cloudos-cli 2.92.0__tar.gz → 2.93.1__tar.gz

{cloudos_cli-2.92.0 → cloudos_cli-2.93.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.92.0
+Version: 2.93.1
 Summary: Python package for interacting with the Lifebit Platform
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -2182,9 +2182,9 @@ cloudos interactive-session create \
 - `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`, default: `12h`)
 
 **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 file or folder into the session for read access (AWS only). Supports S3 files/folders (e.g., `s3://my-bucket/data/file.csv`, `s3://my-bucket/data/`) and File Explorer files/folders (e.g., `my-project/Data/file.csv`, `my-project/Data/results`). S3 paths whose last segment contains a `.` are treated as files; paths ending with `/` or without an extension are treated as folders. Multiple items 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.
+- `--link`: Link a file or folder into the session for read access (AWS only). Supports S3 files/folders (e.g., `s3://my-bucket/data/file.csv`, `s3://my-bucket/data/`) and File Explorer files/folders (e.g., `my-project/Data/file.csv`, `my-project/Data/results`). S3 paths whose last segment contains a `.` are treated as files; paths ending with `/` or without an extension are treated as folders. Multiple items can be specified using multiple `--link` flags or as comma-separated paths in a single `--link` argument. Use `--copy` to copy data into the session instead.
+- `--copy`: Copy data into the session instead of linking for read access. When specified, the paths provided by `--link` are copied into the session's data volume. Supports Lifebit Platform datasets (`project_name/Data/file.csv`) and S3 files (`s3://bucket/path/to/file`). AWS only for S3 files.
+**Note:** Linking is not supported on Azure. Use `--link --copy` to copy Lifebit Platform data into the session on Azure.
 
 **Backend-Specific:**
 - `--r-version`: R version for RStudio (options: `4.4.2`, `4.5.2`) - **optional for rstudio** (default: `4.4.2`)
@@ -2197,20 +2197,21 @@ cloudos interactive-session create \
 **Data Management**
 
 CloudOS CLI supports multiple ways to access data in interactive sessions, depending on your execution platform:
-- **Mount files** (`--mount`): Files are copied into the session's mounted-data volume. Supports CloudOS File Explorer files and S3 files (AWS only).
+- **Copy files** (`--link --copy`): Files are copied into the session's data volume. Supports Lifebit Platform File Explorer files and S3 files (AWS only).
 - **Link files/folders** (`--link`): Files and folders are mounted as read-accessible items in the session (AWS only). Supports S3 files, S3 folders, and Lifebit Platform File Explorer files and folders. Linked items appear with unique mount names based on the item name. Maximum 100 items per session.
 
 
-**Data Mounting Examples**
+**Data Management Examples**
 
-Mount a file from File Explorer:
+Copy a file from File Explorer into the session:
 
 ```bash
 cloudos interactive-session create \
   --profile my_profile \
   --name "Data Analysis" \
   --session-type jupyter \
-  --mount "my_project/training_data.csv"
+  --link "my_project/training_data.csv" \
+  --copy
 ```
 
 Link an S3 folder:
@@ -2613,7 +2614,114 @@ All configuration parameters are optional. If not specified, the session resumes
 - `--cost-limit <USD>` - Update compute cost limit (-1 for unlimited)
 - `--shutdown-in <DURATION>` - Update auto-shutdown time (e.g., 8h, 2d)
 
