seqslab-cli 3.2.1__tar.gz → 3.2.1.post0__tar.gz

seqslab-cli-3.2.1.post0/MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md
+global-exclude **/tests/*

seqslab-cli-3.2.1.post0/PKG-INFO

@@ -0,0 +1,297 @@
+Metadata-Version: 2.1
+Name: seqslab-cli
+Version: 3.2.1.post0
+Summary: Atgenomix SeqsLab Command Line Tool
+Home-page: https://github.com/AnomeGAP/seqslab-cli
+Author: Allen Chang
+Author-email: allen.chang@atgenomix.com
+License: MIT license
+Project-URL: Documentation, https://docs.atgenomix.com/
+Project-URL: Repository, https://github.com/AnomeGAP/seqslab-cli
+Description: <!-- PROJECT SHIELDS -->
+        <!--
+        *** I'm using markdown "reference style" links for readability.
+        *** Reference links are enclosed in brackets [ ] instead of parentheses ( ).
+        *** See the bottom of this document for the declaration of the reference variables
+        *** for contributors-url, forks-url, etc. This is an optional, concise syntax you may use.
+        *** https://www.markdownguide.org/basic-syntax/#reference-style-links
+        -->
+        [Contributors][contributors-url]
+        [Stargazers][stars-url]
+        [Issues][issues-url]
+        [License][license-url]
+        [![LinkedIn][linkedin-shield]][linkedin-url]
+        
+        <!-- PROJECT LOGO -->
+        <br />
+        <p align="center">
+          <a href="https://github.com/AnomeGAP/seqslab-cli">
+            <img src="https://static.wixstatic.com/media/f7a6a5_1ad70ed05af04d7eb45ee5e2df347a32~mv2_d_4266_4449_s_4_2.gif" alt="Logo" width="80" height="80">
+          </a>
+        
+        <h2 align="center">Atgenomix SeqsLab V3 CLI</h2>
+        </p>
+        <p align="center">
+          Command-line interface of Atgenomix SeqsLab, a cloud-native biomedical informatics (BioMed IT) platform
+          <br />
+          <a href="https://docs.atgenomix.com"><strong>Explore the docs »</strong></a>
+          <br />
+          <br />
+          <a href="https://github.com/AnomeGAP/seqslab-cli/issues">Report issue</a>
+          ·
+          <a href="https://github.com/AnomeGAP/seqslab-cli/issues">Request feature</a>
+        </p>
+        
+        <!-- TABLE OF CONTENTS -->
+        <details open="open">
+          <summary>Table of Contents</summary>
+          <ol>
+            <li>
+              <a href="#overview">Overview</a>
+              <ul>
+                <li><a href="#underlying-technology">Underlying Technology</a></li>
+              </ul>
+            </li>
+            <li>
+              <a href="#getting-started">Getting Started</a>
+              <ul>
+                <li><a href="#prerequisites">Prerequisites</a></li>
+                <li><a href="#interactive-mode">Interactive Mode</a></li>
+                <li><a href="#cli-mode">CLI Mode</a></li>
+              </ul>
+            </li>
+            <li>
+              <a href="#development">Development</a>
+              <ul>
+                <li><a href="#authentication-with-the-seqslab-api">Authentication with the SeqsLab API</a></li>
+              </ul>
+            </li>
+            <li><a href="#roadmap">Roadmap</a></li>
+            <li><a href="#contributing">Contributing</a></li>
+            <li><a href="#license">License</a></li>
+            <li><a href="#contact">Contact</a></li>
+            <li><a href="#acknowledgements">Acknowledgements</a></li>
+          </ol>
+        </details>
+        
+        ## Overview
+        
+        ![Product Screen Shot](https://github.com/AnomeGAP/seqslab-cli/blob/main/Atgenomix%20SeqsLab%20V3.png)
+        
+        Working alongside the web-based SeqsLab Console, the CLI enables bioinformaticians to easily build custom scripts and automate workflows on SeqsLab.
+        
+        Common use cases for the CLI include the following:
+        
+        * Automate processing of sequencing data, including uploading and downloading of datasets to/from the SeqsLab Data Hub
+        * Submit workflow run requests on demand via SeqsLab Workflow Execution Service (WES) APIs, and integrate with local downstream analysis tools
+        * View records of platform activities for auditing purposes
+        
+        ### Underlying Technology
+        
