cloudos-cli 2.31.1__tar.gz → 2.32.1__tar.gz

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.31.1
+Version: 2.32.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -902,6 +902,26 @@ Please, note that in the above example a preconfigured profile has been used. If
     --project-name $PROJEC_NAME
 ```
 
+#### Renaming files
+
+Files and folders within the `Data` dataset can be renamed using the following command
+
+```
+cloudos datasets rename <path> <new_name>
+```
+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.
+
+Please, be aware that renaming can only happen in files and folders that are present in the `Data` datasets and that were created or uploaded by your user.
+
+Please, note that in the above example a preconfigured profile has been used. If no profile is provided and there is no default profile, the user will need to also provide the following flags
+
+```bash
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --project-name $PROJEC_NAME
+```
+
 ### WDL pipeline support
 
 #### Cromwell server managing

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/README.md

@@ -867,6 +867,26 @@ Please, note that in the above example a preconfigured profile has been used. If
     --project-name $PROJEC_NAME
 ```
 
+#### Renaming files
+
+Files and folders within the `Data` dataset can be renamed using the following command
+
+```
+cloudos datasets rename <path> <new_name>
+```
+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.
+
+Please, be aware that renaming can only happen in files and folders that are present in the `Data` datasets and that were created or uploaded by your user.
+
+Please, note that in the above example a preconfigured profile has been used. If no profile is provided and there is no default profile, the user will need to also provide the following flags
+
+```bash
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --project-name $PROJEC_NAME
+```
+
 ### WDL pipeline support
 
 #### Cromwell server managing

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/cloudos_cli/__main__.py

@@ -16,6 +16,7 @@ from rich.table import Table
 from cloudos_cli.datasets import Datasets
 from cloudos_cli.utils.resources import ssl_selector, format_bytes
 from rich.style import Style
+from cloudos_cli.utils.details import get_path 
 
 
 # GLOBAL VARS
@@ -85,7 +86,8 @@ def run_cloudos_cli(ctx):
             },
             'datasets': {
                 'ls': shared_config,
-                'mv': shared_config
+                'mv': shared_config,
+                'rename': shared_config
             }
         })
     else:
@@ -130,7 +132,8 @@ def run_cloudos_cli(ctx):
             },
             'datasets': {
                 'ls': shared_config,
-                'mv': shared_config
+                'mv': shared_config,
+                'rename': shared_config
             }
         })
 
@@ -942,6 +945,19 @@ def job_details(ctx,
             sys.exit(1)
     j_details_h = json.loads(j_details.content)
 
+    # Determine the execution platform based on jobType
+    executors = {
+        'nextflowAWS': 'Batch AWS',
+        'nextflowAzure': 'Batch Azure',
+        'nextflowGcp': 'GCP',
+        'nextflowHpc': 'HPC',
+        'nextflowKubernetes': 'Kubernetes',
+        'dockerAWS': 'Batch AWS',
+        'cromwellAWS': 'Batch AWS'
+    }
+    execution_platform = executors.get(j_details_h["jobType"], "None")
+    storage_provider = "s3://" if execution_platform == "Batch AWS" else "az://"
+
     # Check if the job details contain parameters
     if j_details_h["parameters"] != []:
         param_kind_map = {
@@ -949,18 +965,15 @@ def job_details(ctx,
             'arrayFileColumn': 'columnName',
             'globPattern': 'globPattern',
             'lustreFileSystem': 'fileSystem',
+            'dataItem': 'dataItem'
         }
         # there are different types of parameters, arrayFileColumn, globPattern, lustreFileSystem
         # get first the type of parameter, then the value based on the parameter kind
         concats = []
         for param in j_details_h["parameters"]:
-            if param['parameterKind'] == 'dataItem':
-                # For dataItem, we need to use specific nested keys
-                concats.append(f"{param['prefix']}{param['name']}={param['dataItem']['item']['name']}")
-            else:
-                # For other parameter kinds, we use the appropriate key from param_kind_map
-                concats.append(f"{param['prefix']}{param['name']}={param[param_kind_map[param['parameterKind']]]}")
+            concats.append(f"{param['prefix']}{param['name']}={get_path(param, param_kind_map, execution_platform, storage_provider, 'asis')}")
         concat_string = '\n'.join(concats)
+
         # If the user requested to save the parameters in a config file
         if parameters:
             # Create a config file with the parameters
@@ -968,7 +981,7 @@ def job_details(ctx,
             with open(config_filename, 'w') as config_file:
                 config_file.write("params {\n")
                 for param in j_details_h["parameters"]:
-                    config_file.write(f"\t{param['name']} = {param['textValue']}\n")
+                    config_file.write(f"\t{param['name']} = {get_path(param, param_kind_map, execution_platform, storage_provider)}\n")
                 config_file.write("}\n")
             print(f"\tJob parameters have been saved to '{config_filename}'")
     else:
@@ -976,18 +989,6 @@ def job_details(ctx,
         if parameters:
             print("\tNo parameters found in the job details, no config file will be created.")
 
