cloudos-cli 2.40.0__tar.gz → 2.42.0__tar.gz

{cloudos_cli-2.40.0 → cloudos_cli-2.42.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.40.0
+Version: 2.42.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -1116,6 +1116,26 @@ where profile `test` is used for all other necessary variables, but `--session-i
 > [!NOTE]
 > If running the CLI inside a jupyter session, the pre-configured CLI installation will have the session ID already installed and only the `--apikey` needs to be added.
 
+#### Linking a File Explorer folder to Interactive Analysis
+
+Linking a File Explorer folder to an Interactive Analysis session can be done using the same subcommand as for the s3 folders:
+
+```console
+cloudos datasets link <File Explorer FOLDER PATH> <options>
+```
+
+Examples (one per line):
+
+```console
+cloudos datasets link Data/ingest_data --profile test
+cloudos datasets link Data/SEQUENCES --session-id 1234
+cloudos datasets link Data/SEQUENCES/HCC --session-id 1234
+cloudos datasets link "Analyses Results/HLA" --session-id 1234
+```
+
+> [!NOTE]
+> Virtual folders in File Explorer, the ones a user has created in File explorer and are not actual storage locations, cannot be linked.
+
 #### Create a (virtual) folder
 
 New folders can be created within the `Data` dataset and its subfolders using the following command

{cloudos_cli-2.40.0 → cloudos_cli-2.42.0}/README.md

@@ -1081,6 +1081,26 @@ where profile `test` is used for all other necessary variables, but `--session-i
 > [!NOTE]
 > If running the CLI inside a jupyter session, the pre-configured CLI installation will have the session ID already installed and only the `--apikey` needs to be added.
 
+#### Linking a File Explorer folder to Interactive Analysis
+
+Linking a File Explorer folder to an Interactive Analysis session can be done using the same subcommand as for the s3 folders:
+
+```console
+cloudos datasets link <File Explorer FOLDER PATH> <options>
+```
+
+Examples (one per line):
+
+```console
+cloudos datasets link Data/ingest_data --profile test
+cloudos datasets link Data/SEQUENCES --session-id 1234
+cloudos datasets link Data/SEQUENCES/HCC --session-id 1234
+cloudos datasets link "Analyses Results/HLA" --session-id 1234
+```
+
+> [!NOTE]
+> Virtual folders in File Explorer, the ones a user has created in File explorer and are not actual storage locations, cannot be linked.
+
 #### Create a (virtual) folder
 
 New folders can be created within the `Data` dataset and its subfolders using the following command

{cloudos_cli-2.40.0 → cloudos_cli-2.42.0}/cloudos_cli/__main__.py

@@ -3415,24 +3415,27 @@ def rm_item(ctx, target_path, apikey, cloudos_url,
 
 
 @datasets.command(name="link")
-@click.argument("s3_path", required=True)
+@click.argument("path", required=True)
 @click.option('-k', '--apikey', help='Your CloudOS API key', required=True)
 @click.option('-c', '--cloudos-url',
               help=(f'The CloudOS url you are trying to access to. Default={CLOUDOS_URL}.'),
               default=CLOUDOS_URL)
+@click.option('--project-name',
+              help='The name of a CloudOS project.',
+              required=False)
 @click.option('--workspace-id', help='The specific CloudOS workspace id.', required=True)
 @click.option('--session-id', help='The specific CloudOS interactive session id.', required=True)
 @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', help='Profile to use from the config file', default='default')
 @click.pass_context
-def link(ctx, s3_path, apikey, cloudos_url, workspace_id, session_id, disable_ssl_verification, ssl_cert, profile):
+def link(ctx, path, apikey, cloudos_url, project_name, workspace_id, session_id, disable_ssl_verification, ssl_cert, profile):
     """
-    Link a S3 folder to an active interactive analysis.
+    Link a folder (S3 or File Explorer) to an active interactive analysis.
 