+        The SeqsLab CLI is built using the following:
+        
+        * [SeqsLab APIs](https://api.seqslab.net/)
+        * [Python-Nubia](https://github.com/facebookincubator/python-nubia)
+        * [MSAL Python](https://msal-python.readthedocs.io/en/latest/)
+        * [Azure SDK](https://github.com/Azure/azure-sdk)
+        * [aiohttp](https://docs.aiohttp.org/en/stable/index.html)
+        
+        **Note**: The mechanisms for secure information storage are built around a [keyring](https://pypi.org/project/keyring/) service.
+        
+        ## Getting Started
+        
+        ### Prerequisites
+        
+        * Python 3.8 or later
+        
+        * A Python virtual environment
+        
+          Install the SeqsLab CLI.
+          ```bash
+          pip3 install seqslab-cli
+          ```
+        * A keyring backend
+        
+          The SeqsLab CLI supports the following keyring backends:
+        
+          * macOS [Keychain](https://en.wikipedia.org/wiki/Keychain_%28software%29)
+          * Freedesktop [Secret Service](http://standards.freedesktop.org/secret-service/) (requires [secretstorage](https://pypi.python.org/pypi/secretstorage))
+          * KDE4 & KDE5 [KWallet](https://en.wikipedia.org/wiki/KWallet) (requires [dbus](https://pypi.python.org/pypi/dbus-python))
+          * [Windows Credential Locker](https://docs.microsoft.com/en-us/windows/uwp/security/credential-locker)
+        
+          **Note**: See the [Python keyring library documentation](https://pypi.org/project/keyring/) for more information about using keyring on a headless Linux system in a Docker container.
+        
+        * (macOS devices) The following packages:
+        
+          * [pkg-config](https://formulae.brew.sh/formula/pkg-config)
+          * [dbus](https://formulae.brew.sh/formula/dbus)
+          * [glib](https://formulae.brew.sh/formula/glib)
+        
+          You can install the required packages using Homebrew.
+          ```bash
+          # install packages:
+          brew install dbus
+          brew install pkg-config 
+          brew install glib
+          ```
+        
+        ### Interactive Mode
+        
+        This mode provides fish-style auto-completion functionality that is user-friendly, especially for beginners.
+        
+        * Run interactive mode.
+          ```bash
+          virtualenv .venv
+          source .venv/bin/activate
+          export PYTHONPATH=$(pwd)
+          python3 seqslab/cli.py
+          ```
+        
+        * Display the available commands.
+          ```bash
+          seqslab> help
+          ```
+        
+        ### CLI Mode
+        
+        In this mode, the SeqsLab CLI works exactly like any traditional Linux-based command-line utility.
+        
+        ## Development
+        
+        Commands are defined as normal Python functions with `@command` and `@argument` decorators. Super commands are implemented as Python class objects, and instance methods decorated with `@command` are sub-commands. In non-interactive mode, you can set `@command`-decorated functions to return an `int`, which is used as the Linux return code.
+        
+        By default, the framework loads commands from the `python/seqslab/commands` module directory. Atgenomix recommends implementing your program structure under the `commands` directory.
+        
+        ```python
+        
+        from termcolor import cprint
+        from nubia import argument, command
+        @command("hello")
+        @argument("name", type=str, positional=True, description="Your name") 
+        def hello(name: str) -> int:
+            """
+            command help, or the command won't be loaded.
+            """
+            cprint(f"Hello {name}!", "green")
+            return 0
+        @command
+        class SuperCommand:
+          """super-command command help"""
+        
+          def __init__(self):
+            self._shared = "shared variable value"
+        
+          @property
+          def shared(self) -> str:
+            return self._shared
+            
+          @command(aliases=["echo"])
+          @argument("first",
+                    type=str,
+                    positional=False,