-    # Determine the execution platform based on jobType
-    executors = {
-        'nextflowAWS': 'Batch AWS',
-        'nextflowAzure': 'Batch Azure',
-        'nextflowGcp': 'GCP',
-        'nextflowHpc': 'HPC',
-        'nextflowKubernetes': 'Kubernetes',
-        'dockerAWS': 'Batch AWS',
-        'cromwellAWS': 'Batch AWS'
-    }
-    execution_platform = executors.get(j_details_h["jobType"], "None")
-
     # revision
     if j_details_h["jobType"] == "dockerAWS":
         revision = j_details_h["revision"]["digest"]
@@ -1010,7 +1011,11 @@ def job_details(ctx,
         table.add_row("Nextflow Version", str(j_details_h.get("nextflowVersion", "None")))
         table.add_row("Execution Platform", execution_platform)
         table.add_row("Profile", str(j_details_h.get("profile", "None")))
-        table.add_row("Master Instance", str(j_details_h["masterInstance"]["usedInstance"]["type"]))
+        # when the job is just running this value might not be present
+        master_instance = j_details_h.get("masterInstance", {})
+        used_instance = master_instance.get("usedInstance", {})
+        instance_type = used_instance.get("type", "N/A")
+        table.add_row("Master Instance", str(instance_type))
         if j_details_h["jobType"] == "nextflowAzure":
             try:
                 table.add_row("Worker Node", str(j_details_h["azureBatch"]["vmType"]))
@@ -1037,7 +1042,6 @@ def job_details(ctx,
             "Nextflow Version": str(j_details_h.get("nextflowVersion", "None")),
             "Execution Platform": execution_platform,
             "Profile": str(j_details_h.get("profile", "None")),
-            "Master Instance": str(j_details_h["masterInstance"]["usedInstance"]["type"]),
             "Storage": str(j_details_h["storageSizeInGb"]) + " GB",
             "Accelerated File Staging": str(j_details_h.get("usesFusionFileSystem", "None")),
             "Task Resources": f"{str(j_details_h['resourceRequirements']['cpu'])} CPUs, " +
@@ -1045,6 +1049,12 @@ def job_details(ctx,
 
         }
 
+        # when the job is just running this value might not be present
+        master_instance = j_details_h.get("masterInstance", {})
+        used_instance = master_instance.get("usedInstance", {})
+        instance_type = used_instance.get("type", "N/A")
+        job_details_json["Master Instance"] = str(instance_type)
+
         # Conditionally add the "Command" key if the jobType is "dockerAWS"
         if j_details_h["jobType"] == "dockerAWS":
             job_details_json["Command"] = str(j_details_h["command"])
@@ -2351,8 +2361,7 @@ def move_files(ctx, source_path, destination_path, apikey, cloudos_url, workspac
     """
 
