From 8f1f69e8276976de06ff556a98b06c17eaf723db Mon Sep 17 00:00:00 2001 From: Krishna Kumar Date: Tue, 1 Oct 2024 07:48:44 -0500 Subject: [PATCH] TAPIS v3 update to README --- README.md | 8 +- dapi/__init__.py | 27 ++- dapi/jobs/__init__.py | 4 +- docs/dapi.html | 103 +++++++-- docs/dapi/jobs.html | 8 +- docs/search.js | 2 +- examples/mpm/template-mpm-run.ipynb | 342 ---------------------------- 7 files changed, 116 insertions(+), 378 deletions(-) delete mode 100644 examples/mpm/template-mpm-run.ipynb diff --git a/README.md b/README.md index 79f1c8a..3123ee5 100644 --- a/README.md +++ b/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. @@ -131,10 +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 diff --git a/dapi/__init__.py b/dapi/__init__.py index 7d609d2..66053e9 100644 --- a/dapi/__init__.py +++ b/dapi/__init__.py @@ -1,13 +1,34 @@ """ -`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 diff --git a/dapi/jobs/__init__.py b/dapi/jobs/__init__.py index 526fa3e..8dfcb52 100644 --- a/dapi/jobs/__init__.py +++ b/dapi/jobs/__init__.py @@ -1,10 +1,10 @@ """ -`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. diff --git a/docs/dapi.html b/docs/dapi.html index fb5bae4..1e246f8 100644 --- a/docs/dapi.html +++ b/docs/dapi.html @@ -49,15 +49,57 @@

Submodules

dapi

-

dapi is a library that simplifies the process of submitting, running, and monitoring TAPIS v2 / AgavePy jobs on DesignSafe via Jupyter Notebooks.

+

dapi` is a library that simplifies the process of submitting, running, and monitoring TAPIS v3 jobs on DesignSafe via Jupyter Notebooks.

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.

+

Database

+ +

Connects to SQL databases on DesignSafe:

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Databasedbnameenv_prefix
NGLngl| NGL_
Earthake RecoveryeqEQ_
VpvpVP_
+ +

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

@@ -71,25 +113,46 @@

Installation

 1"""
- 2`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).
+ 2dapi` 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).
  3
- 4
- 5## Features
- 6
- 7* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
- 8
- 9* Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
-10
-11## Installation
-12
-13```shell
-14pip3 install dapi
-15```
-16
-17"""
-18from . import auth
-19from . import db
-20from . import jobs
+ 4## Features
+ 5
+ 6### Jobs
+ 7
+ 8* Get TAPIS v3 templates for jobs: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
+ 9
+10* Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
+11
+12### Database
+13
+14Connects to SQL databases on DesignSafe:
+15
+16| Database | dbname | env_prefix |
+17|----------|--------|------------|
+18| NGL | `ngl`| `NGL_` |
+19| Earthake Recovery | `eq` | `EQ_` |
+20| Vp | `vp` | `VP_` |
+21
+22Define the following environment variables:
+23```
+24{env_prefix}DB_USER
+25{env_prefix}DB_PASSWORD
+26{env_prefix}DB_HOST
+27{env_prefix}DB_PORT
+28```
+29
+30For 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"`.
+31
+32## Installation
+33
+34```shell
+35pip3 install dapi
+36```
+37
+38"""
+39from . import auth
+40from . import db
+41from . import jobs
diff --git a/docs/dapi/jobs.html b/docs/dapi/jobs.html index 0811927..cf51fe8 100644 --- a/docs/dapi/jobs.html +++ b/docs/dapi/jobs.html @@ -53,12 +53,12 @@

Submodules

dapi.jobs

-

dapi job submodule simplifies the process of submitting, running, and monitoring TAPIS v2 / AgavePy jobs on DesignSafe via Jupyter Notebooks.

+

dapi job submodule simplifies the process of submitting, running, and monitoring Tapis v3 jobs on DesignSafe via Jupyter Notebooks.

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.

