Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/run_data_managers.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 #!/usr/bin/env python
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2 """Run-data-managers is a tool for provisioning data on a galaxy instance.
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3
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4 Run-data-managers has the ability to run multiple data managers that are interdependent.
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5 When a reference genome is needed for bwa-mem for example, Run-data-managers
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6 can first run a data manager to fetch the fasta file and run
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7 another data manager that indexes the fasta file for bwa-mem.
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8 This functionality depends on the "watch_tool_data_dir" setting in galaxy.ini to be True.
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9 Also, if a new data manager is installed, galaxy needs to be restarted in order for it's tool_data_dir to be watched.
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10
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11 Run-data-managers needs a yaml that specifies what data managers are run and with which settings.
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12 Example files can be found `here <https://github.com/galaxyproject/ephemeris/blob/master/tests/run_data_managers.yaml.sample>`_,
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13 `here <https://github.com/galaxyproject/ephemeris/blob/master/tests/run_data_managers.yaml.sample.advanced>`_,
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14 and `here <https://github.com/galaxyproject/ephemeris/blob/master/tests/run_data_managers.yaml.test>`_.
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15
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16 By default run-data-managers skips entries in the yaml file that have already been run.
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17 It checks it in the following way:
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18
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19 * If the data manager has input variables "name" or "sequence_name" it will check if the "name" column in the data table already has this entry.
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20 "name" will take precedence over "sequence_name".
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21 * If the data manager has input variables "value", "sequence_id" or 'dbkey' it will check if the "value"
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22 column in the data table already has this entry.
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23 Value takes precedence over sequence_id which takes precedence over dbkey.
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24 * If none of the above input variables are specified the data manager will always run.
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25 """
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26 import argparse
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27 import json
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28 import logging
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29 import time
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30 from collections import namedtuple
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31
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32 from bioblend.galaxy.tool_data import ToolDataClient
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33 from bioblend.galaxy.tools import ToolClient
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34 from jinja2 import Template
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35
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36 from . import get_galaxy_connection
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37 from . import load_yaml_file
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38 from .common_parser import get_common_args
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39 from .ephemeris_log import disable_external_library_logging, setup_global_logger
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40
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41 DEFAULT_URL = "http://localhost"
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42 DEFAULT_SOURCE_TABLES = ["all_fasta"]
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43
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44
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45 def wait(gi, job_list, log):
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46 """
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47 Waits until all jobs in a list are finished or failed.
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48 It will check the state of the created datasets every 30s.
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49 It will return a tuple: ( finished_jobs, failed_jobs )
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50 """
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51
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52 failed_jobs = []
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53 successful_jobs = []
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54
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55 # Empty list returns false and stops the loop.
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56 while bool(job_list):
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57 finished_jobs = []
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58 for job in job_list:
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59 job_hid = job['outputs'][0]['hid']
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60 # check if the output of the running job is either in 'ok' or 'error' state
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61 state = gi.datasets.show_dataset(job['outputs'][0]['id'])['state']
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62 if state == 'ok':
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63 log.info('Job %i finished with state %s.' % (job_hid, state))
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64 successful_jobs.append(job)
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65 finished_jobs.append(job)
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66 if state == 'error':
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67 log.error('Job %i finished with state %s.' % (job_hid, state))
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68 job_id = job['jobs'][0]['id']
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69 job_details = gi.jobs.show_job(job_id, full_details=True)
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70 log.error(
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71 "Job {job_hid}: Tool '{tool_id}' finished with exit code: {exit_code}. Stderr: {stderr}".format(
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72 job_hid=job_hid,
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73 **job_details
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74 ))
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75 log.debug("Job {job_hid}: Tool '{tool_id}' stdout: {stdout}".format(
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76 job_hid=job_hid,
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77 **job_details
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78 ))
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79 failed_jobs.append(job)
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80 finished_jobs.append(job)
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81 else:
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82 log.debug('Job %i still running.' % job_hid)
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83 # Remove finished jobs from job_list.
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84 for finished_job in finished_jobs:
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85 job_list.remove(finished_job)
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86 # only sleep if job_list is not empty yet.
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87 if bool(job_list):
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88 time.sleep(30)
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89 return successful_jobs, failed_jobs
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90
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91
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92 def get_first_valid_entry(input_dict, key_list):
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93 """Iterates over key_list and returns the value of the first key that exists in the dictionary. Or returns None"""
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94 for key in key_list:
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95 if key in input_dict:
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96 return input_dict.get(key)
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97 return None
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98
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99
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100 class DataManagers:
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101 def __init__(self, galaxy_instance, configuration):
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102 """
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103 :param galaxy_instance: A GalaxyInstance object (import from bioblend.galaxy)
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104 :param configuration: A dictionary. Examples in the ephemeris documentation.
