cloudos-cli 2.88.2__tar.gz → 2.89.0__tar.gz

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.88.2
+Version: 2.89.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -753,9 +753,8 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 Please note that HPC execution does not support the following parameters and all of them will be ignored:
 
 - `--job-queue`
-- `--resumable | --do-not-save-logs`
+- `--resumable` | `--do-not-save-logs`
 - `--instance-type` | `--instance-disk` | `--cost-limit`
-- `--storage-mode` | `--lustre-size`
 - `--wdl-mainfile` | `--wdl-importsfile` | `--cromwell-token`
 
 #### Check Job Status

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/README.md

@@ -718,9 +718,8 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 Please note that HPC execution does not support the following parameters and all of them will be ignored:
 
 - `--job-queue`
-- `--resumable | --do-not-save-logs`
+- `--resumable` | `--do-not-save-logs`
 - `--instance-type` | `--instance-disk` | `--cost-limit`
-- `--storage-mode` | `--lustre-size`
 - `--wdl-mainfile` | `--wdl-importsfile` | `--cromwell-token`
 
 #### Check Job Status

cloudos_cli-2.89.0/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.89.0'

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/cloudos_cli/bash/cli.py

@@ -75,15 +75,7 @@ def bash():
               help='The amount of memory, in GB, to use for the task\'s master node. Default=4.',
               type=int,
               default=4)
-@click.option('--storage-mode',
-              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
-                    'regular or lustre storage. Default=regular.'),
-              default='regular')
-@click.option('--lustre-size',
-              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
-                    'be 1200 or a multiple of it. Default=1200.'),
-              type=int,
-              default=1200)
+
 @click.option('--wait-completion',
               help=('Whether to wait to job completion and report final ' +
                     'job status.'),
@@ -136,8 +128,6 @@ def run_bash_job(ctx,
                  instance_disk,
                  cpus,
                  memory,
-                 storage_mode,
-                 lustre_size,
                  wait_completion,
                  wait_time,
                  repository_platform,
@@ -194,8 +184,6 @@ def run_bash_job(ctx,
                       nextflow_version=None,
                       instance_type=instance_type,
                       instance_disk=instance_disk,
-                      storage_mode=storage_mode,
-                      lustre_size=lustre_size,
                       execution_platform=execution_platform,
                       hpc_id=None,
                       cost_limit=cost_limit,
@@ -296,15 +284,6 @@ def run_bash_job(ctx,
               help='The amount of memory, in GB, to use for the task\'s master node. Default=4.',
               type=int,
               default=4)
-@click.option('--storage-mode',
-              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
-                    'regular or lustre storage. Default=regular.'),
-              default='regular')
-@click.option('--lustre-size',
-              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
-                    'be 1200 or a multiple of it. Default=1200.'),
-              type=int,
-              default=1200)
 @click.option('--wait-completion',
               help=('Whether to wait to job completion and report final ' +
                     'job status.'),
@@ -391,8 +370,6 @@ def run_bash_array_job(ctx,
                        instance_disk,
                        cpus,
                        memory,
-                       storage_mode,
-                       lustre_size,
                        wait_completion,
                        wait_time,
                        repository_platform,
@@ -525,8 +502,6 @@ def run_bash_array_job(ctx,
                       nextflow_version=None,
                       instance_type=instance_type,
                       instance_disk=instance_disk,
-                      storage_mode=storage_mode,
-                      lustre_size=lustre_size,
                       execution_platform=execution_platform,
                       hpc_id=None,
                       cost_limit=cost_limit,