-> To link or mount data to a running session, use `cloudos link` or `cloudos datasets link` after the session has resumed.
+> To link or copy data to a running session, use `cloudos interactive-session link` after the session has resumed.
+
+### Link
+
+The `cloudos interactive-session link` command provides a unified interface for linking files and folders to interactive analysis sessions. It consolidates functionality previously available through separate commands (`cloudos job results --link`, `cloudos job workdir --link`, `cloudos job logs --link`, and `cloudos datasets link`) into a single, intuitive interface.
+
+#### Link Files and Folders to Interactive Analysis
+
+Link job-related folders or custom S3/File Explorer paths (files and folders) to your interactive analysis sessions for direct access to data without needing to copy files.
+
+**Two modes of operation:**
+
+1. **Job-based linking** (`--job-id`): Links folders from a completed or running job
+   - 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 specific S3 or File Explorer paths (files or folders). Supports a single path or comma-separated multiple paths.
+   - S3 paths whose last segment contains a `.` are treated as files (e.g., `s3://bucket/data/file.csv`)
+   - S3 paths ending with `/` or without an extension are treated as folders
+   - File Explorer paths can point to either files or folders — the CLI detects the type automatically
+   - If the first path segment is a standard top-level folder name (`Data`, `AnalysesResults`, `Analyses_Results`, `Analyses-Results`, `Cohorts`), the path is resolved against the profile project. Otherwise the first segment is treated as the project name (e.g. `other-project/Data/file.csv`).
+
+**Basic usage:**
+
+```bash
+# Link all job folders (results, workdir, logs) - default behavior
+cloudos interactive-session link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
+
+# Link only specific folders from a job
+cloudos interactive-session link --job-id <JOB_ID> --session-id <SESSION_ID> --results --profile my_profile
+cloudos interactive-session link --job-id <JOB_ID> --session-id <SESSION_ID> --workdir --logs --profile my_profile
+
+# Link a single S3 folder
+cloudos interactive-session link s3://bucket/folder/ --session-id <SESSION_ID> --profile my_profile
+
+# Link a single S3 file
+cloudos interactive-session link s3://bucket/data/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Link multiple S3 paths (comma-separated, files and folders mixed)
+cloudos interactive-session link s3://bucket1/data/,s3://bucket2/results/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Link a File Explorer folder from the profile project
+cloudos interactive-session link Data/MyFolder --session-id <SESSION_ID> --profile my_profile
+
+# Link a File Explorer file from a different project
+cloudos interactive-session link other-project/Data/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Mix paths from the profile project, another project, and S3
+cloudos interactive-session link Data/MultiQC,other-project/Data/file.csv,s3://bucket/results/ --session-id <SESSION_ID> --profile my_profile
+```
+
+**Command options:**
+
+- `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)
+- `--session-id`: The specific Lifebit Platform interactive session ID (required)
+- `--job-id`: The job ID in Lifebit Platform (links results, workdir, and logs by default)
+- `--project-name`: Lifebit Platform project name (used as fallback for job-based linking)
+- `--results`: Link only results folder (only works with `--job-id`)
+- `--workdir`: Link only working directory (only works with `--job-id`)
+- `--logs`: Link only logs folder (only works with `--job-id`)
+- `--verbose`: Print detailed information messages
+- `--disable-ssl-verification`: Disable SSL certificate verification
+- `--ssl-cert`: Path to your SSL certificate file
+- `--profile`: Profile to use from the config file
+
+**Examples:**
+
+```bash
+# Link all folders from a completed job
+cloudos interactive-session link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --profile my_profile
+
+# Link only results from a job
+cloudos interactive-session link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --results --profile my_profile
+
+# Link workdir and logs (but not results)
+cloudos interactive-session link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --workdir --logs --profile my_profile
+
+# Link a single S3 bucket folder
+cloudos interactive-session link s3://my-bucket/analysis-results/2024 --session-id abc123 --profile my_profile
+
+# Link multiple S3 folders in one command
+cloudos interactive-session link s3://bucket1/data,s3://bucket2/results,s3://bucket3/final-output --session-id abc123 --profile my_profile
+
+# Link File Explorer paths from the profile project
+cloudos interactive-session link Data/MultiQC --session-id abc123 --profile my_profile
+
+# Link File Explorer paths from multiple projects in one command
+cloudos interactive-session link leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv --session-id abc123 --profile my_profile
+```
+
+**Error handling:**
+
+The command provides clear error messages for common scenarios:
+- Job not completed (for results linking)
+- Folders not available or deleted
+- Job still initializing
+- Invalid paths or permissions
+
+> [!NOTE]
+> If running the CLI inside a Jupyter session, the pre-configured CLI installation will have the session ID already configured and only the `--apikey` needs to be added.
+
+> [!NOTE]
+> Azure Blob Storage paths (az://) are not supported for linking in Azure environments.
+
+---
 