+                    description="firstname",
+                    aliases=["f"])
+          @argument("last",
+                    type=str,
+                    positional=False,
+                    description="lastname",
+                    aliases=["l"])
+          def cprint(self, first: str, last: str) -> int:
+              """
+              sub-command help message.
+              """
+              cprint(f"{first} {last}", "red")
+              return 0
+        ```
+        
+        ### Authentication with the SeqsLab API
+        
+        Regardless of the mode (interactive or non-interactive) that you intend to use, you must sign in to authenticate the session. The SeqsLab CLI follows the OAuth 2.0 Device Authorization Grant (external URL) process.
+        
+        * Specify the platform backend to be used when launching the SeqsLab CLI. The default value is `azure`.
+        
+          ```bash
+          seqslab --backend azure
+          ```
+        
+        * Sign in to the SeqsLab API and obtain API tokens with a single command. By default, the sign-in command uses the Device Code Flow for browserless systems.
+        
+          ```bash
+          auth signin
+          ```
+        
+          Set the device-code argument to `True`. By default, the sign-in process uses the Authorization Code Flow.
+        
+          ```bash
+          auth signin device-code=True
+          ```
+        
+        * Obtain an API access token for interacting with SeqsLab API apps.
+        
+          ```python
+          from seqslab.auth.commands import Auth
+          
+          token = Auth.get_token()
+          access = token.get("tokens").get("access")
+          # use token in your request header, ex: Authorization: Bearer {access}
+          attrs = token.get("attrs")
+          # attrs is a dictionary containing the information about the signing-in user.
+          ```
+        
+          `Auth.get_token()` automatically refreshes the access token upon expiration. When users attempt to sign in to the SeqsLab API before a new access token is generated, the function returns `None`.
+        
+          Access tokens are persistently cached in the system-supported secret service, such as Freedesktop Secret Service and macOS Keychain. As a result, valid access tokens can be used across multiple SeqsLab CLI sessions.
+        
+        ## Roadmap
+        
+        See the [list](https://github.com/AnomeGAP/seqslab-cli/issues) of proposed features and known issues.
+        
+        ## Contributing
+        
+        The repository currently does not accept contributions but will eventually be opened to the community.
+        
+        ## License
+        
+        See `License`.
+        
+        ## Contact 
+        
+        Main contact: [Allen Chang](https://www.linkedin.com/in/allen-chang/) 
+        
+        Email: allen.chang@atgenomix.com
+        
+        Project repository: [https://github.com/atgenomix](https://github.com/atgenomix)
+        
+        ## Acknowledgements
+        
+        * [Facebook Incubator](https://github.com/facebookincubator)
+        * [Microsoft identity platform](https://docs.microsoft.com/en-us/azure/active-directory/develop/active-directory-v2-protocols)
+        * [GA4GH](https://www.ga4gh.org/)
+        * [Best-README-Template](https://github.com/othneildrew/Best-README-Template)
+        
+        <!-- MARKDOWN LINKS & IMAGES -->
+        <!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
+        
+        [contributors-url]: https://github.com/AnomeGAP/seqslab-cli/graphs/contributors
+        
+        [stars-url]: https://github.com/AnomeGAP/seqslab-cli/stargazers
+        
+        [issues-url]: https://github.com/AnomeGAP/seqslab-cli/issues
+        
+        [license-url]: https://github.com/AnomeGAP/seqslab-cli/blob/main/LICENSE.txt
+        
+        [linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555
+        
+        [linkedin-url]: https://www.linkedin.com/company/atgenomix
+        
+        [product-screenshot]: https://github.com/AnomeGAP/seqslab-cli/blob/main/Atgenomix%20SeqsLab%20V3.png
+        
+Platform: UNKNOWN
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown

