Source code for pyiron.base.database.jobtable

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

import pandas
import sys
import os
import numpy as np
from pyiron.base.settings.generic import Settings

"""
The Jobtable module provides a set of top level functions to interact with the database.
"""

__author__ = "Jan Janssen"
__copyright__ = (
    "Copyright 2019, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Jan Janssen"
__email__ = "janssen@mpie.de"
__status__ = "production"
__date__ = "Sep 1, 2017"

s = Settings()


def _job_dict(
    database,
    sql_query,
    user,
    project_path,
    recursive,
    job=None,
    sub_job_name="%",
    element_lst=None,
):
    """
    Internal function to access the database from the project directly.

    Args:
        database (DatabaseAccess): Database object
        sql_query (str): SQL query to enter a more specific request
        user (str): username of the user whoes user space should be searched
        project_path (str): root_path - this is in contrast to the project_path in GenericPath
        recursive (bool): search subprojects [True/False]
        job (str): job_name - by default None
        sub_job_name (str): path inside the HDF5 file - "%" by default to accept any path
        element_lst (list): list of elements required in the chemical formular - by default None

    Returns:
        list: the function returns a list of dicts like get_items_sql, but it does not format datetime:
             [{'chemicalformula': u'Ni108',
              'computer': u'mapc157',
              'hamilton': u'LAMMPS',
              'hamversion': u'1.1',
              'id': 24,
              'job': u'DOF_1_0',
              'parentid': 21L,
              'project': u'lammps.phonons.Ni_fcc',
              'projectpath': u'D:/PyIron/PyIron_data/projects',
              'status': u'finished',
              'timestart': datetime.datetime(2016, 6, 24, 10, 17, 3, 140000),
              'timestop': datetime.datetime(2016, 6, 24, 10, 17, 3, 173000),
              'totalcputime': 0.033,
              'username': u'test'},
             {'chemicalformula': u'Ni108',
              'computer': u'mapc157',
              'hamilton': u'LAMMPS',
              'hamversion': u'1.1',
              'id': 21,
              'job': u'ref',
              'parentid': 20L,
              'project': u'lammps.phonons.Ni_fcc',
              'projectpath': u'D:/PyIron/PyIron_data/projects',
              'status': u'finished',
              'timestart': datetime.datetime(2016, 6, 24, 10, 17, 2, 429000),
              'timestop': datetime.datetime(2016, 6, 24, 10, 17, 2, 463000),
              'totalcputime': 0.034,
              'username': u'test'},.......]

    """
    dict_clause = {}
    # FOR GET_ITEMS_SQL: clause = []
    if user is not None:
        dict_clause["username"] = str(user)
        # FOR GET_ITEMS_SQL: clause.append("username = '" + self.user + "'")
    if sql_query is not None:
        # FOR GET_ITEMS_SQL: clause.append(self.sql_query)
        if "AND" in sql_query:
            cl_split = sql_query.split(" AND ")
        elif "and" in sql_query:
            cl_split = sql_query.split(" and ")
        else:
            cl_split = [sql_query]
        dict_clause.update(
            {str(element.split()[0]): element.split()[2] for element in cl_split}
        )
    if job is not None:
        dict_clause["job"] = str(job)

    if recursive:
        dict_clause["project"] = str(project_path) + "%"
    else:
        dict_clause["project"] = str(project_path)
    if sub_job_name is None:
        dict_clause["subjob"] = None
    elif sub_job_name != "%":
        dict_clause["subjob"] = str(sub_job_name)
    if element_lst is not None:
        dict_clause["element_lst"] = element_lst

    s.logger.debug("sql_query: %s", str(dict_clause))
    return database.get_items_dict(dict_clause)