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/cloudos_cli/jobs/cli.py

@@ -119,15 +119,6 @@ def job():
               help='The disk space of the master node instance, in GB. Default=500.',
               type=int,
               default=500)
-@click.option('--storage-mode',
-              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
-                    'regular or lustre storage. Default=regular.'),
-              default='regular')
-@click.option('--lustre-size',
-              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
-                    'be 1200 or a multiple of it. Default=1200.'),
-              type=int,
-              default=1200)
 @click.option('--wait-completion',
               help=('Whether to wait to job completion and report final ' +
                     'job status.'),
@@ -219,8 +210,6 @@ def run(ctx,
         nextflow_version,
         instance_type,
         instance_disk,
-        storage_mode,
-        lustre_size,
         wait_completion,
         wait_time,
         wdl_mainfile,
@@ -267,11 +256,9 @@ def run(ctx,
               '\t--job-queue\n' +
               '\t--resumable | --do-not-save-logs\n' +
               '\t--instance-type | --instance-disk | --cost-limit\n' +
-              '\t--storage-mode | --lustre-size\n' +
               '\t--wdl-mainfile | --wdl-importsfile | --cromwell-token\n')
         wdl_mainfile = None
         wdl_importsfile = None
-        storage_mode = 'regular'
         save_logs = False
     if accelerate_file_staging:
         if execution_platform != 'aws':
@@ -377,7 +364,7 @@ def run(ctx,
                                 'Docker account to CloudOS before using ' +
                                 '--use-private-docker-repository option.')
             print('Use private Docker repository has been selected. A custom job ' +
-                  'queue to support private Docker containers and/or Lustre FSx will be created for ' +
+                  'queue to support private Docker containers will be created for ' +
                   'your job. The selected job queue will serve as a template.')
             docker_login = True
     else:
@@ -402,8 +389,6 @@ def run(ctx,
                       nextflow_version=nextflow_version,
                       instance_type=instance_type,
                       instance_disk=instance_disk,
-                      storage_mode=storage_mode,
-                      lustre_size=lustre_size,
                       execution_platform=execution_platform,
                       hpc_id=hpc_id,
                       workflow_type=workflow_type,

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/cloudos_cli/jobs/job.py

@@ -309,8 +309,6 @@ class Job(Cloudos):
                                  nextflow_version,
                                  instance_type,
                                  instance_disk,
-                                 storage_mode,
-                                 lustre_size,
                                  execution_platform,
                                  hpc_id,
                                  workflow_type,
@@ -381,12 +379,6 @@ class Job(Cloudos):
             Name of the instance type to be used for the job master node, for example for AWS EC2 c5.xlarge
         instance_disk : int
             The disk space of the master node instance, in GB.
-        storage_mode : string
-            Either 'lustre' or 'regular'. Indicates if the user wants to select regular
-            or lustre storage.
-        lustre_size : int
-            The lustre storage to be used when --storage-mode=lustre, in GB. It should be 1200 or
-            a multiple of it.
         execution_platform : string ['aws'|'azure'|'hpc']
             The execution platform implemented in your CloudOS.
         hpc_id : string
@@ -511,15 +503,6 @@ class Job(Cloudos):
         if len(example_parameters) > 0:
             for example_param in example_parameters:
                 workflow_params.append(example_param)
-        if storage_mode == "lustre":
-            click.secho('\nLustre storage has been selected. Please, be sure that this kind of ' +
-                  'storage is available in your CloudOS workspace.\n', fg='yellow', bold=True)
-            if lustre_size % 1200:
-                raise ValueError('Please, specify a lustre storage size of 1200 or a multiple of it. ' +
-                                 f'{lustre_size} is not a valid number.')
-        if storage_mode not in ['lustre', 'regular']:
-            raise ValueError('Please, use either \'lustre\' or \'regular\' for --storage-mode ' +
-                             f'{storage_mode} is not allowed')
         params = {
             "parameters": workflow_params,
             "project": project_id,
@@ -534,8 +517,6 @@ class Job(Cloudos):
                 "computeCostLimit": cost_limit,
                 "optim": "test"
             },
-            "lusterFsxStorageSizeInGb": lustre_size,
-            "storageMode": storage_mode,
             "instanceType": instance_type,
             "usesFusionFileSystem": use_mountpoints,
             "accelerateSavingResults": accelerate_saving_results
@@ -610,8 +591,6 @@ class Job(Cloudos):
                  nextflow_version='22.10.8',
                  instance_type='c5.xlarge',
                  instance_disk=500,
-                 storage_mode='regular',
-                 lustre_size=1200,
                  execution_platform='aws',
                  hpc_id=None,
                  workflow_type='nextflow',
@@ -676,12 +655,6 @@ class Job(Cloudos):
             Name of the instance type to be used for the job master node, for example for AWS EC2 c5.xlarge
         instance_disk : int
             The disk space of the master node instance, in GB.
-        storage_mode : string
-            Either 'lustre' or 'regular'. Indicates if the user wants to select regular
-            or lustre storage.
-        lustre_size : int
-            The lustre storage to be used when --storage-mode=lustre, in GB. It should be 1200 or
-            a multiple of it.
         execution_platform : string ['aws'|'azure'|'hpc']
             The execution platform implemented in your CloudOS.
         hpc_id : string
@@ -751,8 +724,6 @@ class Job(Cloudos):
                                                nextflow_version,
                                                instance_type,
                                                instance_disk,
-                                               storage_mode,
-                                               lustre_size,
                                                execution_platform,
                                                hpc_id,
                                                workflow_type,