@@ -75,12 +75,12 @@

Installation

 1"""
- 2`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).
+ 2`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).
  3
  4
  5## Features
  6
- 7* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
+ 7* Simplified TAPIS v3 Calls: No need to fiddle with complex API requests. `dapi` abstracts away the complexities.
  8
  9* Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
 10
diff --git a/docs/search.js b/docs/search.js
index 22c2c8c..9712b25 100644
--- a/docs/search.js
+++ b/docs/search.js
@@ -1,6 +1,6 @@
 window.pdocSearch = (function(){
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\n\n
Features
\n\n
    \n
  • Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. dapi abstracts away the complexities.
    • \n
  • Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
    • \n
\n\n
Installation
\n\n
\n
pip3 install dapi\n
\n
\n"}, {"fullname": "dapi.auth", "modulename": "dapi.auth", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.auth.auth", "modulename": "dapi.auth.auth", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.auth.auth.init", "modulename": "dapi.auth.auth", "qualname": "init", "kind": "function", "doc": "
Initialize a Tapis object with authentication.\nTries to read credentials from environment variables first.\nIf not found, prompts the user for input.
\n\n
Returns:\n    object: The authenticated Tapis object.
\n", "signature": "():", "funcdef": "def"}, {"fullname": "dapi.db", "modulename": "dapi.db", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.db.name", "modulename": "dapi.db", "qualname": "name", "kind": "variable", "doc": "
\n", "default_value": "'designsafe_db'"}, {"fullname": "dapi.db.config", "modulename": "dapi.db.config", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.db.config.db_config", "modulename": "dapi.db.config", "qualname": "db_config", "kind": "variable", "doc": "
\n", "default_value": "{'ngl': {'dbname': 'sjbrande_ngl_db', 'env_prefix': 'NGL_'}, 'vp': {'dbname': 'sjbrande_vpdb', 'env_prefix': 'VP_'}, 'eq': {'dbname': 'post_earthquake_recovery', 'env_prefix': 'EQ_'}}"}, {"fullname": "dapi.db.db", "modulename": "dapi.db.db", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase", "modulename": "dapi.db.db", "qualname": "DSDatabase", "kind": "class", "doc": "
A database utility class for connecting to a DesignSafe SQL database.
\n\n
This class provides functionality to connect to a MySQL database using\nSQLAlchemy and PyMySQL. It supports executing SQL queries and returning\nresults in different formats.
\n\n
Attributes:\n    user (str): Database username, defaults to 'dspublic'.\n    password (str): Database password, defaults to 'R3ad0nlY'.\n    host (str): Database host address, defaults to '129.114.52.174'.\n    port (int): Database port, defaults to 3306.\n    db (str): Database name, can be 'sjbrande_ngl_db', 'sjbrande_vpdb', or 'post_earthquake_recovery'.\n    recycle_time (int): Time in seconds to recycle database connections.\n    engine (Engine): SQLAlchemy engine for database connection.\n    Session (sessionmaker): SQLAlchemy session maker bound to the engine.
\n"}, {"fullname": "dapi.db.db.DSDatabase.__init__", "modulename": "dapi.db.db", "qualname": "DSDatabase.__init__", "kind": "function", "doc": "
Initializes the DSDatabase instance with environment variables and creates the database engine.
\n\n
Args:\n    dbname (str): Shorthand for the database name. Must be one of 'ngl', 'vp', or 'eq'.
\n", "signature": "(dbname='ngl')"}, {"fullname": "dapi.db.db.DSDatabase.user", "modulename": "dapi.db.db", "qualname": "DSDatabase.user", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.password", "modulename": "dapi.db.db", "qualname": "DSDatabase.password", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.host", "modulename": "dapi.db.db", "qualname": "DSDatabase.host", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.port", "modulename": "dapi.db.db", "qualname": "DSDatabase.port", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.db", "modulename": "dapi.db.db", "qualname": "DSDatabase.db", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.engine", "modulename": "dapi.db.db", "qualname": "DSDatabase.engine", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.Session", "modulename": "dapi.db.db", "qualname": "DSDatabase.Session", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.read_sql", "modulename": "dapi.db.db", "qualname": "DSDatabase.read_sql", "kind": "function", "doc": "
Executes a SQL query and returns the results.
\n\n