     profile = profile or ctx.default_map['datasets']['move'].get('profile')
-    destination_project_name = destination_project_name or project_name
-
+    
     # Validate destination constraint
     if not destination_path.strip("/").startswith("Data/") and destination_path.strip("/") != "Data":
         click.echo("[ERROR] Destination path must begin with 'Data/' or be 'Data'.", err=True)
@@ -2388,6 +2397,8 @@ def move_files(ctx, source_path, destination_path, apikey, cloudos_url, workspac
     )
 
     verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+
+    destination_project_name = destination_project_name or project_name
     # Initialize Datasets clients
     source_client = Datasets(
         cloudos_url=cloudos_url,
@@ -2479,5 +2490,111 @@ def move_files(ctx, source_path, destination_path, apikey, cloudos_url, workspac
         sys.exit(1)
 
 
+@datasets.command(name="rename")
+@click.argument("source_path", required=True)
+@click.argument("new_name", required=True)
+@click.option('-k', '--apikey', required=True, help='Your CloudOS API key.')
+@click.option('-c', '--cloudos-url', default=CLOUDOS_URL, required=True, help='The CloudOS URL.')
+@click.option('--workspace-id', required=True, help='The CloudOS workspace ID.')
+@click.option('--project-name', required=True, help='The project name.')
+@click.option('--disable-ssl-verification', is_flag=True, help='Disable SSL certificate verification.')
+@click.option('--ssl-cert', help='Path to your SSL certificate file.')
+@click.option('--profile', default=None, help='Profile to use from the config file.')
+@click.pass_context
+def renaming_item(ctx, source_path, new_name, apikey, cloudos_url,
+                    workspace_id, project_name,
+                    disable_ssl_verification, ssl_cert, profile):
+    """
+    Rename a file or folder in a CloudOS project.
+
+    SOURCE_PATH [path]: the full path to the file or folder to rename. It must be a 'Data' folder path.
+     E.g.: 'Data/folderA/old_name.txt'\n
+    NEW_NAME [name]: the new name to assign to the file or folder. E.g.: 'new_name.txt'
+    """
+    if not source_path.strip("/").startswith("Data/"):
+        click.echo("[ERROR] SOURCE_PATH must start with 'Data/', pointing to a file/folder in that dataset.", err=True)
+        sys.exit(1)
+    click.echo("Loading configuration profile...")
+    config_manager = ConfigurationProfile()
+    required_dict = {
+        'apikey': True,
+        'workspace_id': True,
+        'workflow_name': False,
+        'project_name': True
+    }
+
+    apikey, cloudos_url, workspace_id, workflow_name, repository_platform, execution_platform, project_name = (
+        config_manager.load_profile_and_validate_data(
+            ctx,
+            INIT_PROFILE,
+            CLOUDOS_URL,
+            profile=profile,
+            required_dict=required_dict,
+            apikey=apikey,
+            cloudos_url=cloudos_url,
+            workspace_id=workspace_id,
+            workflow_name=None,
+            repository_platform=None,
+            execution_platform=None,
+            project_name=project_name
+        )
+    )
+
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    # Initialize Datasets clients
+    client = Datasets(
+        cloudos_url=cloudos_url,
+        apikey=apikey,
+        workspace_id=workspace_id,
+        project_name=project_name,
+        verify=verify_ssl,
+        cromwell_token=None
+    )
+
+    parts = source_path.strip("/").split("/")
+
+    parent_path = "/".join(parts[:-1])
+    target_name = parts[-1]
+
+    try:
+        contents = client.list_folder_content(parent_path)
+    except Exception as e:
+        click.echo(f"[ERROR] Could not list contents at '{parent_path or '[project root]'}': {str(e)}", err=True)
+        sys.exit(1)
+
+    # Search for file/folder
+    found_item = None
+    for category in ["files", "folders"]:
+        for item in contents.get(category, []):
+            if item.get("name") == target_name:
+                found_item = item
+                break
+        if found_item:
+            break
+
+    if not found_item:
+        click.echo(f"[ERROR] Item '{target_name}' not found in '{parent_path or '[project root]'}'", err=True)
+        sys.exit(1)
+
+    item_id = found_item["_id"]
+    kind = "Folder" if "folderType" in found_item else "File"
+
+    click.echo(f"Renaming {kind} '{target_name}' to '{new_name}'...")
+    try:
+        response = client.rename_item(item_id=item_id, new_name=new_name, kind=kind)
+        if response.ok:
+            click.secho(
+                f"[SUCCESS] {kind} '{target_name}' renamed to '{new_name}' in folder '{parent_path}'.",
+                fg="green",
+                bold=True
+            )
+        else:
+            click.echo(f"[ERROR] Rename failed: {response.status_code} - {response.text}", err=True)
+            sys.exit(1)
+    except Exception as e:
+        click.echo(f"[ERROR] Rename operation failed: {str(e)}", err=True)
+        sys.exit(1)
+
+
 if __name__ == "__main__":
     run_cloudos_cli()

