cloudos-cli 2.81.0__tar.gz → 2.81.1__tar.gz

{cloudos_cli-2.81.0 → cloudos_cli-2.81.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.81.0
+Version: 2.81.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -554,6 +554,16 @@ cloudos job run \
   --resumable
 ```
 
+Azure Blob example:
+
+```bash
+cloudos job run \
+  --profile my_profile \
+  --workflow-name rnatoy \
+  --params-file az://6480f3db916489d248956a5f.blob.core.windows.net/cloudos-66607e71e8cffa9985592c10/dataset/697b7341c69bacdd8b0b700d/rnatoy_params.json \
+  --resumable
+```
+
 Example JSON params file:
 
 ```json
@@ -577,7 +587,7 @@ annot:
 
 > NOTE: options `--job-config`, `--parameter` and `--params-file` are completely compatible and complementary, so you can use a `--job-config` or `--params-file` and add additional parameters using `--parameter` in the same call.
 
-> NOTE: when using `--params-file`, the value must be an S3 URI or a File Explorer relative path (e.g., `Data/file.json`). Local file paths are not supported.
+> NOTE: when using `--params-file`, the value must be an S3 URI, an Azure Blob URI (`az://<account>.blob.core.windows.net/<container>/<blob>`), or a File Explorer relative path (e.g., `Data/file.json`). Local file paths are not supported.
 
 If everything went well, you should see something like:
 

{cloudos_cli-2.81.0 → cloudos_cli-2.81.1}/README.md

@@ -519,6 +519,16 @@ cloudos job run \
   --resumable
 ```
 
+Azure Blob example:
+
+```bash
+cloudos job run \
+  --profile my_profile \
+  --workflow-name rnatoy \
+  --params-file az://6480f3db916489d248956a5f.blob.core.windows.net/cloudos-66607e71e8cffa9985592c10/dataset/697b7341c69bacdd8b0b700d/rnatoy_params.json \
+  --resumable
+```
+
 Example JSON params file:
 
 ```json
@@ -542,7 +552,7 @@ annot:
 
 > NOTE: options `--job-config`, `--parameter` and `--params-file` are completely compatible and complementary, so you can use a `--job-config` or `--params-file` and add additional parameters using `--parameter` in the same call.
 
-> NOTE: when using `--params-file`, the value must be an S3 URI or a File Explorer relative path (e.g., `Data/file.json`). Local file paths are not supported.
+> NOTE: when using `--params-file`, the value must be an S3 URI, an Azure Blob URI (`az://<account>.blob.core.windows.net/<container>/<blob>`), or a File Explorer relative path (e.g., `Data/file.json`). Local file paths are not supported.
 
 If everything went well, you should see something like:
 

cloudos_cli-2.81.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.81.1'

{cloudos_cli-2.81.0 → cloudos_cli-2.81.1}/cloudos_cli/clos.py

@@ -1236,7 +1236,7 @@ class Cloudos:
                     if not queue_id:
                         raise ValueError(f"Queue with name '{filter_queue}' not found in workspace '{workspace_id}'")
 
-                    all_jobs = [job for job in all_jobs if job.get("batch", {}).get("jobQueue", {}).get("id") == queue_id]
+                    all_jobs = [job for job in all_jobs if job.get("batch", {}).get("jobQueue", {}) == queue_id]
                 else:
                     raise ValueError(f"The environment is not a batch environment so queues do not exist. Please remove the --filter-queue option.")
             except Exception as e:
@@ -1284,7 +1284,7 @@ class Cloudos:
                    'nextflowVersion',
                    'batch.enabled',
                    'storageSizeInGb',
-                   'batch.jobQueue.id',
+                   'batch.jobQueue',
                    'usesFusionFileSystem'
                    ]
         df_full = pd.json_normalize(r)
@@ -1416,7 +1416,7 @@ class Cloudos:
             "nextflowVersion": "Nextflow version",
             "batch.enabled": "Executor",
             "storageSizeInGb": "Storage size",
-            "batch.jobQueue.id": "Job queue ID",
+            "batch.jobQueue": "Job queue ID",
             "usesFusionFileSystem": "Accelerated file staging"
         }
 

{cloudos_cli-2.81.0 → cloudos_cli-2.81.1}/cloudos_cli/jobs/cli.py

@@ -68,7 +68,8 @@ def job():
               help=('A file containing the parameters to pass to the job call. ' +
                     'It should be a .json or .yaml file with a dictionary structure ' +
                     'where keys are parameter names and values are parameter values. ' +
-                    'This expects an S3 URI file path or a File Explorer relative path ' +
+                    'This expects an S3 URI, Azure Blob URI (az://<account>.blob.core.windows.net/<container>/<blob>) ' +
+                    'or a File Explorer relative path ' +
                     '(e.g., Data/params_file.json) and does not work with local files.'))
 @click.option('-p',
               '--parameter',