Args:\n    sql (str): The SQL query string to be executed.\n    output_type (str, optional): The format for the query results. Defaults to 'DataFrame'.\n        Possible values are 'DataFrame' for a pandas DataFrame, or 'dict' for a list of dictionaries.
\n\n
Returns:\n    pandas.DataFrame or list of dict: The result of the SQL query.
\n\n
Raises:\n    ValueError: If the SQL query string is empty or if the output type is not valid.\n    SQLAlchemyError: If an error occurs during query execution.
\n", "signature": "(self, sql, output_type='DataFrame'):", "funcdef": "def"}, {"fullname": "dapi.db.db.DSDatabase.close", "modulename": "dapi.db.db", "qualname": "DSDatabase.close", "kind": "function", "doc": "
Close the database connection.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "dapi.jobs", "modulename": "dapi.jobs", "kind": "module", "doc": "
dapi job submodule simplifies the process of submitting, running, and monitoring TAPIS v2 / AgavePy jobs on DesignSafe via Jupyter Notebooks.
\n\n
Features
\n\n
    \n
  • Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. dapi abstracts away the complexities.
    • \n
  • Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
    • \n
\n\n
Installation
\n\n
\n
pip3 install dapi\n
\n
\n"}, {"fullname": "dapi.jobs.dir", "modulename": "dapi.jobs.dir", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.jobs.dir.get_ds_path_uri", "modulename": "dapi.jobs.dir", "qualname": "get_ds_path_uri", "kind": "function", "doc": "
Given a path on DesignSafe, determine the correct input URI for Tapis v3.
\n\n
Args:\nt (Tapis): Tapis object to fetch profiles or metadata.\npath (str): The directory path.
\n\n
Returns:\nstr: The corresponding input URI.
\n\n
Raises:\nValueError: If no matching directory pattern is found.
\n", "signature": "(t: tapipy.tapis.Tapis, path: str) -> str:", "funcdef": "def"}, {"fullname": "dapi.jobs.jobs", "modulename": "dapi.jobs.jobs", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.jobs.jobs.generate_job_info", "modulename": "dapi.jobs.jobs", "qualname": "generate_job_info", "kind": "function", "doc": "
Generates a job info dictionary based on the provided application name, job name, input URI, input file, and optional allocation.
\n\n
Args:\n    t (object): The Tapis API client object.\n    app_name (str): The name of the application to use for the job.\n    input_uri (str): The URI of the input data for the job.\n    input_file (str): The local file path to the input data for the job.\n    job_name (str, optional): The name of the job to be created. Defaults to None.\n    max_minutes (int, optional): The maximum number of minutes the job can run. Defaults to None.\n    node_count (int, optional): The number of nodes to use for the job. Defaults to None.\n    cores_per_node (int, optional): The number of cores per node for the job. Defaults to None.\n    queue (str, optional): The queue to use for the job. Defaults to None.\n    allocation (str, optional): The allocation to use for the job. Defaults to None.
\n\n
Returns:\n    dict: The job info dictionary.
\n", "signature": "(\tt: Any,\tapp_name: str,\tinput_uri: str,\tinput_file: str,\tjob_name: str = None,\tmax_minutes: Optional[int] = None,\tnode_count: Optional[int] = None,\tcores_per_node: Optional[int] = None,\tqueue: Optional[str] = None,\tallocation: Optional[str] = None) -> Dict[str, Any]:", "funcdef": "def"}, {"fullname": "dapi.jobs.jobs.get_status", "modulename": "dapi.jobs.jobs", "qualname": "get_status", "kind": "function", "doc": "
Retrieves and monitors the status of a job using Tapis API.\nThis function waits for the job to start, then monitors it for up to maxMinutes.
\n\n
Args:\nt (object): The Tapis API client object.\nmjobUuid (str): The unique identifier of the job to monitor.\ntlapse (int, optional): Time interval, in seconds, to wait between status checks. Defaults to 15 seconds.
\n\n
Returns:\nstr: The final status of the job (FINISHED, FAILED, or STOPPED).
\n", "signature": "(t, mjobUuid, tlapse=15):", "funcdef": "def"}, {"fullname": "dapi.jobs.jobs.runtime_summary", "modulename": "dapi.jobs.jobs", "qualname": "runtime_summary", "kind": "function", "doc": "
Get the runtime of a job.\nArgs:\nt (object): The Tapis v3 client object.\njob_uuid (str): The UUID of the job for which the runtime needs to be determined.\nverbose (bool): If True, prints all history events. Otherwise, prints only specific statuses.\nReturns:\nNone: This function doesn't return a value, but it prints the runtime details.
\n", "signature": "(t, job_uuid, verbose=False):", "funcdef": "def"}];