cloudos_cli-2.32.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.32.1'

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/cloudos_cli/datasets/datasets.py

@@ -365,5 +365,42 @@ class Datasets(Cloudos):
                 "item": target_id
             }
         }
+        response = retry_requests_put(url, headers=headers, data=json.dumps(payload), verify=self.verify)
+        return response
+
+    def rename_item(self, item_id: str, new_name: str, kind: str):
+        """
+        Rename a file or folder in CloudOS.
+
+        Parameters
+        ----------
+        item_id : str
+            The ID of the file or folder to rename.
+        new_name : str
+            The new name to assign to the item.
+        kind : str
+            Either "File" or "Folder"
+
+        Returns
+        -------
+        response : requests.Response
+            The response object from the CloudOS API.
+        """
+        if kind not in ("File", "Folder"):
+            raise ValueError("Invalid kind provided. Must be 'File' or 'Folder'.")
+
+        endpoint = "files" if kind == "File" else "folders"
+        url = f"{self.cloudos_url}/api/v1/{endpoint}/{item_id}?teamId={self.workspace_id}"
+
+        headers = {
+            "accept": "application/json",
+            "content-type": "application/json",
+            "ApiKey": self.apikey
+        }
+
+        payload = {
+            "name": new_name
+        }
+
         response = retry_requests_put(url, headers=headers, data=json.dumps(payload), verify=self.verify)
         return response

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/cloudos_cli/utils/__init__.py

@@ -7,5 +7,6 @@ from .requests import retry_requests_get, retry_requests_post, retry_requests_pu
 from .resources import format_bytes, ssl_selector
 from .cloud import find_cloud
 from .cloud import find_cloud
+from .details import get_path
 
-__all__ = ['errors', 'requests', 'resources', 'cloud']
+__all__ = ['errors', 'requests', 'resources', 'cloud', 'details']