seqslab-cli-3.2.1.post0/README.md

@@ -0,0 +1,277 @@
+<!-- PROJECT SHIELDS -->
+<!--
+*** I'm using markdown "reference style" links for readability.
+*** Reference links are enclosed in brackets [ ] instead of parentheses ( ).
+*** See the bottom of this document for the declaration of the reference variables
+*** for contributors-url, forks-url, etc. This is an optional, concise syntax you may use.
+*** https://www.markdownguide.org/basic-syntax/#reference-style-links
+-->
+[Contributors][contributors-url]
+[Stargazers][stars-url]
+[Issues][issues-url]
+[License][license-url]
+[![LinkedIn][linkedin-shield]][linkedin-url]
+
+<!-- PROJECT LOGO -->
+<br />
+<p align="center">
+  <a href="https://github.com/AnomeGAP/seqslab-cli">
+    <img src="https://static.wixstatic.com/media/f7a6a5_1ad70ed05af04d7eb45ee5e2df347a32~mv2_d_4266_4449_s_4_2.gif" alt="Logo" width="80" height="80">
+  </a>
+
+<h2 align="center">Atgenomix SeqsLab V3 CLI</h2>
+</p>
+<p align="center">
+  Command-line interface of Atgenomix SeqsLab, a cloud-native biomedical informatics (BioMed IT) platform
+  <br />
+  <a href="https://docs.atgenomix.com"><strong>Explore the docs »</strong></a>
+  <br />
+  <br />
+  <a href="https://github.com/AnomeGAP/seqslab-cli/issues">Report issue</a>
+  ·
+  <a href="https://github.com/AnomeGAP/seqslab-cli/issues">Request feature</a>
+</p>
+
+<!-- TABLE OF CONTENTS -->
+<details open="open">
+  <summary>Table of Contents</summary>
+  <ol>
+    <li>
+      <a href="#overview">Overview</a>
+      <ul>
+        <li><a href="#underlying-technology">Underlying Technology</a></li>
+      </ul>
+    </li>
+    <li>
+      <a href="#getting-started">Getting Started</a>
+      <ul>
+        <li><a href="#prerequisites">Prerequisites</a></li>
+        <li><a href="#interactive-mode">Interactive Mode</a></li>
+        <li><a href="#cli-mode">CLI Mode</a></li>
+      </ul>
+    </li>
+    <li>
+      <a href="#development">Development</a>
+      <ul>
+        <li><a href="#authentication-with-the-seqslab-api">Authentication with the SeqsLab API</a></li>
+      </ul>
+    </li>
+    <li><a href="#roadmap">Roadmap</a></li>
+    <li><a href="#contributing">Contributing</a></li>
+    <li><a href="#license">License</a></li>
+    <li><a href="#contact">Contact</a></li>
+    <li><a href="#acknowledgements">Acknowledgements</a></li>
+  </ol>
+</details>
+
+## Overview
+
+![Product Screen Shot](https://github.com/AnomeGAP/seqslab-cli/blob/main/Atgenomix%20SeqsLab%20V3.png)
+
+Working alongside the web-based SeqsLab Console, the CLI enables bioinformaticians to easily build custom scripts and automate workflows on SeqsLab.
+
+Common use cases for the CLI include the following:
+
+* Automate processing of sequencing data, including uploading and downloading of datasets to/from the SeqsLab Data Hub
+* Submit workflow run requests on demand via SeqsLab Workflow Execution Service (WES) APIs, and integrate with local downstream analysis tools
+* View records of platform activities for auditing purposes
+
+### Underlying Technology
+
+The SeqsLab CLI is built using the following:
+
+* [SeqsLab APIs](https://api.seqslab.net/)
+* [Python-Nubia](https://github.com/facebookincubator/python-nubia)
+* [MSAL Python](https://msal-python.readthedocs.io/en/latest/)
+* [Azure SDK](https://github.com/Azure/azure-sdk)
+* [aiohttp](https://docs.aiohttp.org/en/stable/index.html)
+
+**Note**: The mechanisms for secure information storage are built around a [keyring](https://pypi.org/project/keyring/) service.
+
+## Getting Started
+
+### Prerequisites
+
+* Python 3.8 or later
+
+* A Python virtual environment
+
+  Install the SeqsLab CLI.
+  ```bash
+  pip3 install seqslab-cli
+  ```
+* A keyring backend
+
+  The SeqsLab CLI supports the following keyring backends:
+
+  * macOS [Keychain](https://en.wikipedia.org/wiki/Keychain_%28software%29)
+  * Freedesktop [Secret Service](http://standards.freedesktop.org/secret-service/) (requires [secretstorage](https://pypi.python.org/pypi/secretstorage))
+  * KDE4 & KDE5 [KWallet](https://en.wikipedia.org/wiki/KWallet) (requires [dbus](https://pypi.python.org/pypi/dbus-python))
+  * [Windows Credential Locker](https://docs.microsoft.com/en-us/windows/uwp/security/credential-locker)
+
+  **Note**: See the [Python keyring library documentation](https://pypi.org/project/keyring/) for more information about using keyring on a headless Linux system in a Docker container.
+
+* (macOS devices) The following packages:
+
+  * [pkg-config](https://formulae.brew.sh/formula/pkg-config)
+  * [dbus](https://formulae.brew.sh/formula/dbus)
+  * [glib](https://formulae.brew.sh/formula/glib)
+
+  You can install the required packages using Homebrew.
+  ```bash
+  # install packages:
+  brew install dbus
+  brew install pkg-config 
+  brew install glib
+  ```
+
+### Interactive Mode
+
+This mode provides fish-style auto-completion functionality that is user-friendly, especially for beginners.
