From 992ea3e426bed22df5dbbe0408e4a5075a145c9a Mon Sep 17 00:00:00 2001 From: Krishna Kumar Date: Tue, 1 Oct 2024 08:24:24 -0500 Subject: [PATCH] Set numpy and pandas to be compatible --- dapi/auth/auth.py | 6 ++ docs/dapi/auth/auth.html | 110 ++++++++++++++----------- docs/search.js | 2 +- poetry.lock | 174 ++++++++++++++++----------------------- pyproject.toml | 4 +- 5 files changed, 145 insertions(+), 151 deletions(-) diff --git a/dapi/auth/auth.py b/dapi/auth/auth.py index 42d2470..eb1d67f 100644 --- a/dapi/auth/auth.py +++ b/dapi/auth/auth.py @@ -10,6 +10,12 @@ def init(): Tries to read credentials from environment variables first. If not found, prompts the user for input. + Save the user credentials in the .env file. + ``` + DESIGNSAFE_USERNAME= + DESIGNSAFE_PASSWORD= + ``` + Returns: object: The authenticated Tapis object. """ diff --git a/docs/dapi/auth/auth.html b/docs/dapi/auth/auth.html index 2e5fd8e..3f05c87 100644 --- a/docs/dapi/auth/auth.html +++ b/docs/dapi/auth/auth.html @@ -66,30 +66,36 @@

10 Tries to read credentials from environment variables first. 11 If not found, prompts the user for input. 12 -13 Returns: -14 object: The authenticated Tapis object. -15 """ -16 base_url = "https://designsafe.tapis.io" -17 -18 # Load environment variables from .env file -19 load_dotenv() -20 -21 # Try to get credentials from environment variables -22 username = os.getenv("DESIGNSAFE_USERNAME") -23 password = os.getenv("DESIGNSAFE_PASSWORD") -24 -25 # If environment variables are not set, prompt user for input -26 if not username: -27 username = input("Enter username: ") -28 if not password: -29 password = getpass("Enter password: ") +13 Save the user credentials in the .env file. +14 ``` +15 DESIGNSAFE_USERNAME=<username> +16 DESIGNSAFE_PASSWORD=<password> +17 ``` +18 +19 Returns: +20 object: The authenticated Tapis object. +21 """ +22 base_url = "https://designsafe.tapis.io" +23 +24 # Load environment variables from .env file +25 load_dotenv() +26 +27 # Try to get credentials from environment variables +28 username = os.getenv("DESIGNSAFE_USERNAME") +29 password = os.getenv("DESIGNSAFE_PASSWORD") 30 -31 # Initialize Tapis object -32 t = Tapis(base_url=base_url, username=username, password=password) -33 -34 t.get_tokens() -35 -36 return t +31 # If environment variables are not set, prompt user for input +32 if not username: +33 username = input("Enter username: ") +34 if not password: +35 password = getpass("Enter password: ") +36 +37 # Initialize Tapis object +38 t = Tapis(base_url=base_url, username=username, password=password) +39 +40 t.get_tokens() +41 +42 return t @@ -111,30 +117,36 @@

11 Tries to read credentials from environment variables first. 12 If not found, prompts the user for input. 13 -14 Returns: -15 object: The authenticated Tapis object. -16 """ -17 base_url = "https://designsafe.tapis.io" -18 -19 # Load environment variables from .env file -20 load_dotenv() -21 -22 # Try to get credentials from environment variables -23 username = os.getenv("DESIGNSAFE_USERNAME") -24 password = os.getenv("DESIGNSAFE_PASSWORD") -25 -26 # If environment variables are not set, prompt user for input -27 if not username: -28 username = input("Enter username: ") -29 if not password: -30 password = getpass("Enter password: ") +14 Save the user credentials in the .env file. +15 ``` +16 DESIGNSAFE_USERNAME=<username> +17 DESIGNSAFE_PASSWORD=<password> +18 ``` +19 +20 Returns: +21 object: The authenticated Tapis object. +22 """ +23 base_url = "https://designsafe.tapis.io" +24 +25 # Load environment variables from .env file +26 load_dotenv() +27 +28 # Try to get credentials from environment variables +29 username = os.getenv("DESIGNSAFE_USERNAME") +30 password = os.getenv("DESIGNSAFE_PASSWORD") 31 -32 # Initialize Tapis object -33 t = Tapis(base_url=base_url, username=username, password=password) -34 -35 t.get_tokens() -36 -37 return t +32 # If environment variables are not set, prompt user for input +33 if not username: +34 username = input("Enter username: ") +35 if not password: +36 password = getpass("Enter password: ") +37 +38 # Initialize Tapis object +39 t = Tapis(base_url=base_url, username=username, password=password) +40 +41 t.get_tokens() +42 +43 return t @@ -142,6 +154,12 @@

Tries to read credentials from environment variables first. If not found, prompts the user for input.

+

Save the user credentials in the .env file.

+ +
DESIGNSAFE_USERNAME=<username>
+DESIGNSAFE_PASSWORD=<password>
+
+

Returns: object: The authenticated Tapis object.

diff --git a/docs/search.js b/docs/search.js index 0706b2b..273fa56 100644 --- a/docs/search.js +++ b/docs/search.js @@ -1,6 +1,6 @@ window.pdocSearch = (function(){ /** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. 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e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();odapi` 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"}]; + /** 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

Save the user credentials in the .env file.

\n\n
DESIGNSAFE_USERNAME=<username>\nDESIGNSAFE_PASSWORD=<password>\n
\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": "

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\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.

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