-    S3_PATH [path]: the full path to the S3 folder to link. E.g.: 's3://bucket-name/folder/subfolder'\n
+    PATH [path]: the full path to the S3 folder to link or relative to File Explorer. 
+    E.g.: 's3://bucket-name/folder/subfolder', 'Data/Downloads' or 'Data'.
     """
-    print(link.__doc__ + '\n')
 
     profile = profile or ctx.default_map['datasets']['link']['profile']
 
@@ -3455,7 +3458,8 @@ def link(ctx, s3_path, apikey, cloudos_url, workspace_id, session_id, disable_ss
             apikey=apikey,
             cloudos_url=cloudos_url,
             workspace_id=workspace_id,
-            session_id=session_id
+            session_id=session_id,
+            project_name=project_name
         )
     )
     # Unpack the user options
@@ -3463,17 +3467,23 @@ def link(ctx, s3_path, apikey, cloudos_url, workspace_id, session_id, disable_ss
     cloudos_url = user_options['cloudos_url']
     workspace_id = user_options['workspace_id']
     session_id = user_options['session_id']
+    project_name = user_options['project_name']
+
+    if not path.startswith("s3://") and project_name is None:
+        # for non-s3 paths we need the project, for S3 we don't
+        raise click.UsageError("When using File Explorer paths '--project-name' needs to be defined")
 
     verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+
     link_p = Link(
         cloudos_url=cloudos_url,
         apikey=apikey,
         workspace_id=workspace_id,
         cromwell_token=None,
-        project_name=None,
+        project_name=project_name,
         verify=verify_ssl
     )
-    link_p.link_S3_folder(s3_path, session_id)
+    link_p.link_folder(path, session_id)
 
 
 if __name__ == "__main__":

cloudos_cli-2.42.0/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.42.0'

{cloudos_cli-2.40.0 → cloudos_cli-2.42.0}/cloudos_cli/datasets/datasets.py

@@ -489,7 +489,7 @@ class Datasets(Cloudos):
         return response
     
     def copy_item(self, item, destination_id, destination_kind):
-        """Copy a file or folder (S3 or Virtual) to a destination in CloudOS."""
+        """Copy a file or folder (S3, Azure or Virtual) to a destination in CloudOS."""
         headers = {
             "accept": "application/json",
             "content-type": "application/json",
@@ -526,6 +526,29 @@ class Datasets(Cloudos):
                 "sizeInBytes": item.get("sizeInBytes", 0)
             }
             url = f"{self.cloudos_url}/api/v1/files/s3?teamId={self.workspace_id}"
+        # Azure folder
+        elif item.get("folderType") == "AzureBlobFolder":
+            payload = {
+                "blobContainerName": item["blobContainerName"],
+                "blobPrefix": item["blobPrefix"],
+                "blobStorageAccountName": item["blobStorageAccountName"],
+                "name": item["name"],
+                "parent": parent
+            }
+            url = f"{self.cloudos_url}/api/v1/folders/azure-blob?teamId={self.workspace_id}"
+        # Azure file
+        elif item.get("fileType") == "AzureBlobFile":
+            payload = {
+                "blobContainerName": item["blobContainerName"],
+                "blobName": item["blobName"],
+                "blobStorageAccountName": item["blobStorageAccountName"],
+                "name": item["name"],
+                "parent": parent,
+                "isManagedByLifebit": item.get("isManagedByLifebit", False),
+                "sizeInBytes": item.get("sizeInBytes", 0)
+            }
+            url = f"{self.cloudos_url}/api/v1/files/azure-blob?teamId={self.workspace_id}"
+
         else:
             raise ValueError(f"Unknown item type for copy: {item.get('name')}")
         response = retry_requests_post(url, headers=headers, json=payload)

{cloudos_cli-2.40.0 → cloudos_cli-2.42.0}/cloudos_cli/link/link.py

@@ -7,6 +7,8 @@ from typing import Union
 from cloudos_cli.clos import Cloudos
 from cloudos_cli.utils.requests import retry_requests_post
 from urllib.parse import urlparse
+from cloudos_cli.utils.array_job import extract_project, get_file_or_folder_id
+import json
 
 
 @dataclass
@@ -30,24 +32,24 @@ class Link(Cloudos):
     project_name: str
     verify: Union[bool, str] = True
 
-    def link_S3_folder(self,
-                       s3_folder: str,
-                       session_id: str) -> dict:
-        """Link an S3 folder to an interactive session.
+    def link_folder(self,
+                    folder: str,
+                    session_id: str) -> dict:
+        """Link a folder (S3 or File Explorer) to an interactive session.
 
         Parameters
         ----------
-        s3_folder : str
-            The S3 folder to link.
+        folder : str
+            The folder to link.
         session_id : str
             The interactive session ID.
 