+    /** pdoc search index */const docs = [{"fullname": "dapi", "modulename": "dapi", "kind": "module", "doc": "
dapi` is a library that simplifies the process of submitting, running, and monitoring TAPIS v3 jobs on DesignSafe via Jupyter Notebooks.
\n\n
Features
\n\n
Jobs
\n\n
    \n
  • Get TAPIS v3 templates for jobs: No need to fiddle with complex API requests. dapi abstracts away the complexities.
    • \n
  • Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
    • \n
\n\n
Database
\n\n
Connects to SQL databases on DesignSafe:
\n\n\n\n\n  \n  \n  \n\n\n\n\n  \n  \n\n\n  \n  \n  \n\n\n  \n  \n  \n\n\n
Databasedbnameenv_prefix
NGLngl| NGL_
Earthake RecoveryeqEQ_
VpvpVP_
\n\n
Define the following environment variables:
\n\n
{env_prefix}DB_USER\n{env_prefix}DB_PASSWORD\n{env_prefix}DB_HOST\n{env_prefix}DB_PORT\n
\n\n
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\".
\n\n
Installation
\n\n
\n
pip3 install dapi\n
\n
\n"}, {"fullname": "dapi.auth", "modulename": "dapi.auth", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.auth.auth", "modulename": "dapi.auth.auth", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.auth.auth.init", "modulename": "dapi.auth.auth", "qualname": "init", "kind": "function", "doc": "
Initialize a Tapis object with authentication.\nTries to read credentials from environment variables first.\nIf not found, prompts the user for input.
\n\n
Returns:\n    object: The authenticated Tapis object.
\n", "signature": "():", "funcdef": "def"}, {"fullname": "dapi.db", "modulename": "dapi.db", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.db.name", "modulename": "dapi.db", "qualname": "name", "kind": "variable", "doc": "
\n", "default_value": "'designsafe_db'"}, {"fullname": "dapi.db.config", "modulename": "dapi.db.config", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.db.config.db_config", "modulename": "dapi.db.config", "qualname": "db_config", "kind": "variable", "doc": "
\n", "default_value": "{'ngl': {'dbname': 'sjbrande_ngl_db', 'env_prefix': 'NGL_'}, 'vp': {'dbname': 'sjbrande_vpdb', 'env_prefix': 'VP_'}, 'eq': {'dbname': 'post_earthquake_recovery', 'env_prefix': 'EQ_'}}"}, {"fullname": "dapi.db.db", "modulename": "dapi.db.db", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase", "modulename": "dapi.db.db", "qualname": "DSDatabase", "kind": "class", "doc": "
A database utility class for connecting to a DesignSafe SQL database.
\n\n
This class provides functionality to connect to a MySQL database using\nSQLAlchemy and PyMySQL. It supports executing SQL queries and returning\nresults in different formats.
\n\n
Attributes:\n    user (str): Database username, defaults to 'dspublic'.\n    password (str): Database password, defaults to 'R3ad0nlY'.\n    host (str): Database host address, defaults to '129.114.52.174'.\n    port (int): Database port, defaults to 3306.\n    db (str): Database name, can be 'sjbrande_ngl_db', 'sjbrande_vpdb', or 'post_earthquake_recovery'.\n    recycle_time (int): Time in seconds to recycle database connections.\n    engine (Engine): SQLAlchemy engine for database connection.\n    Session (sessionmaker): SQLAlchemy session maker bound to the engine.
\n"}, {"fullname": "dapi.db.db.DSDatabase.__init__", "modulename": "dapi.db.db", "qualname": "DSDatabase.__init__", "kind": "function", "doc": "
Initializes the DSDatabase instance with environment variables and creates the database engine.
\n\n
Args:\n    dbname (str): Shorthand for the database name. Must be one of 'ngl', 'vp', or 'eq'.
\n", "signature": "(dbname='ngl')"}, {"fullname": "dapi.db.db.DSDatabase.user", "modulename": "dapi.db.db", "qualname": "DSDatabase.user", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.password", "modulename": "dapi.db.db", "qualname": "DSDatabase.password", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.host", "modulename": "dapi.db.db", "qualname": "DSDatabase.host", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.port", "modulename": "dapi.db.db", "qualname": "DSDatabase.port", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.db", "modulename": "dapi.db.db", "qualname": "DSDatabase.db", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.engine", "modulename": "dapi.db.db", "qualname": "DSDatabase.engine", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.Session", "modulename": "dapi.db.db", "qualname": "DSDatabase.Session", "kind": "variable", "doc": "
\n"}, {"fullname": "dapi.db.db.DSDatabase.read_sql", "modulename": "dapi.db.db", "qualname": "DSDatabase.read_sql", "kind": "function", "doc": "
Executes a SQL query and returns the results.
\n\n