 ### Datasets
 
@@ -2807,113 +2915,6 @@ cloudos datasets rm <path> --profile my_profile
 
 ---
 
-### Link
-
-The `cloudos link` command provides a unified interface for linking files and folders to interactive analysis sessions. This command consolidates functionality previously available through separate commands (`cloudos job results --link`, `cloudos job workdir --link`, `cloudos job logs --link`, and `cloudos datasets link`) into a single, intuitive interface.
-
-#### Link Files and Folders to Interactive Analysis
-
-Link job-related folders or custom S3/File Explorer paths (files and folders) to your interactive analysis sessions for direct access to data without needing to copy files.
-
-**Two modes of operation:**
-
-1. **Job-based linking** (`--job-id`): Links folders from a completed or running job
-   - 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 specific S3 or File Explorer paths (files or folders). Supports a single path or comma-separated multiple paths.
-   - S3 paths whose last segment contains a `.` are treated as files (e.g., `s3://bucket/data/file.csv`)
-   - S3 paths ending with `/` or without an extension are treated as folders
-   - File Explorer paths can point to either files or folders — the CLI detects the type automatically
-
-**Basic usage:**
-
-```bash
-# Link all job folders (results, workdir, logs) - default behavior
-cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
-
-# Link only specific folders from a job
-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 single S3 folder
-cloudos link s3://bucket/folder/ --session-id <SESSION_ID> --profile my_profile
-
-# Link a single S3 file
-cloudos link s3://bucket/data/file.csv --session-id <SESSION_ID> --profile my_profile
-
-# Link multiple S3 paths (comma-separated, files and folders mixed)
-cloudos link s3://bucket1/data/,s3://bucket2/results/file.csv --session-id <SESSION_ID> --profile my_profile
-
-# Link a File Explorer folder (path is RELATIVE to --project-name; do NOT prepend the project)
-cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID> --profile my_profile
-
-# Link a File Explorer file (path is RELATIVE to --project-name)
-cloudos link "Data/file.csv" --project-name my-project --session-id <SESSION_ID> --profile my_profile
-
-# Link several File Explorer items at once (all in the same project)
-cloudos link "Data/MyFolder,Data/file.csv,Results/run-1" --project-name my-project --session-id <SESSION_ID> --profile my_profile
-```
-
-> [!IMPORTANT]
-> **`cloudos link` is single-project for File Explorer paths.** All File Explorer items linked in one invocation must belong to the project named in `--project-name`. The path must be relative to that project — prepending the project name to the path (e.g. `my-project/Data/file.csv`) is rejected. To link items from a different project, run `cloudos link` again with a different `--project-name`.
-
-**Command options:**
-
-
-- `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)
-- `--session-id`: The specific Lifebit Platform interactive session ID (required)
-- `--job-id`: The job ID in Lifebit Platform (links results, workdir, and logs by default)
-- `--project-name`: Lifebit Platform project name. Required when any PATH is a File Explorer path. All FE paths in one invocation must belong to this project and must be RELATIVE to it (do not prepend the project name)
-- `--results`: Link only results folder (only works with `--job-id`)
-- `--workdir`: Link only working directory (only works with `--job-id`)
-- `--logs`: Link only logs folder (only works with `--job-id`)
-- `--verbose`: Print detailed information messages
-- `--disable-ssl-verification`: Disable SSL certificate verification
-- `--ssl-cert`: Path to your SSL certificate file
-- `--profile`: Profile to use from the config file
-
-**Examples:**
-
-```bash
-# Link all folders from a completed job
-cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --profile my_profile
-
-# Link only results from a job
-cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --results --profile my_profile
-
-# Link workdir and logs (but not results)
-cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --workdir --logs --profile my_profile
-
-# 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:**
-
-The command provides clear error messages for common scenarios:
-- Job not completed (for results linking)
-- Folders not available or deleted
-- Job still initializing
-- Invalid paths or permissions
-
-> [!NOTE]
-> If running the CLI inside a Jupyter session, the pre-configured CLI installation will have the session ID already configured and only the `--apikey` needs to be added.
-
-> [!NOTE]
-> Azure Blob Storage paths (az://) are not supported for linking in Azure environments.
-
----
-
 ### Procurement
 
 Lifebit Platform supports procurement functionality to manage and list images associated with organizations within a given procurement. This feature is useful for administrators and users who need to view available container images across different organizations in their procurement.