         Raises
         ------
         ValueError
-            If the S3 URL already exists with 'mounted' status
+            If the URL already exists with 'mounted' status
             If the API key is invalid or permissions are insufficient
-            If the S3 URL is invalid or the session is not active.
+            If the URL is invalid or the session is not active.
         """
         url = (
             f"{self.cloudos_url}/api/v1/"
@@ -58,22 +60,35 @@ class Link(Cloudos):
             "Content-type": "application/json",
             "apikey": self.apikey
         }
-        data = self.parse_s3_path(s3_folder)
+        # determine if is file explorer or s3
+        if folder.startswith('s3://'):
+            data = self.parse_s3_path(folder)
+            type_folder = "S3"
+        else:
+            data = self.parse_file_explorer_path(folder)
+            type_folder = "File Explorer"
         r = retry_requests_post(url, headers=headers, json=data, verify=self.verify)
-
         if r.status_code == 403:
-            raise ValueError(f"Provided folder already exists with 'mounted' status")
+            raise ValueError(f"Provided {type_folder} folder already exists with 'mounted' status")
         elif r.status_code == 401:
             raise ValueError(f"Forbidden: Invalid API key or insufficient permissions")
         elif r.status_code == 400:
-            raise ValueError("Bad request: please make sure the S3 URL is valid, and the session is active")
+            r_content = json.loads(r.content)
+            if r_content["message"] == "Invalid Supported DataItem folderType. Supported values are S3Folder":
+                raise ValueError(f"Invalid Supported DataItem '{type_folder}' folderType. Virtual folders cannot be linked.")
+            elif r_content["message"] == "Request failed with status code 403":
+                raise ValueError(f"Interactive Analysis session is not active")
+            else:
+                raise ValueError(f"Cannot link folder")
         elif r.status_code == 204:
-            full_path = (
-                f"s3://{data['dataItem']['data']['s3BucketName']}/"
-                f"{data['dataItem']['data']['s3Prefix']}"
-            )
-            print(f"Succesfully linked S3 folder: {full_path}")
-
+            if type_folder == "S3":
+                full_path = (
+                    f"s3://{data['dataItem']['data']['s3BucketName']}/"
+                    f"{data['dataItem']['data']['s3Prefix']}"
+                )
+            else:
+                full_path = folder
+            print(f"Succesfully linked {type_folder} folder: {full_path}")
 
     def parse_s3_path(self, s3_url):
         """
@@ -123,3 +138,40 @@ class Link(Cloudos):
             }
         }
 
+    def parse_file_explorer_path(self, path):
+        """
+        Parses a file path and returns the base name and full path.
+
+        Parameters
+        ----------
+        file_path : str
+            The file path to parse.
+
+        Returns
+        -------
+        dict: A dictionary containing the parsed file information structured as:
+                "dataItem": {
+                    "type": "File",
+                    "data": {
+                        "name": str,          # The base name of the file.
+                        "fullPath": str      # The full path of the file.
+        """
+        # get folder id
+        folder_id = get_file_or_folder_id(
+            self.cloudos_url,
+            self.apikey,
+            self.workspace_id,
+            self.project_name,
+            self.verify,
+            path.strip("/"),
+            "",
+            is_file=False
+        )
+        parts = path.strip("/").split("/")
+        return {
+            "dataItem": {
+                "kind": "Folder",
+                "item": f"{folder_id}",
+                "name": f"{parts[-1]}"
+            }
+        }

{cloudos_cli-2.40.0 → cloudos_cli-2.42.0}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.40.0
+Version: 2.42.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -1116,6 +1116,26 @@ where profile `test` is used for all other necessary variables, but `--session-i
 > [!NOTE]
 > If running the CLI inside a jupyter session, the pre-configured CLI installation will have the session ID already installed and only the `--apikey` needs to be added.
 
+#### Linking a File Explorer folder to Interactive Analysis
+
+Linking a File Explorer folder to an Interactive Analysis session can be done using the same subcommand as for the s3 folders:
+
+```console
+cloudos datasets link <File Explorer FOLDER PATH> <options>
+```
+
+Examples (one per line):
+
+```console
+cloudos datasets link Data/ingest_data --profile test
+cloudos datasets link Data/SEQUENCES --session-id 1234
+cloudos datasets link Data/SEQUENCES/HCC --session-id 1234
+cloudos datasets link "Analyses Results/HLA" --session-id 1234
+```
+
+> [!NOTE]
+> Virtual folders in File Explorer, the ones a user has created in File explorer and are not actual storage locations, cannot be linked.
+
 #### Create a (virtual) folder
 
 New folders can be created within the `Data` dataset and its subfolders using the following command

cloudos_cli-2.40.0/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.40.0'