+
+* Run interactive mode.
+  ```bash
+  virtualenv .venv
+  source .venv/bin/activate
+  export PYTHONPATH=$(pwd)
+  python3 seqslab/cli.py
+  ```
+
+* Display the available commands.
+  ```bash
+  seqslab> help
+  ```
+
+### CLI Mode
+
+In this mode, the SeqsLab CLI works exactly like any traditional Linux-based command-line utility.
+
+## Development
+
+Commands are defined as normal Python functions with `@command` and `@argument` decorators. Super commands are implemented as Python class objects, and instance methods decorated with `@command` are sub-commands. In non-interactive mode, you can set `@command`-decorated functions to return an `int`, which is used as the Linux return code.
+
+By default, the framework loads commands from the `python/seqslab/commands` module directory. Atgenomix recommends implementing your program structure under the `commands` directory.
+
+```python
+
+from termcolor import cprint
+from nubia import argument, command
+@command("hello")
+@argument("name", type=str, positional=True, description="Your name") 
+def hello(name: str) -> int:
+    """
+    command help, or the command won't be loaded.
+    """
+    cprint(f"Hello {name}!", "green")
+    return 0
+@command
+class SuperCommand:
+  """super-command command help"""
+
+  def __init__(self):
+    self._shared = "shared variable value"
+
+  @property
+  def shared(self) -> str:
+    return self._shared
+    
+  @command(aliases=["echo"])
+  @argument("first",
+            type=str,
+            positional=False,
+            description="firstname",
+            aliases=["f"])
+  @argument("last",
+            type=str,
+            positional=False,
+            description="lastname",
+            aliases=["l"])
+  def cprint(self, first: str, last: str) -> int:
+      """
+      sub-command help message.
+      """
+      cprint(f"{first} {last}", "red")
+      return 0
+```
+
+### Authentication with the SeqsLab API
+
+Regardless of the mode (interactive or non-interactive) that you intend to use, you must sign in to authenticate the session. The SeqsLab CLI follows the OAuth 2.0 Device Authorization Grant (external URL) process.
+
+* Specify the platform backend to be used when launching the SeqsLab CLI. The default value is `azure`.
+
+  ```bash
+  seqslab --backend azure
+  ```
+
+* Sign in to the SeqsLab API and obtain API tokens with a single command. By default, the sign-in command uses the Device Code Flow for browserless systems.
+
+  ```bash
+  auth signin
+  ```
+
+  Set the device-code argument to `True`. By default, the sign-in process uses the Authorization Code Flow.
+
+  ```bash
+  auth signin device-code=True
+  ```
+
+* Obtain an API access token for interacting with SeqsLab API apps.
+
+  ```python
+  from seqslab.auth.commands import Auth
+  
+  token = Auth.get_token()
+  access = token.get("tokens").get("access")
+  # use token in your request header, ex: Authorization: Bearer {access}
+  attrs = token.get("attrs")
+  # attrs is a dictionary containing the information about the signing-in user.
+  ```
+
+  `Auth.get_token()` automatically refreshes the access token upon expiration. When users attempt to sign in to the SeqsLab API before a new access token is generated, the function returns `None`.
+
+  Access tokens are persistently cached in the system-supported secret service, such as Freedesktop Secret Service and macOS Keychain. As a result, valid access tokens can be used across multiple SeqsLab CLI sessions.
+
+## Roadmap
+
+See the [list](https://github.com/AnomeGAP/seqslab-cli/issues) of proposed features and known issues.
+
+## Contributing
+
+The repository currently does not accept contributions but will eventually be opened to the community.
+
+## License
+
+See `License`.
+
+## Contact 
+
+Main contact: [Allen Chang](https://www.linkedin.com/in/allen-chang/) 
+
+Email: allen.chang@atgenomix.com
+
+Project repository: [https://github.com/atgenomix](https://github.com/atgenomix)
+
+## Acknowledgements
+
+* [Facebook Incubator](https://github.com/facebookincubator)
+* [Microsoft identity platform](https://docs.microsoft.com/en-us/azure/active-directory/develop/active-directory-v2-protocols)
+* [GA4GH](https://www.ga4gh.org/)
+* [Best-README-Template](https://github.com/othneildrew/Best-README-Template)
+
+<!-- MARKDOWN LINKS & IMAGES -->
+<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
+
+[contributors-url]: https://github.com/AnomeGAP/seqslab-cli/graphs/contributors
+
+[stars-url]: https://github.com/AnomeGAP/seqslab-cli/stargazers
+
+[issues-url]: https://github.com/AnomeGAP/seqslab-cli/issues
+
+[license-url]: https://github.com/AnomeGAP/seqslab-cli/blob/main/LICENSE.txt
+
+[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555
+
+[linkedin-url]: https://www.linkedin.com/company/atgenomix
+
+[product-screenshot]: https://github.com/AnomeGAP/seqslab-cli/blob/main/Atgenomix%20SeqsLab%20V3.png