Args:\n    sql (str): The SQL query string to be executed.\n    output_type (str, optional): The format for the query results. Defaults to 'DataFrame'.\n        Possible values are 'DataFrame' for a pandas DataFrame, or 'dict' for a list of dictionaries.
\n\n
Returns:\n    pandas.DataFrame or list of dict: The result of the SQL query.
\n\n
Raises:\n    ValueError: If the SQL query string is empty or if the output type is not valid.\n    SQLAlchemyError: If an error occurs during query execution.
\n", "signature": "(self, sql, output_type='DataFrame'):", "funcdef": "def"}, {"fullname": "dapi.db.db.DSDatabase.close", "modulename": "dapi.db.db", "qualname": "DSDatabase.close", "kind": "function", "doc": "
Close the database connection.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "dapi.jobs", "modulename": "dapi.jobs", "kind": "module", "doc": "
dapi job submodule simplifies the process of submitting, running, and monitoring Tapis v3 jobs on DesignSafe via Jupyter Notebooks.
\n\n
Features
\n\n
    \n
  • Simplified TAPIS v3 Calls: No need to fiddle with complex API requests. dapi abstracts away the complexities.
    • \n
  • Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
    • \n
\n\n
Installation
\n\n
\n
pip3 install dapi\n
\n
\n"}, {"fullname": "dapi.jobs.dir", "modulename": "dapi.jobs.dir", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.jobs.dir.get_ds_path_uri", "modulename": "dapi.jobs.dir", "qualname": "get_ds_path_uri", "kind": "function", "doc": "
Given a path on DesignSafe, determine the correct input URI for Tapis v3.
\n\n
Args:\nt (Tapis): Tapis object to fetch profiles or metadata.\npath (str): The directory path.
\n\n
Returns:\nstr: The corresponding input URI.
\n\n
Raises:\nValueError: If no matching directory pattern is found.
\n", "signature": "(t: tapipy.tapis.Tapis, path: str) -> str:", "funcdef": "def"}, {"fullname": "dapi.jobs.jobs", "modulename": "dapi.jobs.jobs", "kind": "module", "doc": "
\n"}, {"fullname": "dapi.jobs.jobs.generate_job_info", "modulename": "dapi.jobs.jobs", "qualname": "generate_job_info", "kind": "function", "doc": "
Generates a job info dictionary based on the provided application name, job name, input URI, input file, and optional allocation.
\n\n
Args:\n    t (object): The Tapis API client object.\n    app_name (str): The name of the application to use for the job.\n    input_uri (str): The URI of the input data for the job.\n    input_file (str): The local file path to the input data for the job.\n    job_name (str, optional): The name of the job to be created. Defaults to None.\n    max_minutes (int, optional): The maximum number of minutes the job can run. Defaults to None.\n    node_count (int, optional): The number of nodes to use for the job. Defaults to None.\n    cores_per_node (int, optional): The number of cores per node for the job. Defaults to None.\n    queue (str, optional): The queue to use for the job. Defaults to None.\n    allocation (str, optional): The allocation to use for the job. Defaults to None.
\n\n
Returns:\n    dict: The job info dictionary.
\n", "signature": "(\tt: Any,\tapp_name: str,\tinput_uri: str,\tinput_file: str,\tjob_name: str = None,\tmax_minutes: Optional[int] = None,\tnode_count: Optional[int] = None,\tcores_per_node: Optional[int] = None,\tqueue: Optional[str] = None,\tallocation: Optional[str] = None) -> Dict[str, Any]:", "funcdef": "def"}, {"fullname": "dapi.jobs.jobs.get_status", "modulename": "dapi.jobs.jobs", "qualname": "get_status", "kind": "function", "doc": "
Retrieves and monitors the status of a job using Tapis API.\nThis function waits for the job to start, then monitors it for up to maxMinutes.
\n\n
Args:\nt (object): The Tapis API client object.\nmjobUuid (str): The unique identifier of the job to monitor.\ntlapse (int, optional): Time interval, in seconds, to wait between status checks. Defaults to 15 seconds.
\n\n
Returns:\nstr: The final status of the job (FINISHED, FAILED, or STOPPED).
\n", "signature": "(t, mjobUuid, tlapse=15):", "funcdef": "def"}, {"fullname": "dapi.jobs.jobs.runtime_summary", "modulename": "dapi.jobs.jobs", "qualname": "runtime_summary", "kind": "function", "doc": "
Get the runtime of a job.\nArgs:\nt (object): The Tapis v3 client object.\njob_uuid (str): The UUID of the job for which the runtime needs to be determined.\nverbose (bool): If True, prints all history events. Otherwise, prints only specific statuses.\nReturns:\nNone: This function doesn't return a value, but it prints the runtime details.
\n", "signature": "(t, job_uuid, verbose=False):", "funcdef": "def"}];
 
