cloudos-cli 2.89.2__tar.gz → 2.90.1__tar.gz

{cloudos_cli-2.89.2 → cloudos_cli-2.90.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.89.2
+Version: 2.90.1
 Summary: Python package for interacting with the Lifebit Platform
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -2183,7 +2183,8 @@ cloudos interactive-session create \
 
 **Data & Storage Management:**
 - `--mount`: Mount a data file into the session. Supports both Lifebit Platform datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.
-- `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders and Lifebit Platform folders. Format: `s3://bucket/prefix` (e.g., `s3://my-bucket/data/`) or `project_name/folder_path` (e.g., `leila-test/AnalysesResults/analysis_id/results`). Can be used multiple times. **Note:** Linking is not supported on Azure. Use Lifebit Platform file explorer for data access.
+- `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders (e.g., `s3://my-bucket/data/`) and File Explorer folders (e.g., `my-project/Data/results`). Multiple folders can be specified using multiple `--link` flags or as comma-separated paths in a single `--link` argument. 
+**Note:** Linking is not supported on Azure. Use Lifebit Platform File Explorer for data access.
 
 **Backend-Specific:**
 - `--r-version`: R version for RStudio (options: `4.4.2`, `4.5.2`) - **optional for rstudio** (default: `4.4.2`)
@@ -2196,8 +2197,8 @@ cloudos interactive-session create \
 **Data Management**
 
 CloudOS CLI supports multiple ways to access data in interactive sessions, depending on your execution platform:
-- you can load data directly into the session (i.e. files are copied into the session's mounted-data volume)
-- you can link folders to your session  (i.e the folders are sym-linked to the session). This works only for folders (S3-based) and only in AWS enviornments. 
+- **Mount files** (`--mount`): Files are copied into the session's mounted-data volume. Supports CloudOS File Explorer files and S3 files (AWS only).
+- **Link folders** (`--link`): Folders are mounted as read/write accessible directories in the session (AWS only). Supports both S3 folders and Lifebit Platform File Explorer folders. Linked folders appear with unique mount names based on the folder path. 
 
 
 **Data Mounting Examples**
@@ -2212,7 +2213,7 @@ cloudos interactive-session create \
   --mount "my_project/training_data.csv"
 ```
 
-Link an S3 bucket:
+Link an S3 folder:
 
 ```bash
 cloudos interactive-session create \
@@ -2222,15 +2223,36 @@ cloudos interactive-session create \
   --link "s3://my-results-bucket/output/"
 ```
 
-Link multiple S3 buckets:
+Link a File Explorer folder:
 
 ```bash
 cloudos interactive-session create \
   --profile my_profile \
-  --name "Multi-S3 Session" \
+  --name "File Explorer Access" \
+  --session-type jupyter \
+  --link "my-project/Data/results"
+```
+
+Link multiple folders (using multiple --link flags):
+
+```bash
+cloudos interactive-session create \
+  --profile my_profile \
+  --name "Multi-Folder Session" \
   --session-type jupyter \
   --link "s3://input-bucket/data/" \
-  --link "s3://output-bucket/results/"
+  --link "s3://output-bucket/results/" \
+  --link "my-project/AnalysesResults/analysis_123/output"
+```
+
+Link multiple folders (using comma-separated paths):
+
+```bash
+cloudos interactive-session create \
+  --profile my_profile \
+  --name "Multi-Folder Session" \
+  --session-type jupyter \
+  --link "s3://bucket-1/data/,s3://bucket-2/results/,my-project/Data/analysis"
 ```
 
 
@@ -2797,7 +2819,8 @@ Link job-related folders or custom S3 paths to your interactive analysis session
    - By default, links results, workdir, and logs folders
    - Use `--results`, `--workdir`, or `--logs` flags to link only specific folders
 
-2. **Direct path linking** (PATH argument): Links a specific S3 path
+2. **Direct path linking** (PATH argument): Links specific S3 or File Explorer paths. It supports a single path or comma-separated multiple paths.
+   
 
 **Basic usage:**
 
@@ -2809,16 +2832,20 @@ cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
 cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --results --profile my_profile
 cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --workdir --logs --profile my_profile
 
-# Link a specific S3 path
+# Link a single S3 path
 cloudos link s3://bucket/folder --session-id <SESSION_ID> --profile my_profile
 
+# Link multiple S3 paths (comma-separated)
+cloudos link s3://bucket1/data,s3://bucket2/results,s3://bucket3/output --session-id <SESSION_ID> --profile my_profile
+
 # Link a File Explorer path (requires project name)
 cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID> --profile my_profile
 ```
 
 **Command options:**
 
-- `PATH`: S3 path to link (positional argument, required if `--job-id` is not provided)
+
+- `PATH`: S3 or File Explorer path(s) to link (positional argument, required if `--job-id` is not provided). Supports comma-separated multiple paths for batch linking (e.g., `s3://bucket1/path1,s3://bucket2/path2`)
 - `--apikey` / `-k`: Your Lifebit Platform API key (required)
 - `--cloudos-url` / `-c`: The Lifebit Platform URL (default: https://cloudos.lifebit.ai)
 - `--workspace-id`: The specific Lifebit Platform workspace ID (required)
@@ -2845,9 +2872,14 @@ cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --results --p
 # Link workdir and logs (but not results)
 cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --workdir --logs --profile my_profile
 
-# Link an S3 bucket folder
+# Link a single S3 bucket folder
 cloudos link s3://my-bucket/analysis-results/2024 --session-id abc123 --profile my_profile
 
+# Link multiple S3 folders in one command
+cloudos link s3://bucket1/data,s3://bucket2/results,s3://bucket3/final-output --session-id abc123 --profile my_profile
+
+# Mix different S3 prefixes from the same or different buckets
+cloudos link s3://lifebit-datasets/pipelines/vep/,s3://lifebit-datasets/pipelines/phewas/,s3://my-results/output/ --session-id abc123 --profile my_profile
 ```
 
 **Error handling:**

{cloudos_cli-2.89.2 → cloudos_cli-2.90.1}/README.md

@@ -2148,7 +2148,8 @@ cloudos interactive-session create \
 
 **Data & Storage Management:**
 - `--mount`: Mount a data file into the session. Supports both Lifebit Platform datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.
-- `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders and Lifebit Platform folders. Format: `s3://bucket/prefix` (e.g., `s3://my-bucket/data/`) or `project_name/folder_path` (e.g., `leila-test/AnalysesResults/analysis_id/results`). Can be used multiple times. **Note:** Linking is not supported on Azure. Use Lifebit Platform file explorer for data access.
+- `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders (e.g., `s3://my-bucket/data/`) and File Explorer folders (e.g., `my-project/Data/results`). Multiple folders can be specified using multiple `--link` flags or as comma-separated paths in a single `--link` argument. 
+**Note:** Linking is not supported on Azure. Use Lifebit Platform File Explorer for data access.
 
 **Backend-Specific:**
 - `--r-version`: R version for RStudio (options: `4.4.2`, `4.5.2`) - **optional for rstudio** (default: `4.4.2`)
@@ -2161,8 +2162,8 @@ cloudos interactive-session create \
 **Data Management**
 
 CloudOS CLI supports multiple ways to access data in interactive sessions, depending on your execution platform:
-- you can load data directly into the session (i.e. files are copied into the session's mounted-data volume)
-- you can link folders to your session  (i.e the folders are sym-linked to the session). This works only for folders (S3-based) and only in AWS enviornments. 
+- **Mount files** (`--mount`): Files are copied into the session's mounted-data volume. Supports CloudOS File Explorer files and S3 files (AWS only).
+- **Link folders** (`--link`): Folders are mounted as read/write accessible directories in the session (AWS only). Supports both S3 folders and Lifebit Platform File Explorer folders. Linked folders appear with unique mount names based on the folder path. 
 
 
 **Data Mounting Examples**
@@ -2177,7 +2178,7 @@ cloudos interactive-session create \
   --mount "my_project/training_data.csv"
 ```
 
-Link an S3 bucket:
+Link an S3 folder:
 
 ```bash
 cloudos interactive-session create \
@@ -2187,15 +2188,36 @@ cloudos interactive-session create \
   --link "s3://my-results-bucket/output/"
 ```
 
-Link multiple S3 buckets:
+Link a File Explorer folder:
 
 ```bash
 cloudos interactive-session create \
   --profile my_profile \
-  --name "Multi-S3 Session" \
+  --name "File Explorer Access" \
+  --session-type jupyter \
+  --link "my-project/Data/results"
+```
+
+Link multiple folders (using multiple --link flags):
+
+```bash
+cloudos interactive-session create \
+  --profile my_profile \
+  --name "Multi-Folder Session" \
   --session-type jupyter \
   --link "s3://input-bucket/data/" \
-  --link "s3://output-bucket/results/"
+  --link "s3://output-bucket/results/" \
+  --link "my-project/AnalysesResults/analysis_123/output"
+```
+
+Link multiple folders (using comma-separated paths):
+
+```bash
+cloudos interactive-session create \
+  --profile my_profile \
+  --name "Multi-Folder Session" \
+  --session-type jupyter \
+  --link "s3://bucket-1/data/,s3://bucket-2/results/,my-project/Data/analysis"
 ```
 
 
@@ -2762,7 +2784,8 @@ Link job-related folders or custom S3 paths to your interactive analysis session
    - By default, links results, workdir, and logs folders
    - Use `--results`, `--workdir`, or `--logs` flags to link only specific folders
 
-2. **Direct path linking** (PATH argument): Links a specific S3 path
+2. **Direct path linking** (PATH argument): Links specific S3 or File Explorer paths. It supports a single path or comma-separated multiple paths.
+   
 
 **Basic usage:**
 
@@ -2774,16 +2797,20 @@ cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
 cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --results --profile my_profile
 cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --workdir --logs --profile my_profile
 
-# Link a specific S3 path
+# Link a single S3 path
 cloudos link s3://bucket/folder --session-id <SESSION_ID> --profile my_profile
 
