpreter in the executable command:
|
|
@@ -2021,7 +2021,7 @@ Interactive sessions allow you to work within the platform using different virtu
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You can get a list of all interactive sessions in your workspace by running `cloudos interactive-session list`. The command can produce three different output formats that can be selected using the `--output-format` option:
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|
|
2024
|
-
- **stdout** (default): Displays a table directly in the terminal with interactive pagination
|
|
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|
+
- **stdout** (default): Displays a table directly in the terminal with interactive pagination
|
|
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|
- **csv**: Saves session data to a CSV file with a minimum predefined set of columns by default, or all available columns using the `--all-fields` parameter
|
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|
- **json**: Saves complete session information to a JSON file with all available fields
|
|
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2027
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|
|
@@ -2036,7 +2036,7 @@ cloudos interactive-session list --profile my_profile --output-format stdout
|
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The table displays sessions with pagination controls (press `n` for next page, `p` for previous page, or `q` to quit):
|
|
2037
2037
|
|
|
2038
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|
```console
|
|
2039
|
-
Interactive Sessions
|
|
2039
|
+
Interactive Sessions
|
|
2040
2040
|
┏━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━┓
|
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┃ Status ┃ Name ┃ Type ┃ ID ┃ Owner ┃
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┡━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━┩
|
|
@@ -2646,7 +2646,7 @@ The `datasets ls` command supports different output formats using the `--output-
|
|
|
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|
- **`stdout` (default)**: Displays results in the console with Rich formatting
|
|
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|
- Without `--details`: Simple list of file/folder names with color coding (blue underlined for folders)
|
|
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|
- With `--details`: Rich formatted table with all file information
|
|
2649
|
-
|
|
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|
+
|
|
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|
- **`csv`**: Saves results to a CSV file
|
|
2651
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|
- Without `--details`: CSV with two columns: "Name,Storage Path"
|
|
2652
2652
|
- With `--details`: CSV with columns "Type, Owner, Size, Size (bytes), Last Updated, Virtual Name, Storage Path"
|
|
@@ -2696,7 +2696,7 @@ Any of the `source_path` must be a full path, starting from the `Data` datasets
|
|
|
2696
2696
|
An example of such command is:
|
|
2697
2697
|
|
|
2698
2698
|
```
|
|
2699
|
-
cloudos datasets mv Data/results/my_plot.png Data/plots
|
|
2699
|
+
cloudos datasets mv Data/results/my_plot.png Data/plots
|
|
2700
2700
|
```
|
|
2701
2701
|
|
|
2702
2702
|
#### Rename Files
|
|
@@ -2707,7 +2707,7 @@ Change file and folder names while keeping them in the same location. This helps
|
|
|
2707
2707
|
> Files and folders within the `Data` dataset can be renamed using the following command
|
|
2708
2708
|
|
|
2709
2709
|
```bash
|
|
2710
|
-
cloudos datasets rename <path> <new_name> --profile my_profile
|
|
2710
|
+
cloudos datasets rename <path> <new_name> --profile my_profile
|
|
2711
2711
|
```
|
|
2712
2712
|
where `path` is the full path to the file/folder to be renamed and `new_name` is just the name, no path required, as the file will not be moved.
|
|
2713
2713
|
|
|
@@ -2733,12 +2733,12 @@ or it can happen **across different projects** within the same workspace
|
|
|
2733
2733
|
cloudos datasets cp <source_path> <destination_path> --profile <profile> --destination-project-name <project>
|
|
2734
2734
|
```
|
|
2735
2735
|
|
|
2736
|
-
Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder.
|
|
2736
|
+
Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder.
|
|
2737
2737
|
|
|
2738
2738
|
An example of such command is:
|
|
2739
2739
|
|
|
2740
2740
|
```
|
|
2741
|
-
cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
|
|
2741
|
+
cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
|
|
2742
2742
|
```
|
|
2743
2743
|
|
|
2744
2744
|
|
|
@@ -2789,7 +2789,7 @@ Create new organizational folders within your projects to maintain structured da
|
|
|
2789
2789
|
> New folders can be created within the `Data` dataset and its subfolders.
|
|
2790
2790
|
|
|
2791
2791
|
```bash
|
|
2792
|
-
cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
2792
|
+
cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
2793
2793
|
```
|
|
2794
2794
|
|
|
2795
2795
|
#### Remove Files or Folders
|
|
@@ -2797,14 +2797,14 @@ cloudos datasets mkdir <new_folder_path> --profile my_profile
|
|
|
2797
2797
|
Remove unnecessary files or empty folders from your File Explorer. Note that this removes files from Lifebit Platform but not from underlying cloud storage.
|
|
2798
2798
|
|
|
2799
2799
|
> [!NOTE]
|
|
2800
|
-
> Files and folders can be removed in the `Data` datasets and its subfolders.