     // mirrored in build-search-index.js (part 1)
     // Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/examples/mpm/template-mpm-run.ipynb b/examples/mpm/template-mpm-run.ipynb
deleted file mode 100644
index c9480cf..0000000
--- a/examples/mpm/template-mpm-run.ipynb
+++ /dev/null
@@ -1,342 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "4efabb5e",
-   "metadata": {},
-   "source": [
-    "# Templatized notebook for running CB-Geo MPM TAPIS job"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "abe5d8a3-32da-4233-b605-9fd51d053ec1",
-   "metadata": {},
-   "source": [
-    "## Install DSJobs"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "b7fa3e9a-7bf3-441c-917f-fb57a94ee017",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m23.3.2\u001b[0m\n",
-      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n"
-     ]
-    }
-   ],
-   "source": [
-    "!pip install dapi --quiet"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "dd802d14-8cb5-49e7-b43c-1c21ac253961",
-   "metadata": {},
-   "source": [
-    "## Modify MPM Job parameters\n",
-    "\n",
-    "> Only change the cell below"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "8593c08c-c96a-4a66-9b52-80b8b5c27e44",
-   "metadata": {
-    "tags": [
-     "parameters"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "# Default parameters for the MPM template notebook\n",
-    "path: str = \"/MyData/mpm-benchmarks/2d/uniaxial_stress/\"  # path to input file\n",
-    "\n",
-    "input_file: str = \"mpm.json\"  # input file.json\n",
-    "\n",
-    "duration: str = \"00:10:00\"  # Runtime duration ('HH:MM:SS')\n",
-    "\n",
-    "# The parameters modified in your job will be included in the cell below."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "89d9596b-1c14-4d0c-a127-ee6c46da2671",
-   "metadata": {},
-   "source": [
-    "## Imports"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "91b811a4-45d9-4223-a145-c0f4e393af66",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from agavepy.agave import Agave\n",
-    "import dapi\n",
-    "import json\n",
-    "import os"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "14a18561-3bf7-4605-a6f4-98ab0b99af10",
-   "metadata": {},
-   "source": [
-    "## Configure and run MPM job"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "0153c5cc-f4b9-460b-b4c6-d92eb8c6ede5",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "---Job Info---\n",
-      "\n",
-      "{\n",
-      "  \"appId\": \"mpm-1.1.0u3\",\n",
-      "  \"name\": \"mpm-uniaxial\",\n",
-      "  \"batchQueue\": \"development\",\n",
-      "  \"nodeCount\": 1,\n",
-      "  \"processorsPerNode\": 1,\n",
-      "  \"memoryPerNode\": \"1\",\n",
-      "  \"maxRunTime\": \"00:10:00\",\n",
-      "  \"archive\": true,\n",
-      "  \"inputs\": {\n",
-      "    \"inputDirectory\": [\n",
-      "      \"agave://designsafe.storage.default/kks32/mpm-benchmarks/2d/uniaxial_stress/\"\n",
-      "    ]\n",
-      "  },\n",
-      "  \"parameters\": {\n",
-      "    \"inputfile\": [\n",
-      "      \"mpm.json\"\n",
-      "    ]\n",
-      "  }\n",
-      "}\n"
-     ]
-    }
-   ],
-   "source": [
-    "# authenticate\n",
-    "ag = Agave.restore()\n",
-    "\n",
-    "# generate and modify job info\n",
-    "job_info = dapi.jobs.generate_job_info(\n",
-    "    ag, appid=\"mpm-1.1.0u3\", jobname=\"mpm-uniaxial\", runtime=duration\n",
-    ")\n",
-    "\n",
-    "# specify input path and file\n",
-    "job_info[\"inputs\"] = {\"inputDirectory\": [dapi.jobs.get_ds_path_uri(ag, path)]}\n",
-    "job_info[\"parameters\"] = {\"inputfile\": [input_file]}\n",
-    "print(\"\\n---Job Info---\\n\\n\" + json.dumps(job_info, indent=2))"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "9851e692-2ba8-4cb0-887f-b639ba8832d2",
-   "metadata": {},
-   "source": [
-    "## Submit and monitor job status"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "4e6dc010-d821-45d5-805b-84620363f468",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "job = ag.jobs.submit(body=job_info)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "06dd17dc-2540-46b3-9036-3245a9b6cfae",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Waiting for job to start: 2it [00:30, 15.14s/it, Status: RUNNING]\n",
-      "Monitoring job:   0%|                                                        | 0/40 [00:00