{cloudos_cli-2.81.0 → cloudos_cli-2.81.1}/cloudos_cli/jobs/job.py

@@ -11,6 +11,7 @@ from cloudos_cli.utils.requests import retry_requests_post, retry_requests_get,
 from pathlib import Path
 from urllib.parse import urlparse
 import base64
+import re
 from cloudos_cli.utils.array_job import classify_pattern, get_file_or_folder_id, extract_project
 import os
 import click
@@ -183,11 +184,7 @@ class Job(Cloudos):
             if len(params_file) != 1:
                 raise ValueError('Please, provide a single file for --params-file.')
             params_file = params_file[0]
-
-        ext = os.path.splitext(params_file)[1].lower()
         allowed_ext = {'.json', '.yaml', '.yml'}
-        if ext not in allowed_ext:
-            raise ValueError('Please, provide a .json or .yaml file for --params-file.')
 
         if params_file.startswith('s3://'):
             parsed = urlparse(params_file)
@@ -196,6 +193,9 @@ class Job(Cloudos):
             if not bucket or not s3_key:
                 raise ValueError('Invalid S3 URL. Please, provide a full s3://bucket/key path.')
             name = s3_key.rstrip('/').split('/')[-1]
+            ext = os.path.splitext(name)[1].lower()
+            if ext not in allowed_ext:
+                raise ValueError('Please, provide a .json or .yaml file for --params-file.')
             return {
                 "parametersFile": {
                     "dataItemEmbedded": {
@@ -209,9 +209,57 @@ class Job(Cloudos):
                 }
             }
 
+        if params_file.startswith('az://'):
+            parsed = urlparse(params_file)
+            if parsed.query:
+                raise ValueError('Azure URL with query parameters is not supported for --params-file.')
+
+            host = parsed.netloc
+            if not host.endswith('.blob.core.windows.net'):
+                raise ValueError('Invalid Azure URL. Expected format: az://<account>.blob.core.windows.net/<container>/<blobName>')
+
+            blob_storage_account_name = host[:-len('.blob.core.windows.net')]
+            path_parts = parsed.path.lstrip('/').split('/', 1)
+            if len(path_parts) != 2:
+                raise ValueError('Invalid Azure URL. Expected format: az://<account>.blob.core.windows.net/<container>/<blobName>')
+
+            blob_container_name, blob_name = path_parts
+            blob_name = blob_name.rstrip('/')
+            if not blob_storage_account_name or not blob_container_name or not blob_name:
+                raise ValueError('Invalid Azure URL. Expected format: az://<account>.blob.core.windows.net/<container>/<blobName>')
+
+            blob_leaf = blob_name.split('/')[-1]
+            uuid_suffix_match = re.match(r'^(.*)_([0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12})$', blob_leaf)
+            if uuid_suffix_match:
+                name = uuid_suffix_match.group(1)
+            else:
+                name = blob_leaf
+
+            ext = os.path.splitext(name)[1].lower()
+            if ext not in allowed_ext:
+                raise ValueError('Please, provide a .json or .yaml file for --params-file.')
+
+            return {
+                "parametersFile": {
+                    "dataItemEmbedded": {
+                        "data": {
+                            "name": name,
+                            "blobStorageAccountName": blob_storage_account_name,
+                            "blobContainerName": blob_container_name,
+                            "blobName": blob_name
+                        },
+                        "type": "AzureBlobFile"
+                    }
+                }
+            }
+
         if not self.project_name:
             raise ValueError('Please, provide --project-name to resolve --params-file paths.')
 
+        ext = os.path.splitext(params_file)[1].lower()
+        if ext not in allowed_ext:
+            raise ValueError('Please, provide a .json or .yaml file for --params-file.')
+
         normalized_path = params_file.lstrip('/')
         allowed_prefixes = ('Data', 'Analyses Results', 'Cohorts')
         if not normalized_path.startswith(allowed_prefixes):

{cloudos_cli-2.81.0 → cloudos_cli-2.81.1}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.81.0
+Version: 2.81.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -554,6 +554,16 @@ cloudos job run \
   --resumable
 ```
 
+Azure Blob example:
+
+```bash
+cloudos job run \
+  --profile my_profile \
+  --workflow-name rnatoy \
+  --params-file az://6480f3db916489d248956a5f.blob.core.windows.net/cloudos-66607e71e8cffa9985592c10/dataset/697b7341c69bacdd8b0b700d/rnatoy_params.json \
+  --resumable
+```
+
 Example JSON params file:
 
 ```json
@@ -577,7 +587,7 @@ annot:
 
 > NOTE: options `--job-config`, `--parameter` and `--params-file` are completely compatible and complementary, so you can use a `--job-config` or `--params-file` and add additional parameters using `--parameter` in the same call.
 
-> NOTE: when using `--params-file`, the value must be an S3 URI or a File Explorer relative path (e.g., `Data/file.json`). Local file paths are not supported.
+> NOTE: when using `--params-file`, the value must be an S3 URI, an Azure Blob URI (`az://<account>.blob.core.windows.net/<container>/<blob>`), or a File Explorer relative path (e.g., `Data/file.json`). Local file paths are not supported.
 
 If everything went well, you should see something like:
 

cloudos_cli-2.81.0/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.81.0'