{seqslab-cli-3.2.1 → seqslab-cli-3.2.1.post0}/python/seqslab/__init__.py

@@ -23,7 +23,7 @@ __all__ = [
 ]
 
 
-__version__ = "3.2.1"
+__version__ = "3.2.1.post0"
 
 LOGGING = {
     "DIR_PATH": "/var/log/seqslab"

{seqslab-cli-3.2.1 → seqslab-cli-3.2.1.post0}/python/seqslab/drs/commands.py

@@ -584,29 +584,44 @@ class BaseDatahub:
         return results
 
     @command(aliases=["clean"])
+    @argument("ids",
+              type=List[str],
+              positional=False,
+              description="Specify the IDs of the DRS object that you want to delete "
+                          "(optional).")
     @argument("names",
               type=List[str],
               positional=False,
-              description="Generate a list of DRS object names "
+              description="Specify the names of the DRS object that you want to delete "
                           "(optional).")
     @argument("tags",
               type=List[str],
               positional=False,
-              description="Specify the label of the DRS object that you want to delete "
+              description="Specify the labels of the DRS object that you want to delete "
                           "(optional).")
+    @argument("backend_resource",
+              type=str,
+              positional=False,
+              description="Specify whether or not you want to delete the associated computing resources (default = true, optional).",
+              aliases=["purge"],
+              choices=['true', 'false'])
     def delete(
             self,
+            ids: List[str] = [],
             tags: List[str] = [],
             names: List[str] = [],
+            backend_resource: str = "true"
     ) -> int:
         """
-        Delete DRS objects either by name or by tag.
+        Delete DRS objects by DRS id, by DRS name or by DRS tag.
         """
-        if not names and not tags:
-            cprint("Either give names or tags to do DRS query", "red")
+        if not ids and not names and not tags:
+            cprint("Must specify one of the ids, names or tags to identify DRS objects for deletion", "red")
             return errno.ENOENT
 
-        asyncio.run(utils.drs_delete(names, tags))
+        resps = asyncio.run(utils.drs_delete(ids, names, tags, query_opts=f"?backend_content={backend_resource}"))
+        for r in resps:
+            print(r)
 
         return 0
 

{seqslab-cli-3.2.1 → seqslab-cli-3.2.1.post0}/python/seqslab/drs/internal/aiocopy.py

@@ -54,12 +54,12 @@ class CopyResult(NamedTuple):
         }
 
     @staticmethod
-    def access_method(access_methods_type, access_tier, dst, region, Authorization=None):
+    def access_method(access_methods_type, access_tier, dst, region):
         return {
             "type": access_methods_type,
             "access_url": {
                 "url": dst,
-                "headers": {"Authorization": Authorization}
+                "headers": {}
             },
             "access_tier": access_tier,
             "region": region

{seqslab-cli-3.2.1 → seqslab-cli-3.2.1.post0}/python/seqslab/drs/internal/utils.py

@@ -70,9 +70,11 @@ async def drs_crud(drs_id: str, method: str, **kwargs) -> dict:
     except KeyError:
         raise KeyError(f"No tokens, Please signin first!")
 
+    query_opts = kwargs.get("query_opts", None)
+    url = os.path.join(DRS_OBJECT_URL, drs_id, query_opts) if query_opts else os.path.join(DRS_OBJECT_URL, drs_id)
     async with RetryClient(client_session=ClientSession(raise_for_status=False),
                            retry_options=RandomRetry(attempts=3)).request(
-            method=method, url=os.path.join(DRS_OBJECT_URL, drs_id), proxy=kwargs.get("proxy", None),
+            method=method, url=url, proxy=kwargs.get("proxy", None),
             headers={"Authorization": f"Bearer {token}"},
     ) as response:
         resp = await response.content.read()
@@ -102,10 +104,10 @@ async def drs_existence(path: URL, label_check: bool = True) -> bool:
 
 
 @async_exception_handler
-async def drs_delete(names: List[str], labels: List[str], **kwargs):
+async def drs_delete(ids: List[str], names: List[str], labels: List[str], **kwargs):
     search = [drs_search(names=names, labels=[]), drs_search(names=[], labels=labels)]
     resps = await asyncio.gather(*search, return_exceptions=False)
-    drs_ids = [ob.get('id') for res in resps for ob in res.get('objects')]
+    drs_ids = list(set([ob.get('id') for res in resps for ob in res.get('objects')] + ids))
     if not drs_ids:
         cprint(f'No object to be delete')
     else: