Merge pull request #1 from DesignSafe-CI/tapisv3

Tapisv3

Author: kks32

README.md

@@ -6,13 +6,13 @@
 [![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.md)
 [![Docs](https://img.shields.io/badge/view-docs-8A2BE2?color=8A2BE2)](https://designsafe-ci.github.io/dapi/dapi/index.html)
 
-`dapi` is a library that simplifies the process of submitting, running, and monitoring [TAPIS v2 / AgavePy](https://agavepy.readthedocs.io/en/latest/index.html) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
+`dapi` is a library that simplifies the process of submitting, running, and monitoring [TAPIS v3](https://tapis.readthedocs.io/en/latest/) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
 
 ## Features
 
 ### Jobs
 
-* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
+* Get TAPIS v3 templates for jobs: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
 
 * Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
 
@@ -53,6 +53,15 @@ pip install git+https://github.com/DesignSafe-CI/dapi.git --quiet
 
 ## Example usage:
 
+### Storing credentials
+
+Dapi uses the Tapis v3 SDK to authenticate with the DesignSafe API. To store your credentials, create a `.env` file in the root of your project with the following content:
+
+```shell
+DESIGNSAFE_USERNAME=<your_designsafe_username>
+DESIGNSAFE_PASSWORD=<your_designsafe_password>
+```
+
 ### Jobs
 
 * [Jupyter Notebook Templates](example-notebooks/template-mpm-run.ipynb) using dapi.
@@ -66,7 +75,7 @@ Install the latest version of `dapi` and restart the kernel (Kernel >> Restart K
 ```python
 # Remove any previous installations
 !pip uninstall dapi -y
-# Install 
+# Install
 !pip install dapi --quiet
 ```
 
@@ -122,10 +131,6 @@ To run the unit test
 poetry run pytest -v
 ```
 
-## Known Issues
-
-The project only works on `Python 3.9` due to AgavePy Issue [#125](https://github.com/TACC/agavepy/issues/125).
-
 
 ## License
 

dapi/__init__.py

@@ -1,20 +1,42 @@
 """
-`dapi` is a library that simplifies the process of submitting, running, and monitoring [TAPIS v2 / AgavePy](https://agavepy.readthedocs.io/en/latest/index.html) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
-
+dapi` is a library that simplifies the process of submitting, running, and monitoring [TAPIS v3](https://tapis.readthedocs.io/en/latest/) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
 
 ## Features
 
-* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
+### Jobs
+
+* Get TAPIS v3 templates for jobs: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
 
 * Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
 
+### Database
+
+Connects to SQL databases on DesignSafe:
+
+| Database | dbname | env_prefix |
+|----------|--------|------------|
+| NGL | `ngl`| `NGL_` |
+| Earthake Recovery | `eq` | `EQ_` |
+| Vp | `vp` | `VP_` |
+
+Define the following environment variables:
+```
+{env_prefix}DB_USER
+{env_prefix}DB_PASSWORD
+{env_prefix}DB_HOST
+{env_prefix}DB_PORT
+```
+
+For e.g., to add the environment variable `NGL_DB_USER` edit `~/.bashrc`, `~/.zshrc`, or a similar shell-specific configuration file for the current user and add `export NGL_DB_USER="dspublic"`.
+
 ## Installation
 