+# Link multiple S3 paths (comma-separated)
+cloudos link s3://bucket1/data,s3://bucket2/results,s3://bucket3/output --session-id <SESSION_ID> --profile my_profile
+
 # Link a File Explorer path (requires project name)
 cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID> --profile my_profile
 ```
 
 **Command options:**
 
-- `PATH`: S3 path to link (positional argument, required if `--job-id` is not provided)
+
+- `PATH`: S3 or File Explorer path(s) to link (positional argument, required if `--job-id` is not provided). Supports comma-separated multiple paths for batch linking (e.g., `s3://bucket1/path1,s3://bucket2/path2`)
 - `--apikey` / `-k`: Your Lifebit Platform API key (required)
 - `--cloudos-url` / `-c`: The Lifebit Platform URL (default: https://cloudos.lifebit.ai)
 - `--workspace-id`: The specific Lifebit Platform workspace ID (required)
@@ -2810,9 +2837,14 @@ cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --results --p
 # Link workdir and logs (but not results)
 cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --workdir --logs --profile my_profile
 
-# Link an S3 bucket folder
+# Link a single S3 bucket folder
 cloudos link s3://my-bucket/analysis-results/2024 --session-id abc123 --profile my_profile
 
+# Link multiple S3 folders in one command
+cloudos link s3://bucket1/data,s3://bucket2/results,s3://bucket3/final-output --session-id abc123 --profile my_profile
+
+# Mix different S3 prefixes from the same or different buckets
+cloudos link s3://lifebit-datasets/pipelines/vep/,s3://lifebit-datasets/pipelines/phewas/,s3://my-results/output/ --session-id abc123 --profile my_profile
 ```
 
 **Error handling:**

cloudos_cli-2.90.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.90.1'

{cloudos_cli-2.89.2 → cloudos_cli-2.90.1}/cloudos_cli/bash/cli.py

@@ -341,6 +341,7 @@ def run_bash_job(ctx,
               is_flag=True)
 @click.option('-a', '--array-parameter',
               multiple=True,
+              required=True,
               help=('A single parameter to pass to the job call only for specifying array columns. ' +
                     'It should be in the following form: parameter_name=array_file_column_name. E.g.: ' +
                     '-a --test=value or -a -test=value or -a test=value or -a =value (for no prefix). ' +

{cloudos_cli-2.89.2 → cloudos_cli-2.90.1}/cloudos_cli/clos.py

@@ -2548,4 +2548,71 @@ class Cloudos:
         # Return the status code (204 No Content is success)
         return r.status_code
     
+    def mount_fuse_filesystem_v2(self, session_id, team_id, payload, verify=True):
+        """Mount a FUSE filesystem into an interactive session (API v2).
+
+        Parameters
+        ----------
+        session_id : string
+            The session ID (MongoDB ObjectId) to mount filesystem to.
+        team_id : string
+            The CloudOS team id (workspace id).
+        payload : dict
+            FuseFileSystemMount payload with dataItems array configuration.
+            For S3: {"dataItems": [{"type": "S3Folder", "data": {"name": str, "s3BucketName": str, "s3Prefix": str}}, ...]}
+            For File Explorer: {"dataItems": [{"kind": "Folder", "item": str, "name": str}, ...]}
+        verify: [bool|string], default=True
+            Whether to use SSL verification or not. Alternatively, if
+            a string is passed, it will be interpreted as the path to
+            the SSL certificate file.
+
+        Returns
+        -------
+        int
+            HTTP status code (204 for successful mount, no content returned).
+        """
+        # Validate inputs
+        if not session_id or not isinstance(session_id, str):
+            raise ValueError("Invalid session_id: must be a non-empty string")
+        if not team_id or not isinstance(team_id, str):
+            raise ValueError("Invalid team_id: must be a non-empty string")
+
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
+
+        # Build URL with v2 endpoint and teamId query parameter
+        url = f"{self.cloudos_url}/api/v2/interactive-sessions/{session_id}/fuse-filesystem/mount?teamId={team_id}"
+        
+        # Make the API request with POST method
+        try:
+            r = retry_requests_post(
+                url,
+                headers=headers,
+                json=payload,
+                verify=verify,
+                timeout=30
+            )
+        except Exception as e:
+            raise Exception(f"Failed to mount FUSE filesystem: {str(e)}")
+        
+        if r.status_code >= 400:
+            if r.status_code == 404:
+                # Try to determine if it's a missing session or missing endpoint
+                try:
+                    error_body = r.json() if r.content else {}
+                    error_message = error_body.get("message", "").lower()
+                    # If error mentions session, it's a session-not-found error
+                    if "session" in error_message:
+                        raise ValueError(f"Session not found: {session_id}")
+                except (json.JSONDecodeError, AttributeError):
+                    pass
+                # Otherwise, likely endpoint not available - raise generic 404
+                raise BadRequestException(r)
+            raise BadRequestException(r)
+        
+        # Return the status code (204 No Content is success)
+        return r.status_code
+