cloudos_cli-2.32.1/cloudos_cli/utils/details.py

@@ -0,0 +1,66 @@
+def get_path(param, param_kind_map, execution_platform, storage_provider, mode="parameters"):
+    """
+    Constructs a storage path based on the parameter kind and execution platform.
+
+    Parameters
+    ----------
+    param : dict
+        A dictionary containing parameter details. Expected keys include:
+            - 'parameterKind': Specifies the kind of parameter (e.g., 'dataItem', 'globPattern').
+            - For 'dataItem': Contains nested keys such as 'item', which includes:
+                - 's3BucketName', 's3ObjectKey', 's3Prefix' (for AWS Batch).
+                - 'blobStorageAccountName', 'blobContainerName', 'blobName' (for other platforms).
+            - For 'globPattern': Contains nested keys such as 'folder', which includes:
+                - 's3BucketName', 's3Prefix' (for AWS Batch).
+                - 'blobStorageAccountName', 'blobContainerName', 'blobPrefix' (for other platforms).
+    param_kind_map : dict
+        A mapping of parameter kinds to their corresponding keys in the `param` dictionary.
+    execution_platform : str
+        The platform on which the execution is taking place. 
+        Expected values include "Batch AWS" or other non-AWS platforms.
+    storage_provider : str
+        Either s3:// or az://
+    mode : str
+        For "parameters" is creating the '*.config' file and it adds the complete path, for "asis"
+        leaves the constructed path as generated from the API
+
+    Returns
+    -------
+    str: A constructed storage path based on the parameter kind and execution platform.
+        - For 'dataItem' on AWS Batch: "s3BucketName/s3ObjectKey" or "s3BucketName/s3Prefix".
+        - For 'dataItem' on other platforms: "blobStorageAccountName/blobContainerName/blobName".
+        - For 'globPattern' on AWS Batch: "s3BucketName/s3Prefix/globPattern".
+        - For 'globPattern' on other platforms: "blobStorageAccountName/blobContainerName/blobPrefix/globPattern".
+    """
+    value = param[param_kind_map[param['parameterKind']]]
+    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)
+            if mode == "parameters":
+                value = storage_provider + value['item']['s3BucketName'] + '/' + s3_object_key
+            else:
+                value = value['item']['s3BucketName'] + '/' + s3_object_key
+        else:
+            account_name = value['item']['blobStorageAccountName'] + ".blob.core.windows.net"
+            container_name = value['item']['blobContainerName']
+            blob_name = value['item']['blobName']
+            if mode == "parameters":
+                value = storage_provider + account_name + '/' + container_name + '/' + blob_name
+            else:
+                value = value['item']['blobStorageAccountName'] + '/' + container_name + '/' + blob_name
+    elif param['parameterKind'] == 'globPattern':
+        if execution_platform == "Batch AWS":
+            if mode == "parameters":
+                value = storage_provider + param['folder']['s3BucketName'] + '/' + param['folder']['s3Prefix'] + '/' + param['globPattern']
+            else:
+                value = param['folder']['s3BucketName'] + '/' + param['folder']['s3Prefix'] + '/' + param['globPattern']
+        else:
+            account_name = param['folder']['blobStorageAccountName'] + ".blob.core.windows.net"
+            container_name = param['folder']['blobContainerName']
+            blob_name = param['folder']['blobPrefix']
+            if mode == "parameters":
+                value = storage_provider + account_name + '/' + container_name + '/' + blob_name + '/' + param['globPattern']
+            else:
+                value = param['folder']['blobStorageAccountName'] + '/' + container_name + '/' + blob_name + '/' + param['globPattern']
+
+    return value

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.31.1
+Version: 2.32.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -902,6 +902,26 @@ Please, note that in the above example a preconfigured profile has been used. If
     --project-name $PROJEC_NAME
 ```
 
+#### Renaming files
+
+Files and folders within the `Data` dataset can be renamed using the following command
+
+```
+cloudos datasets rename <path> <new_name>
+```
+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.
+
+Please, be aware that renaming can only happen in files and folders that are present in the `Data` datasets and that were created or uploaded by your user.
+
+Please, note that in the above example a preconfigured profile has been used. If no profile is provided and there is no default profile, the user will need to also provide the following flags
+
+```bash
+    --cloudos-url $CLOUDOS \
+    --apikey $MY_API_KEY \
+    --workspace-id $WORKSPACE_ID \
+    --project-name $PROJEC_NAME
+```
+
 ### WDL pipeline support
 
 #### Cromwell server managing

{cloudos_cli-2.31.1 → cloudos_cli-2.32.1}/cloudos_cli.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ cloudos_cli/queue/__init__.py
 cloudos_cli/queue/queue.py
 cloudos_cli/utils/__init__.py
 cloudos_cli/utils/cloud.py
+cloudos_cli/utils/details.py
 cloudos_cli/utils/errors.py
 cloudos_cli/utils/requests.py
 cloudos_cli/utils/resources.py

cloudos_cli-2.31.1/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.31.1'