 ```shell
 pip3 install dapi
 ```
 
 """
+from . import apps
 from . import auth
 from . import db
 from . import jobs

dapi/apps/__init__.py

@@ -0,0 +1,3 @@
+from .apps import find_apps, get_app_version
+
+__all__ = ["find_apps", "get_app_version"]

dapi/apps/apps.py

@@ -0,0 +1,57 @@
+from tapipy.tapis import Tapis
+from typing import List, Dict, Any, Optional
+
+
+def find_apps(
+    t: Tapis, search_term: str, list_type: str = "ALL", verbose: bool = True
+) -> List[Any]:
+    """
+    Search for Tapis apps matching a search term.
+
+    Args:
+        t (Tapis): Tapis client instance
+        search_term (str): Name or partial name to search for
+        list_type (str): One of 'OWNED', 'SHARED_PUBLIC', 'SHARED_DIRECT', 'READ_PERM', 'MINE', 'ALL'
+        verbose (bool): If True, prints all found apps
+
+    Returns:
+        List[Any]: List of matching app objects
+    """
+    results = t.apps.getApps(search=f"(id.like.*{search_term}*)", listType=list_type)
+
+    if verbose:
+        if not results:
+            print(f"No apps found matching '{search_term}'")
+        else:
+            print(f"\nFound {len(results)} matching apps:")
+            for app in results:
+                print(f"- {app.id}")
+            print()
+
+    return results
+
+
+def get_app_version(t: Tapis, app_id: str, verbose: bool = True) -> Optional[Any]:
+    """
+    Get latest version info for a specific app ID.
+
+    Args:
+        t (Tapis): Tapis client instance
+        app_id (str): Exact app ID to look up
+        verbose (bool): If True, prints basic app info
+
+    Returns:
+        Optional[Any]: Latest version info for the app, or None if not found
+    """
+    try:
+        app_info = t.apps.getAppLatestVersion(appId=app_id)
+        if verbose:
+            print(f"App: {app_info.id}")
+            print(f"Version: {app_info.version}")
+            print(f"System: {app_info.jobAttributes.execSystemId}")
+        return app_info
+    except Exception as e:
+        print(f"Error getting app info for '{app_id}': {str(e)}")
+        print("\nCouldn't find exact match. Here are similar apps:")
+        _ = find_apps(t, app_id)
+        return None

dapi/auth/auth.py

@@ -1,30 +1,42 @@
-from agavepy.agave import Agave
-from collections.abc import Mapping
+import os
+from getpass import getpass
+from tapipy.tapis import Tapis
+from dotenv import load_dotenv
 
 
-def init(username, password):
+def init():
     """
-    Initialize an Agave object with a new client and an active token.
+    Initialize a Tapis object with authentication.
+    Tries to read credentials from environment variables first.
+    If not found, prompts the user for input.
 
-    Args:
-        username (str): The username.
-        password (str): The password.
+    Save the user credentials in the .env file.
+    ```
+    DESIGNSAFE_USERNAME=<username>
+    DESIGNSAFE_PASSWORD=<password>
+    ```
 
     Returns:
-        object: The Agave object.
+        object: The authenticated Tapis object.
     """
-    # Authenticate with Agave
-    ag = Agave(
-        base_url="https://agave.designsafe-ci.org", username=username, password=password
-    )
-    # Create a new client
-    new_client = ag.clients_create()
-    # create a new ag object with the new client, at this point ag will have a new token
-    ag = Agave(
-        base_url="https://agave.designsafe-ci.org",
-        username=username,
-        password=password,
-        api_key=new_client["api_key"],
-        api_secret=new_client["api_secret"],
-    )
-    return ag
+    base_url = "https://designsafe.tapis.io"
+
+    # Load environment variables from .env file
+    load_dotenv()
+
+    # Try to get credentials from environment variables
+    username = os.getenv("DESIGNSAFE_USERNAME")
+    password = os.getenv("DESIGNSAFE_PASSWORD")
+
+    # If environment variables are not set, prompt user for input
+    if not username:
+        username = input("Enter username: ")
+    if not password:
+        password = getpass("Enter password: ")
+
+    # Initialize Tapis object
+    t = Tapis(base_url=base_url, username=username, password=password)
+
+    t.get_tokens()
+
+    return t

dapi/jobs/__init__.py

@@ -1,19 +1,19 @@
 """
-`dapi` job submodule simplifies the process of submitting, running, and monitoring [TAPIS v2 / AgavePy](https://agavepy.readthedocs.io/en/latest/index.html) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
+`dapi` job submodule simplifies the process of submitting, running, and monitoring [Tapis v3](https://tapis.readthedocs.io/en/latest/) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
 
 
 ## Features
 
-* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
+* Simplified TAPIS v3 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
 
 * Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
 
-## Installation
+# Installation
 
 ```shell
 pip3 install dapi
 ```
 
 """
 from .dir import get_ds_path_uri
-from .jobs import get_status, runtime_summary, generate_job_info, get_archive_path
+from .jobs import get_status, runtime_summary, generate_job_info

dapi/jobs/dir.py

@@ -1,21 +1,21 @@
 import os
+from tapipy.tapis import Tapis
 
 
-def get_ds_path_uri(ag, path):
+def get_ds_path_uri(t: Tapis, path: str) -> str:
     """
-    Given a path on DesignSafe, determine the correct input URI.
+    Given a path on DesignSafe, determine the correct input URI for Tapis v3.
 
     Args:
-        ag (object): Agave object to fetch profiles or metadata.
-        path (str): The directory path.
+    t (Tapis): Tapis object to fetch profiles or metadata.
+    path (str): The directory path.
 
     Returns:
-        str: The corresponding input URI.
+    str: The corresponding input URI.
 
     Raises:
-        ValueError: If no matching directory pattern is found.
+    ValueError: If no matching directory pattern is found.
     """
-
     # If any of the following directory patterns are found in the path,
     # process them accordingly.
     directory_patterns = [
@@ -28,9 +28,9 @@ def get_ds_path_uri(ag, path):
 
     for pattern, storage, use_username in directory_patterns:
         if pattern in path:
-            path = path.split(pattern).pop()
-            input_dir = ag.profiles.get()["username"] + path if use_username else path
-            input_uri = f"agave://{storage}/{input_dir}"
+            path = path.split(pattern, 1)[1].lstrip("/")
+            input_dir = f"{t.username}/{path}" if use_username else path
+            input_uri = f"tapis://{storage}/{input_dir}"
             return input_uri.replace(" ", "%20")
 
     project_patterns = [
@@ -40,12 +40,15 @@ def get_ds_path_uri(ag, path):
 
     for pattern, prefix in project_patterns:
         if pattern in path:
-            path = path.split(pattern + "/").pop()
-            project_id = path.split("/")[0]
-            query = {"value.projectId": str(project_id)}
-            path = path.split(project_id).pop()
-            project_uuid = ag.meta.listMetadata(q=str(query))[0]["uuid"]
-            input_uri = f"agave://{prefix}{project_uuid}{path}"
+            path = path.split(pattern, 1)[1].lstrip("/")
+            project_id, *rest = path.split("/", 1)
+            path = rest[0] if rest else ""
+
+            # Using Tapis v3 to get project UUID
+            resp = t.get(f"https://designsafe-ci.org/api/projects/v2/{project_id}")
+            project_uuid = resp.json()["baseProject"]["uuid"]
+
+            input_uri = f"tapis://{prefix}{project_uuid}/{path}"
             return input_uri.replace(" ", "%20")
 
     raise ValueError(f"No matching directory pattern found for: {path}")