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105 """
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106 self.gi = galaxy_instance
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107 self.config = configuration
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108 self.tool_data_client = ToolDataClient(self.gi)
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109 self.tool_client = ToolClient(self.gi)
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110 self.possible_name_keys = ['name', 'sequence_name'] # In order of importance!
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111 self.possible_value_keys = ['value', 'sequence_id', 'dbkey'] # In order of importance!
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112 self.data_managers = self.config.get('data_managers')
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113 self.genomes = self.config.get('genomes', '')
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114 self.source_tables = DEFAULT_SOURCE_TABLES
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115 self.fetch_jobs = []
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116 self.skipped_fetch_jobs = []
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117 self.index_jobs = []
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118 self.skipped_index_jobs = []
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119
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120 def initiate_job_lists(self):
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121 """
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122 Determines which data managers should be run to populate the data tables.
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123 Distinguishes between fetch jobs (download files) and index jobs.
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124 :return: populate self.fetch_jobs, self.skipped_fetch_jobs, self.index_jobs and self.skipped_index_jobs
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125 """
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126 self.fetch_jobs = []
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127 self.skipped_fetch_jobs = []
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128 self.index_jobs = []
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129 self.skipped_index_jobs = []
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130 for dm in self.data_managers:
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131 jobs, skipped_jobs = self.get_dm_jobs(dm)
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132 if self.dm_is_fetcher(dm):
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133 self.fetch_jobs.extend(jobs)
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134 self.skipped_fetch_jobs.extend(skipped_jobs)
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135 else:
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136 self.index_jobs.extend(jobs)
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137 self.skipped_index_jobs.extend(skipped_jobs)
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138
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139 def get_dm_jobs(self, dm):
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140 """Gets the job entries for a single dm. Puts entries that already present in skipped_job_list.
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141 :returns job_list, skipped_job_list"""
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142 job_list = []
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143 skipped_job_list = []
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144 items = self.parse_items(dm.get('items', ['']))
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145 for item in items:
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146 dm_id = dm['id']
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147 params = dm['params']
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148 inputs = dict()
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149 # Iterate over all parameters, replace occurences of {{item}} with the current processing item
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150 # and create the tool_inputs dict for running the data manager job
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151 for param in params:
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152 key, value = list(param.items())[0]
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153 value_template = Template(value)
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154 value = value_template.render(item=item)
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155 inputs.update({key: value})
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156
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157 job = dict(tool_id=dm_id, inputs=inputs)
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158
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159 data_tables = dm.get('data_table_reload', [])
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160 if self.input_entries_exist_in_data_tables(data_tables, inputs):
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161 skipped_job_list.append(job)
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162 else:
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163 job_list.append(job)
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164 return job_list, skipped_job_list
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165
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166 def dm_is_fetcher(self, dm):
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167 """Checks whether the data manager fetches a sequence instead of indexing.
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168 This is based on the source table.
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169 :returns True if dm is a fetcher. False if it is not."""
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170 data_tables = dm.get('data_table_reload', [])
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171 for data_table in data_tables:
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172 if data_table in self.source_tables:
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173 return True
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174 return False
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175
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176 def data_table_entry_exists(self, data_table_name, entry, column='value'):
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177 """Checks whether an entry exists in the a specified column in the data_table."""
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178 try:
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179 data_table_content = self.tool_data_client.show_data_table(data_table_name)
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180 except Exception:
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181 raise Exception('Table "%s" does not exist' % data_table_name)
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182
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183 try:
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184 column_index = data_table_content.get('columns').index(column)
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185 except IndexError:
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186 raise IndexError('Column "%s" does not exist in %s' % (column, data_table_name))
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187
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188 for field in data_table_content.get('fields'):
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189 if field[column_index] == entry:
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190 return True
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191 return False
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192
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193 def input_entries_exist_in_data_tables(self, data_tables, input_dict):
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194 """Checks whether name and value entries from the input are already present in the data tables.
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195 If an entry is missing in of the tables, this function returns False"""
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196 value_entry = get_first_valid_entry(input_dict, self.possible_value_keys)
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197 name_entry = get_first_valid_entry(input_dict, self.possible_name_keys)
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198
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199 # Return False if name and value entries are both None
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200 if not value_entry and not name_entry:
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201 return False
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202
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203 # Check every data table for existence of name and value
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204 # Return False as soon as entry is not present
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205 for data_table in data_tables:
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206 if value_entry:
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207 if not self.data_table_entry_exists(data_table, value_entry, column='value'):
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208 return False
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209 if name_entry:
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210 if not self.data_table_entry_exists(data_table, name_entry, column='name'):
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211 return False
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212 # If all checks are passed the entries are present in the database tables.