{cloudos_cli-2.92.0 → cloudos_cli-2.93.1}/README.md

@@ -2147,9 +2147,9 @@ cloudos interactive-session create \
 - `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`, default: `12h`)
 
 **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 file or folder into the session for read access (AWS only). Supports S3 files/folders (e.g., `s3://my-bucket/data/file.csv`, `s3://my-bucket/data/`) and File Explorer files/folders (e.g., `my-project/Data/file.csv`, `my-project/Data/results`). S3 paths whose last segment contains a `.` are treated as files; paths ending with `/` or without an extension are treated as folders. Multiple items 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.
+- `--link`: Link a file or folder into the session for read access (AWS only). Supports S3 files/folders (e.g., `s3://my-bucket/data/file.csv`, `s3://my-bucket/data/`) and File Explorer files/folders (e.g., `my-project/Data/file.csv`, `my-project/Data/results`). S3 paths whose last segment contains a `.` are treated as files; paths ending with `/` or without an extension are treated as folders. Multiple items can be specified using multiple `--link` flags or as comma-separated paths in a single `--link` argument. Use `--copy` to copy data into the session instead.
+- `--copy`: Copy data into the session instead of linking for read access. When specified, the paths provided by `--link` are copied into the session's data volume. Supports Lifebit Platform datasets (`project_name/Data/file.csv`) and S3 files (`s3://bucket/path/to/file`). AWS only for S3 files.
+**Note:** Linking is not supported on Azure. Use `--link --copy` to copy Lifebit Platform data into the session on Azure.
 
 **Backend-Specific:**
 - `--r-version`: R version for RStudio (options: `4.4.2`, `4.5.2`) - **optional for rstudio** (default: `4.4.2`)
@@ -2162,20 +2162,21 @@ cloudos interactive-session create \
 **Data Management**
 
 CloudOS CLI supports multiple ways to access data in interactive sessions, depending on your execution platform:
-- **Mount files** (`--mount`): Files are copied into the session's mounted-data volume. Supports CloudOS File Explorer files and S3 files (AWS only).
+- **Copy files** (`--link --copy`): Files are copied into the session's data volume. Supports Lifebit Platform File Explorer files and S3 files (AWS only).
 - **Link files/folders** (`--link`): Files and folders are mounted as read-accessible items in the session (AWS only). Supports S3 files, S3 folders, and Lifebit Platform File Explorer files and folders. Linked items appear with unique mount names based on the item name. Maximum 100 items per session.
 
 
-**Data Mounting Examples**
+**Data Management Examples**
 
-Mount a file from File Explorer:
+Copy a file from File Explorer into the session:
 
 ```bash
 cloudos interactive-session create \
   --profile my_profile \
   --name "Data Analysis" \
   --session-type jupyter \
-  --mount "my_project/training_data.csv"
+  --link "my_project/training_data.csv" \
+  --copy
 ```
 
 Link an S3 folder:
@@ -2578,7 +2579,114 @@ All configuration parameters are optional. If not specified, the session resumes
 - `--cost-limit <USD>` - Update compute cost limit (-1 for unlimited)
 - `--shutdown-in <DURATION>` - Update auto-shutdown time (e.g., 8h, 2d)
 
