--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/ephemeris/run_data_managers.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,318 @@
+#!/usr/bin/env python
+"""Run-data-managers is a tool for provisioning data on a galaxy instance.
+
+Run-data-managers has the ability to run multiple data managers that are interdependent.
+When a reference genome is needed for bwa-mem for example, Run-data-managers
+can first run a data manager to fetch the fasta file and run
+another data manager that indexes the fasta file for bwa-mem.
+This functionality depends on the "watch_tool_data_dir" setting in galaxy.ini to be True.
+Also, if a new data manager is installed, galaxy needs to be restarted in order for it's tool_data_dir to be watched.
+
+Run-data-managers needs a yaml that specifies what data managers are run and with which settings.
+Example files can be found `here <https://github.com/galaxyproject/ephemeris/blob/master/tests/run_data_managers.yaml.sample>`_,
+`here <https://github.com/galaxyproject/ephemeris/blob/master/tests/run_data_managers.yaml.sample.advanced>`_,
+and `here <https://github.com/galaxyproject/ephemeris/blob/master/tests/run_data_managers.yaml.test>`_.
+
+By default run-data-managers skips entries in the yaml file that have already been run.
+It checks it in the following way:
+
+  * 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.
+    "name" will take precedence over "sequence_name".
+  * If the data manager has input variables "value", "sequence_id" or 'dbkey' it will check if the "value"
+    column in the data table already has this entry.
+    Value takes precedence over sequence_id which takes precedence over dbkey.
+  * If none of the above input variables are specified the data manager will always run.
+"""
+import argparse
+import json
+import logging
+import time
+from collections import namedtuple
+
+from bioblend.galaxy.tool_data import ToolDataClient
+from bioblend.galaxy.tools import ToolClient
+from jinja2 import Template
+
+from . import get_galaxy_connection
+from . import load_yaml_file
+from .common_parser import get_common_args
+from .ephemeris_log import disable_external_library_logging, setup_global_logger
+
+DEFAULT_URL = "http://localhost"
+DEFAULT_SOURCE_TABLES = ["all_fasta"]
+
+
+def wait(gi, job_list, log):
+    """
+        Waits until all jobs in a list are finished or failed.
+        It will check the state of the created datasets every 30s.
+        It will return a tuple: ( finished_jobs, failed_jobs )
+    """
+
+    failed_jobs = []
+    successful_jobs = []
+
+    # Empty list returns false and stops the loop.
+    while bool(job_list):
+        finished_jobs = []
+        for job in job_list:
+            job_hid = job['outputs'][0]['hid']
+            # check if the output of the running job is either in 'ok' or 'error' state
+            state = gi.datasets.show_dataset(job['outputs'][0]['id'])['state']
+            if state == 'ok':
+                log.info('Job %i finished with state %s.' % (job_hid, state))
+                successful_jobs.append(job)
+                finished_jobs.append(job)
+            if state == 'error':
+                log.error('Job %i finished with state %s.' % (job_hid, state))
+                job_id = job['jobs'][0]['id']
+                job_details = gi.jobs.show_job(job_id, full_details=True)
+                log.error(
+                    "Job {job_hid}: Tool '{tool_id}' finished with exit code: {exit_code}. Stderr: {stderr}".format(
+                        job_hid=job_hid,
+                        **job_details
+                    ))
+                log.debug("Job {job_hid}: Tool '{tool_id}' stdout: {stdout}".format(
+                    job_hid=job_hid,
+                    **job_details
+                ))
+                failed_jobs.append(job)
+                finished_jobs.append(job)
+            else:
+                log.debug('Job %i still running.' % job_hid)
+        # Remove finished jobs from job_list.
+        for finished_job in finished_jobs:
+            job_list.remove(finished_job)
+        # only sleep if job_list is not empty yet.
+        if bool(job_list):
+            time.sleep(30)
+    return successful_jobs, failed_jobs
+
+
+def get_first_valid_entry(input_dict, key_list):
+    """Iterates over key_list and returns the value of the first key that exists in the dictionary. Or returns None"""
+    for key in key_list:
+        if key in input_dict:
+            return input_dict.get(key)
+    return None
+
+
+class DataManagers:
+    def __init__(self, galaxy_instance, configuration):
+        """
+        :param galaxy_instance: A GalaxyInstance object (import from bioblend.galaxy)
+        :param configuration: A dictionary. Examples in the ephemeris documentation.
+        """
+        self.gi = galaxy_instance
+        self.config = configuration
+        self.tool_data_client = ToolDataClient(self.gi)
+        self.tool_client = ToolClient(self.gi)
+        self.possible_name_keys = ['name', 'sequence_name']  # In order of importance!
+        self.possible_value_keys = ['value', 'sequence_id', 'dbkey']  # In order of importance!