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213 return True
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214
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215 def parse_items(self, items):
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216 """
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217 Parses items with jinja2.
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218 :param items: the items to be parsed
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219 :return: the parsed items
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220 """
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221 if bool(self.genomes):
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222 items_template = Template(json.dumps(items))
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223 rendered_items = items_template.render(genomes=json.dumps(self.genomes))
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224 # Remove trailing " if present
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225 rendered_items = rendered_items.strip('"')
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226 items = json.loads(rendered_items)
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227 return items
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228
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229 def run(self, log=None, ignore_errors=False, overwrite=False):
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230 """
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231 Runs the data managers.
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232 :param log: The log to be used.
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233 :param ignore_errors: Ignore erroring data_managers. Continue regardless.
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234 :param overwrite: Overwrite existing entries in data tables
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235 """
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236 self.initiate_job_lists()
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237 all_succesful_jobs = []
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238 all_failed_jobs = []
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239 all_skipped_jobs = []
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240
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241 if not log:
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242 log = logging.getLogger()
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243
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244 def run_jobs(jobs, skipped_jobs):
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245 job_list = []
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246 for skipped_job in skipped_jobs:
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247 if overwrite:
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248 log.info('%s already run for %s. Entry will be overwritten.' %
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249 (skipped_job["tool_id"], skipped_job["inputs"]))
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250 jobs.append(skipped_job)
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251 else:
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252 log.info('%s already run for %s. Skipping.' % (skipped_job["tool_id"], skipped_job["inputs"]))
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253 all_skipped_jobs.append(skipped_job)
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254 for job in jobs:
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255 started_job = self.tool_client.run_tool(history_id=None, tool_id=job["tool_id"],
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256 tool_inputs=job["inputs"])
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257 log.info('Dispatched job %i. Running DM: "%s" with parameters: %s' %
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258 (started_job['outputs'][0]['hid'], job["tool_id"], job["inputs"]))
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259 job_list.append(started_job)
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260
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261 successful_jobs, failed_jobs = wait(self.gi, job_list, log)
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262 if failed_jobs:
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263 if not ignore_errors:
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264 log.error('Not all jobs successful! aborting...')
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265 raise RuntimeError('Not all jobs successful! aborting...')
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266 else:
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267 log.warning('Not all jobs successful! ignoring...')
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268 all_succesful_jobs.extend(successful_jobs)
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269 all_failed_jobs.extend(failed_jobs)
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270
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271 log.info("Running data managers that populate the following source data tables: %s" % self.source_tables)
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272 run_jobs(self.fetch_jobs, self.skipped_fetch_jobs)
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273 log.info("Running data managers that index sequences.")
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274 run_jobs(self.index_jobs, self.skipped_index_jobs)
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275
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276 log.info('Finished running data managers. Results:')
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277 log.info('Successful jobs: %i ' % len(all_succesful_jobs))
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278 log.info('Skipped jobs: %i ' % len(all_skipped_jobs))
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279 log.info('Failed jobs: %i ' % len(all_failed_jobs))
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280 InstallResults = namedtuple("InstallResults", ["successful_jobs", "failed_jobs", "skipped_jobs"])
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281 return InstallResults(successful_jobs=all_succesful_jobs, failed_jobs=all_failed_jobs,
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282 skipped_jobs=all_skipped_jobs)
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283
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284
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285 def _parser():
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286 """returns the parser object."""
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287 parent = get_common_args(log_file=True)
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288
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289 parser = argparse.ArgumentParser(
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290 parents=[parent],
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291 description='Running Galaxy data managers in a defined order with defined parameters.'
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292 "'watch_tool_data_dir' in galaxy config should be set to true.'")
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293 parser.add_argument("--config", required=True,
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294 help="Path to the YAML config file with the list of data managers and data to install.")
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295 parser.add_argument("--overwrite", action="store_true",
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296 help="Disables checking whether the item already exists in the tool data table.")
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297 parser.add_argument("--ignore_errors", action="store_true",
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298 help="Do not stop running when jobs have failed.")
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299 return parser
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300
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301
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302 def main():
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303 disable_external_library_logging()
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304 parser = _parser()
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305 args = parser.parse_args()
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306 log = setup_global_logger(name=__name__, log_file=args.log_file)
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307 if args.verbose:
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308 log.setLevel(logging.DEBUG)
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309 else:
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310 log.setLevel(logging.INFO)
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311 gi = get_galaxy_connection(args, file=args.config, log=log, login_required=True)
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312 config = load_yaml_file(args.config)
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313 data_managers = DataManagers(gi, config)
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314 data_managers.run(log, args.ignore_errors, args.overwrite)
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315
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316
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317 if __name__ == '__main__':
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318 main()