-> To link or mount data to a running session, use `cloudos link` or `cloudos datasets link` after the session has resumed.
+> To link or copy data to a running session, use `cloudos interactive-session link` after the session has resumed.
+
+### Link
+
+The `cloudos interactive-session link` command provides a unified interface for linking files and folders to interactive analysis sessions. It consolidates functionality previously available through separate commands (`cloudos job results --link`, `cloudos job workdir --link`, `cloudos job logs --link`, and `cloudos datasets link`) into a single, intuitive interface.
+
+#### Link Files and Folders to Interactive Analysis
+
+Link job-related folders or custom S3/File Explorer paths (files and folders) to your interactive analysis sessions for direct access to data without needing to copy files.
+
+**Two modes of operation:**
+
+1. **Job-based linking** (`--job-id`): Links folders from a completed or running job
+   - 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 specific S3 or File Explorer paths (files or folders). Supports a single path or comma-separated multiple paths.
+   - S3 paths whose last segment contains a `.` are treated as files (e.g., `s3://bucket/data/file.csv`)
+   - S3 paths ending with `/` or without an extension are treated as folders
+   - File Explorer paths can point to either files or folders — the CLI detects the type automatically
+   - If the first path segment is a standard top-level folder name (`Data`, `AnalysesResults`, `Analyses_Results`, `Analyses-Results`, `Cohorts`), the path is resolved against the profile project. Otherwise the first segment is treated as the project name (e.g. `other-project/Data/file.csv`).
+
+**Basic usage:**
+
+```bash
+# Link all job folders (results, workdir, logs) - default behavior
+cloudos interactive-session link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
+
+# Link only specific folders from a job
+cloudos interactive-session link --job-id <JOB_ID> --session-id <SESSION_ID> --results --profile my_profile
+cloudos interactive-session link --job-id <JOB_ID> --session-id <SESSION_ID> --workdir --logs --profile my_profile
+
+# Link a single S3 folder
+cloudos interactive-session link s3://bucket/folder/ --session-id <SESSION_ID> --profile my_profile
+
+# Link a single S3 file
+cloudos interactive-session link s3://bucket/data/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Link multiple S3 paths (comma-separated, files and folders mixed)
+cloudos interactive-session link s3://bucket1/data/,s3://bucket2/results/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Link a File Explorer folder from the profile project
+cloudos interactive-session link Data/MyFolder --session-id <SESSION_ID> --profile my_profile
+
+# Link a File Explorer file from a different project
+cloudos interactive-session link other-project/Data/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Mix paths from the profile project, another project, and S3
+cloudos interactive-session link Data/MultiQC,other-project/Data/file.csv,s3://bucket/results/ --session-id <SESSION_ID> --profile my_profile
+```
+
+**Command options:**
+
+- `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)
+- `--session-id`: The specific Lifebit Platform interactive session ID (required)
+- `--job-id`: The job ID in Lifebit Platform (links results, workdir, and logs by default)
+- `--project-name`: Lifebit Platform project name (used as fallback for job-based linking)
+- `--results`: Link only results folder (only works with `--job-id`)
+- `--workdir`: Link only working directory (only works with `--job-id`)
+- `--logs`: Link only logs folder (only works with `--job-id`)
+- `--verbose`: Print detailed information messages
+- `--disable-ssl-verification`: Disable SSL certificate verification
+- `--ssl-cert`: Path to your SSL certificate file
+- `--profile`: Profile to use from the config file
+
+**Examples:**
+
+```bash
+# Link all folders from a completed job
+cloudos interactive-session link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --profile my_profile
+
+# Link only results from a job
+cloudos interactive-session link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --results --profile my_profile
+
+# Link workdir and logs (but not results)
+cloudos interactive-session link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --workdir --logs --profile my_profile
+
+# Link a single S3 bucket folder
+cloudos interactive-session link s3://my-bucket/analysis-results/2024 --session-id abc123 --profile my_profile
+
+# Link multiple S3 folders in one command
+cloudos interactive-session link s3://bucket1/data,s3://bucket2/results,s3://bucket3/final-output --session-id abc123 --profile my_profile
+
+# Link File Explorer paths from the profile project
+cloudos interactive-session link Data/MultiQC --session-id abc123 --profile my_profile
+
+# Link File Explorer paths from multiple projects in one command
+cloudos interactive-session link leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv --session-id abc123 --profile my_profile
+```
+
+**Error handling:**
+
+The command provides clear error messages for common scenarios:
+- Job not completed (for results linking)
+- Folders not available or deleted
+- Job still initializing
+- Invalid paths or permissions
+
+> [!NOTE]
+> If running the CLI inside a Jupyter session, the pre-configured CLI installation will have the session ID already configured and only the `--apikey` needs to be added.
+
+> [!NOTE]
+> Azure Blob Storage paths (az://) are not supported for linking in Azure environments.
+
+---
 