[docs]def get_db_columns(database): """ Get column names Args: database (DatabaseAccess): Database object Returns: list: list of column names like: ['id', 'parentid', 'masterid', 'projectpath', 'project', 'job', 'subjob', 'chemicalformula', 'status', 'hamilton', 'hamversion', 'username', 'computer', 'timestart', 'timestop', 'totalcputime'] """ return database.get_table_headings()
[docs]def job_table( database, sql_query, user, project_path, recursive=True, columns=None, all_columns=False, sort_by="id", max_colwidth=200, full_table=False, element_lst=None, job_name_contains='', ): """ Access the job_table Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath recursive (bool): search subprojects [True/False] columns (list): by default only the columns ['job', 'project', 'chemicalformula'] are selected, but the user can select a subset of ['id', 'status', 'chemicalformula', 'job', 'subjob', 'project', 'projectpath', 'timestart', 'timestop', 'totalcputime', 'computer', 'hamilton', 'hamversion', 'parentid', 'masterid'] all_columns (bool): Select all columns - this overwrites the columns option. sort_by (str): Sort by a specific column max_colwidth (int): set the column width full_table (bool): Whether to show the entire pandas table element_lst (list): list of elements required in the chemical formular - by default None job_name_contains (str): a string which should be contained in every job_name Returns: pandas.Dataframe: Return the result as a pandas.Dataframe object """ if columns is None: columns = ["job", "project", "chemicalformula"] all_db = [ "id", "status", "chemicalformula", "job", "subjob", "projectpath", "project", "timestart", "timestop", "totalcputime", "computer", "hamilton", "hamversion", "parentid", "masterid", ] if all_columns: columns = all_db job_dict = _job_dict( database=database, sql_query=sql_query, user=user, project_path=project_path, recursive=recursive, element_lst=element_lst, ) if full_table: pandas.set_option('display.max_rows', None) pandas.set_option('display.max_columns', None) else: pandas.reset_option('display.max_rows') pandas.reset_option('display.max_columns') pandas.set_option("display.max_colwidth", max_colwidth) df = pandas.DataFrame(job_dict) if len(job_dict) == 0: return df if job_name_contains != '': df = df[df.job.str.contains(job_name_contains)] if sort_by in columns: return df[columns].sort_values(by=sort_by) return df[columns]
[docs]def get_jobs(database, sql_query, user, project_path, recursive=True, columns=None): """ Internal function to return the jobs as dictionary rather than a pandas.Dataframe Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath recursive (bool): search subprojects [True/False] columns (list): by default only the columns ['id', 'project'] are selected, but the user can select a subset of ['id', 'status', 'chemicalformula', 'job', 'subjob', 'project', 'projectpath', 'timestart', 'timestop', 'totalcputime', 'computer', 'hamilton', 'hamversion', 'parentid', 'masterid'] Returns: dict: columns are used as keys and point to a list of the corresponding values """ if columns is None: columns = ["id", "project"] df = job_table(database, sql_query, user, project_path, recursive, columns=columns) if len(df) == 0: dictionary = {} for key in columns: dictionary[key] = list() return dictionary # return {key: list() for key in columns} dictionary = {} for key in df.keys(): dictionary[key] = df[ key ].tolist() # ToDo: Check difference of tolist and to_list return dictionary
# return {key: df[key].tolist() for key in df.keys()}
[docs]def get_job_ids(database, sql_query, user, project_path, recursive=True): """ Return the job IDs matching a specific query Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath recursive (bool): search subprojects [True/False] Returns: list: a list of job IDs """ return get_jobs(database, sql_query, user, project_path, recursive=recursive)["id"]
[docs]def get_child_ids(database, sql_query, user, project_path, job_specifier, status=None): """ Get the childs for a specific job Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath job_specifier (str): name of the master job or the master jobs job ID status (str): filter childs which match a specific status - None by default Returns: list: list of child IDs """ id_master = get_job_id(database, sql_query, user, project_path, job_specifier) if id_master is None: return [] else: search_dict = {"masterid": str(id_master)} if status is not None: search_dict["status"] = status return sorted( [ job["id"] for job in database.get_items_dict( search_dict, return_all_columns=False ) ] )
[docs]def get_job_id(database, sql_query, user, project_path, job_specifier): """ get the job_id for job named job_name in the local project path from database Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath job_specifier (str): name of the job or job ID Returns: int: job ID of the job """ if sys.version_info.major == 2: if isinstance(job_specifier, (int, long, np.integer)): return int(job_specifier) # is id else: if isinstance(job_specifier, (int, np.integer)): return job_specifier # is id job_specifier.replace(".", "_") # if job_specifier[0] is not '/': # sub_job_name = '/' + job_specifier # else: # sub_job_name = job_specifier # job_dict = _job_dict(database, sql_query, user, project_path, recursive=False, # job=job_specifier, # sub_job_name=sub_job_name) # if len(job_dict) == 0: # job_dict = _job_dict(database, sql_query, user, project_path, recursive=True, # job=job_specifier, # sub_job_name=sub_job_name) job_dict = _job_dict( database, sql_query, user, project_path, recursive=False, job=job_specifier ) if len(job_dict) == 0: job_dict = _job_dict( database, sql_query, user, project_path, recursive=True, job=job_specifier ) if len(job_dict) == 0: return None elif len(job_dict) == 1: return job_dict[0]["id"] else: raise ValueError( "job name '{0}' in this project is not unique".format(job_dict) )
[docs]def set_job_status(database, sql_query, user, project_path, job_specifier, status): """ Set the status of a particular job Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath job_specifier (str): name of the job or job ID status (str): job status can be one of the following ['initialized', 'appended', 'created', 'submitted', 'running', 'aborted', 'collect', 'suspended', 'refresh', 'busy', 'finished'] """ database.item_update( {"status": str(status)}, get_job_id(database, sql_query, user, project_path, job_specifier), )
[docs]def get_job_status(database, sql_query, user, project_path, job_specifier): """ Get the status of a particular job Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath job_specifier (str): name of the job or job ID Returns: str: job status can be one of the following ['initialized', 'appended', 'created', 'submitted', 'running', 'aborted', 'collect', 'suspended', 'refresh', 'busy', 'finished'] """ try: return database.get_item_by_id( get_job_id(database, sql_query, user, project_path, job_specifier) )["status"] except KeyError: return None
[docs]def get_job_working_directory(database, sql_query, user, project_path, job_specifier): """ Get the working directory of a particular job Args: database (DatabaseAccess): Database object sql_query (str): SQL query to enter a more specific request user (str): username of the user whoes user space should be searched project_path (str): root_path - this is in contrast to the project_path in GenericPath job_specifier (str): name of the job or job ID Returns: str: working directory as absolute path """ try: db_entry = database.get_item_by_id( get_job_id(database, sql_query, user, project_path, job_specifier) ) if db_entry: job_name = db_entry["subjob"][1:] return os.path.join( db_entry["projectpath"], db_entry["project"], job_name + "_hdf5", job_name, ) else: return None except KeyError: return None