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/cloudos_cli/utils/details.py

@@ -41,7 +41,13 @@ def get_path(param, param_kind_map, execution_platform, storage_provider, mode="
         - For 'globPattern' on AWS Batch: "s3BucketName/s3Prefix/globPattern".
         - For 'globPattern' on other platforms: "blobStorageAccountName/blobContainerName/blobPrefix/globPattern".
     """
-    value = param[param_kind_map[param['parameterKind']]]
+    # Handle unsupported parameter kinds (e.g., legacy 'lustreFileSystem' from historical jobs)
+    parameter_kind = param['parameterKind']
+    if parameter_kind not in param_kind_map:
+        # Return the parameterKind as-is to indicate an unsupported/legacy parameter type
+        return f"<unsupported parameter type: {parameter_kind}>"
+    
+    value = param[param_kind_map[parameter_kind]]
     if param['parameterKind'] == 'dataItem':
         if execution_platform == "Batch AWS":
             s3_object_key = value['item'].get('s3ObjectKey', None) if value['item'].get('s3Prefix', None) is None else value['item'].get('s3Prefix', None)
@@ -140,7 +146,6 @@ def create_job_details(j_details_h, job_id, output_format, output_basename, para
     - 'textValue': Simple text parameters
     - 'arrayFileColumn': Column-based array parameters
     - 'globPattern': File pattern matching parameters
-    - 'lustreFileSystem': Lustre filesystem parameters
     - 'dataItem': Data file/object parameters
 
     Time calculations assume UTC timezone and convert ISO format timestamps
@@ -166,10 +171,9 @@ def create_job_details(j_details_h, job_id, output_format, output_basename, para
             'textValue': 'textValue',
             'arrayFileColumn': 'columnName',
             'globPattern': 'globPattern',
-            'lustreFileSystem': 'fileSystem',
             'dataItem': 'dataItem'
         }
-        # there are different types of parameters, arrayFileColumn, globPattern, lustreFileSystem
+        # there are different types of parameters, arrayFileColumn, globPattern
         # get first the type of parameter, then the value based on the parameter kind
         concats = []
         for param in j_details_h["parameters"]:
@@ -476,8 +480,6 @@ def _build_job_row_values(job, cloudos_url, terminal_width, columns_to_show):
     storage_mode = job.get("storageMode", "N/A")
     if storage_mode == "regular":
         storage_type = "Regular"
-    elif storage_mode == "lustre":
-        storage_type = "Lustre"
     else:
         storage_type = str(storage_mode).capitalize() if storage_mode != "N/A" else "N/A"
 

{cloudos_cli-2.88.2 → cloudos_cli-2.89.0}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.88.2
+Version: 2.89.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -753,9 +753,8 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 Please note that HPC execution does not support the following parameters and all of them will be ignored:
 
 - `--job-queue`
-- `--resumable | --do-not-save-logs`
+- `--resumable` | `--do-not-save-logs`
 - `--instance-type` | `--instance-disk` | `--cost-limit`
-- `--storage-mode` | `--lustre-size`
 - `--wdl-mainfile` | `--wdl-importsfile` | `--cromwell-token`
 
 #### Check Job Status

cloudos_cli-2.88.2/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.88.2'