|
|
2800
|
+
> Files and folders can be removed in the `Data` datasets and its subfolders.
|
|
2801
2801
|
|
|
2802
2802
|
```bash
|
|
2803
2803
|
cloudos datasets rm <path> --profile my_profile
|
|
2804
2804
|
```
|
|
2805
2805
|
> [!NOTE]
|
|
2806
2806
|
> If a file was uploaded by the user, in order to be removed you must use `--force` and that will permanently remove the file. If the file is "linked" (e.g a s3 folder or file), removing it using `cloudos datasets rm` will not remove it from the the s3 bucket.
|
|
2807
|
-
|
|
2807
|
+
|
|
2808
2808
|
---
|
|
2809
2809
|
|
|
2810
2810
|
### Link
|
|
@@ -2926,7 +2926,7 @@ To list images for a specific procurement, use the following command:
|
|
|
2926
2926
|
|
|
2927
2927
|
```bash
|
|
2928
2928
|
cloudos procurement images ls \
|
|
2929
|
-
-- profile procurement_profile
|
|
2929
|
+
-- profile procurement_profile
|
|
2930
2930
|
--procurement-id "your_procurement_id_here"
|
|
2931
2931
|
```
|
|
2932
2932
|
|
|
@@ -2985,12 +2985,10 @@ cloudos procurement images set --profile procurement_profile --image-type "JobDe
|
|
|
2985
2985
|
- `--image-type`: The Lifebit Platform resource image type (required). Possible values:
|
|
2986
2986
|
- `RegularInteractiveSessions`
|
|
2987
2987
|
- `SparkInteractiveSessions`
|
|
2988
|
-
- `RStudioInteractiveSessions`
|
|
2989
|
-
- `JupyterInteractiveSessions`
|
|
2990
2988
|
- `JobDefault`
|
|
2991
2989
|
- `NextflowBatchComputeEnvironment`
|
|
2992
|
-
- `--provider`: The cloud provider (required). Currently only `aws`
|
|
2993
|
-
- `--region`: The cloud region (required). Currently only
|
|
2990
|
+
- `--provider`: The cloud provider (required). Currently only supporting `aws` and `azure`.
|
|
2991
|
+
- `--region`: The cloud region (required). Currently only supporting aws and azure regions.
|
|
2994
2992
|
- `--image-id`: The new image ID value (required)
|
|
2995
2993
|
- `--image-name`: The new image name value (optional)
|
|
2996
2994
|
- `--image-version`: The new image version (required)
|
|
@@ -3023,7 +3021,7 @@ cloudos procurement images reset --profile procurement_profile --image-type "Job
|
|
|
3023
3021
|
- `--organisation-id`: The organization ID where the change will be applied (required)
|
|
3024
3022
|
- `--image-type`: The Lifebit Platform resource image type (required). Same values as for `set` command
|
|
3025
3023
|
- `--provider`: The cloud provider (required). Currently only `aws` is supported
|
|
3026
|
-
- `--region`: The cloud region (required). Currently only
|
|
3024
|
+
- `--region`: The cloud region (required). Currently only supporting aws and azure regions.
|
|
3027
3025
|
- `--disable-ssl-verification`: Disable SSL certificate verification
|
|
3028
3026
|
- `--ssl-cert`: Path to your SSL certificate file
|
|
3029
3027
|
- `--profile`: Profile to use from the config file
|
|
@@ -3052,7 +3050,7 @@ Executing status...
|
|
|
3052
3050
|
Current Cromwell server status is: Stopped
|
|
3053
3051
|
```
|
|
3054
3052
|
|
|
3055
|
-
```bash
|
|
3053
|
+
```bash
|
|
3056
3054
|
# Cromwell start
|
|
3057
3055
|
cloudos cromwell start --profile my_profile
|
|
3058
3056
|
```
|
|
@@ -3278,8 +3276,8 @@ responses>=0.21.0
|
|
|
3278
3276
|
mock>=3.0.5
|
|
3279
3277
|
```
|
|
3280
3278
|
|
|
3281
|
-
Command to run tests from the `cloudos-cli` main folder:
|
|
3279
|
+
Command to run tests from the `cloudos-cli` main folder:
|
|
3282
3280
|
|
|
3283
3281
|
```
|
|
3284
3282
|
python -m pytest -s -v
|
|
3285
|
-
```
|
|
3283
|
+
```
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
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|
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|
|
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|
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|
|
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|
|
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|
|
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|
{cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/cloudos_cli/interactive_session/interactive_session.py
RENAMED
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
|
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|
{cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_interactive_session/test_create_session.py
RENAMED
|
File without changes
|
{cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_interactive_session/test_list_sessions.py
RENAMED
|
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|
|
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|
|
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|
|
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|
|
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|
{cloudos_cli-2.91.0 → cloudos_cli-2.92.0}/tests/test_related_analyses/test_related_analyses.py
RENAMED
|
File without changes
|