 ### Datasets
 
@@ -2772,113 +2880,6 @@ cloudos datasets rm <path> --profile my_profile
 
 ---
 
-### Link
-
-The `cloudos link` command provides a unified interface for linking files and folders to interactive analysis sessions. This command consolidates functionality previously available through separate commands (`cloudos job results --link`, `cloudos job workdir --link`, `cloudos job logs --link`, and `cloudos datasets link`) into a single, intuitive interface.
-
-#### Link Files and Folders to Interactive Analysis
-
-Link job-related folders or custom S3/File Explorer paths (files and folders) to your interactive analysis sessions for direct access to data without needing to copy files.
-
-**Two modes of operation:**
-
-1. **Job-based linking** (`--job-id`): Links folders from a completed or running job
-   - 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 specific S3 or File Explorer paths (files or folders). Supports a single path or comma-separated multiple paths.
-   - S3 paths whose last segment contains a `.` are treated as files (e.g., `s3://bucket/data/file.csv`)
-   - S3 paths ending with `/` or without an extension are treated as folders
-   - File Explorer paths can point to either files or folders — the CLI detects the type automatically
-
-**Basic usage:**
-
-```bash
-# Link all job folders (results, workdir, logs) - default behavior
-cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
-
-# Link only specific folders from a job
-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 single S3 folder
-cloudos link s3://bucket/folder/ --session-id <SESSION_ID> --profile my_profile
-
-# Link a single S3 file
-cloudos link s3://bucket/data/file.csv --session-id <SESSION_ID> --profile my_profile
-
-# Link multiple S3 paths (comma-separated, files and folders mixed)
-cloudos link s3://bucket1/data/,s3://bucket2/results/file.csv --session-id <SESSION_ID> --profile my_profile
-
-# Link a File Explorer folder (path is RELATIVE to --project-name; do NOT prepend the project)
-cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID> --profile my_profile
-
-# Link a File Explorer file (path is RELATIVE to --project-name)
-cloudos link "Data/file.csv" --project-name my-project --session-id <SESSION_ID> --profile my_profile
-
-# Link several File Explorer items at once (all in the same project)
-cloudos link "Data/MyFolder,Data/file.csv,Results/run-1" --project-name my-project --session-id <SESSION_ID> --profile my_profile
-```
-
-> [!IMPORTANT]
-> **`cloudos link` is single-project for File Explorer paths.** All File Explorer items linked in one invocation must belong to the project named in `--project-name`. The path must be relative to that project — prepending the project name to the path (e.g. `my-project/Data/file.csv`) is rejected. To link items from a different project, run `cloudos link` again with a different `--project-name`.
-
-**Command options:**
-
-
-- `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)
-- `--session-id`: The specific Lifebit Platform interactive session ID (required)
-- `--job-id`: The job ID in Lifebit Platform (links results, workdir, and logs by default)
-- `--project-name`: Lifebit Platform project name. Required when any PATH is a File Explorer path. All FE paths in one invocation must belong to this project and must be RELATIVE to it (do not prepend the project name)
-- `--results`: Link only results folder (only works with `--job-id`)
-- `--workdir`: Link only working directory (only works with `--job-id`)
-- `--logs`: Link only logs folder (only works with `--job-id`)
-- `--verbose`: Print detailed information messages
-- `--disable-ssl-verification`: Disable SSL certificate verification
-- `--ssl-cert`: Path to your SSL certificate file
-- `--profile`: Profile to use from the config file
-
-**Examples:**
-
-```bash
-# Link all folders from a completed job
-cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --profile my_profile
-
-# Link only results from a job
-cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --results --profile my_profile
-
-# Link workdir and logs (but not results)
-cloudos link --job-id 62c83a1191fe06013b7ef355 --session-id abc123 --workdir --logs --profile my_profile
-
-# 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:**
-
-The command provides clear error messages for common scenarios:
-- Job not completed (for results linking)
-- Folders not available or deleted
-- Job still initializing
-- Invalid paths or permissions
-
-> [!NOTE]
-> If running the CLI inside a Jupyter session, the pre-configured CLI installation will have the session ID already configured and only the `--apikey` needs to be added.
-
-> [!NOTE]
-> Azure Blob Storage paths (az://) are not supported for linking in Azure environments.
-
----
-
 ### Procurement
 
 Lifebit Platform supports procurement functionality to manage and list images associated with organizations within a given procurement. This feature is useful for administrators and users who need to view available container images across different organizations in their procurement.

{cloudos_cli-2.92.0 → cloudos_cli-2.93.1}/cloudos_cli/__main__.py

@@ -24,7 +24,6 @@ from cloudos_cli.bash.cli import bash
 from cloudos_cli.procurement.cli import procurement
 from cloudos_cli.datasets.cli import datasets
 from cloudos_cli.configure.cli import configure
-from cloudos_cli.link.cli import link
 from cloudos_cli.interactive_session.cli import interactive_session
 
 
@@ -63,7 +62,6 @@ run_cloudos_cli.add_command(bash)
 run_cloudos_cli.add_command(procurement)
 run_cloudos_cli.add_command(datasets)
 run_cloudos_cli.add_command(configure)
-run_cloudos_cli.add_command(link)
 run_cloudos_cli.add_command(interactive_session)
 
 if __name__ == '__main__':

cloudos_cli-2.93.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.93.1'

{cloudos_cli-2.92.0 → cloudos_cli-2.93.1}/cloudos_cli/datasets/cli.py

@@ -4,7 +4,7 @@ import rich_click as click
 import csv
 import sys
 from cloudos_cli.datasets import Datasets
-from cloudos_cli.link import Link
+from cloudos_cli.interactive_session.link import Link
 from cloudos_cli.utils.resources import ssl_selector, format_bytes
 from cloudos_cli.configure.configure import with_profile_config, CLOUDOS_URL
 from cloudos_cli.logging.logger import update_command_context_from_click
@@ -326,8 +326,8 @@ def move_files(ctx, source_path, destination_path, apikey, cloudos_url, workspac
         if folder_type in ("VirtualFolder", "Folder"):
             target_kind = "Folder"
         elif folder_type == "S3Folder":
-            raise ValueError(f"Unable to move item '{source_item_name}' to '{destination_path}'. " +
-                       "The destination is an S3 folder, and only virtual folders can be selected as valid move destinations.")
+            raise ValueError(f"Unable to move item '{source_item_name}' to '{destination_path}'. "
+                             "The destination is an S3 folder, and only virtual folders can be selected as valid move destinations.")
         elif isinstance(folder_type, bool) and folder_type:  # legacy dataset structure
             target_kind = "Dataset"
         else:
@@ -335,8 +335,8 @@ def move_files(ctx, source_path, destination_path, apikey, cloudos_url, workspac
 
     except Exception as e:
         raise ValueError(f"Could not resolve destination path '{destination_path}'. {str(e)}")
-    print(f"Moving {source_kind} '{source_item_name}' to '{destination_path}' " +
-               f"in project '{destination_project_name} ...")
+    print(f"Moving {source_kind} '{source_item_name}' to '{destination_path}' "
+          f"in project '{destination_project_name} ...")
     # === Perform Move ===
     try:
         response = source_client.move_files_and_folders(
@@ -756,11 +756,10 @@ def link(ctx,
     """
     Link a file or folder (S3 or File Explorer) to an active interactive analysis.
 
-    PATH [path]: the full path to the S3 file/folder, or a path RELATIVE to
-    the project named in --project-name for File Explorer items. Do NOT
-    prepend the project name to File Explorer paths.
+    PATH [path]: the full path to the S3 file/folder or relative path in File Explorer
+    (relative to the project specified by --project-name).
     E.g.: 's3://bucket-name/folder/subfolder', 's3://bucket/data/file.csv',
-    'Data/Downloads', 'Data/file.csv'.
+    'Data/Downloads', 'Data', or 'Data/file.csv'.
     """
     if not path.startswith("s3://") and project_name is None:
         raise click.UsageError("When using File Explorer paths '--project-name' needs to be defined")
@@ -777,13 +776,8 @@ def link(ctx,
     )
 
     try:
-        succeeded = link_p.link_folder(path, session_id)
+        success = link_p.link_folder(path, session_id)
     except Exception as e:
         raise ValueError(f"Could not link item. {e}")
-
-    if not succeeded:
-        click.secho(
-            "Linking did not complete successfully. See errors above.",
-            fg='red', err=True,
-        )
-        raise SystemExit(1)
+    if not success:
+        raise click.ClickException("Linking failed: mount verification did not reach 'mounted' status.")

cloudos_cli-2.93.1/cloudos_cli/interactive_session/__init__.py

@@ -0,0 +1,5 @@
+"""CloudOS interactive session module."""
+
+from .link import Link
+
+__all__ = ['Link']