+        self.data_managers = self.config.get('data_managers')
+        self.genomes = self.config.get('genomes', '')
+        self.source_tables = DEFAULT_SOURCE_TABLES
+        self.fetch_jobs = []
+        self.skipped_fetch_jobs = []
+        self.index_jobs = []
+        self.skipped_index_jobs = []
+
+    def initiate_job_lists(self):
+        """
+        Determines which data managers should be run to populate the data tables.
+        Distinguishes between fetch jobs (download files) and index jobs.
+        :return: populate self.fetch_jobs, self.skipped_fetch_jobs, self.index_jobs and self.skipped_index_jobs
+        """
+        self.fetch_jobs = []
+        self.skipped_fetch_jobs = []
+        self.index_jobs = []
+        self.skipped_index_jobs = []
+        for dm in self.data_managers:
+            jobs, skipped_jobs = self.get_dm_jobs(dm)
+            if self.dm_is_fetcher(dm):
+                self.fetch_jobs.extend(jobs)
+                self.skipped_fetch_jobs.extend(skipped_jobs)
+            else:
+                self.index_jobs.extend(jobs)
+                self.skipped_index_jobs.extend(skipped_jobs)
+
+    def get_dm_jobs(self, dm):
+        """Gets the job entries for a single dm. Puts entries that already present in skipped_job_list.
+        :returns job_list, skipped_job_list"""
+        job_list = []
+        skipped_job_list = []
+        items = self.parse_items(dm.get('items', ['']))
+        for item in items:
+            dm_id = dm['id']
+            params = dm['params']
+            inputs = dict()
+            # Iterate over all parameters, replace occurences of {{item}} with the current processing item
+            # and create the tool_inputs dict for running the data manager job
+            for param in params:
+                key, value = list(param.items())[0]
+                value_template = Template(value)
+                value = value_template.render(item=item)
+                inputs.update({key: value})
+
+            job = dict(tool_id=dm_id, inputs=inputs)
+
+            data_tables = dm.get('data_table_reload', [])
+            if self.input_entries_exist_in_data_tables(data_tables, inputs):
+                skipped_job_list.append(job)
+            else:
+                job_list.append(job)
+        return job_list, skipped_job_list
+
+    def dm_is_fetcher(self, dm):
+        """Checks whether the data manager fetches a sequence instead of indexing.
+        This is based on the source table.
+        :returns True if dm is a fetcher. False if it is not."""
+        data_tables = dm.get('data_table_reload', [])
+        for data_table in data_tables:
+            if data_table in self.source_tables:
+                return True
+        return False
+
+    def data_table_entry_exists(self, data_table_name, entry, column='value'):
+        """Checks whether an entry exists in the a specified column in the data_table."""
+        try:
+            data_table_content = self.tool_data_client.show_data_table(data_table_name)
+        except Exception:
+            raise Exception('Table "%s" does not exist' % data_table_name)
+
+        try:
+            column_index = data_table_content.get('columns').index(column)
+        except IndexError:
+            raise IndexError('Column "%s" does not exist in %s' % (column, data_table_name))
+
+        for field in data_table_content.get('fields'):
+            if field[column_index] == entry:
+                return True
+        return False
+
+    def input_entries_exist_in_data_tables(self, data_tables, input_dict):
+        """Checks whether name and value entries from the input are already present in the data tables.
+        If an entry is missing in of the tables, this function returns False"""
+        value_entry = get_first_valid_entry(input_dict, self.possible_value_keys)
+        name_entry = get_first_valid_entry(input_dict, self.possible_name_keys)
+
+        # Return False if name and value entries are both None
+        if not value_entry and not name_entry:
+            return False
+
+        # Check every data table for existence of name and value
+        # Return False as soon as entry is not present
+        for data_table in data_tables:
+            if value_entry:
+                if not self.data_table_entry_exists(data_table, value_entry, column='value'):
+                    return False
+            if name_entry:
+                if not self.data_table_entry_exists(data_table, name_entry, column='name'):
+                    return False
+        # If all checks are passed the entries are present in the database tables.
+        return True
+
+    def parse_items(self, items):
+        """
+        Parses items with jinja2.
+        :param items: the items to be parsed
+        :return: the parsed items
+        """
+        if bool(self.genomes):
+            items_template = Template(json.dumps(items))
+            rendered_items = items_template.render(genomes=json.dumps(self.genomes))
+            # Remove trailing " if present
+            rendered_items = rendered_items.strip('"')
+            items = json.loads(rendered_items)
+        return items
+
+    def run(self, log=None, ignore_errors=False, overwrite=False):
+        """
+        Runs the data managers.
+        :param log: The log to be used.
+        :param ignore_errors: Ignore erroring data_managers. Continue regardless.
+        :param overwrite: Overwrite existing entries in data tables
+        """
+        self.initiate_job_lists()
+        all_succesful_jobs = []
+        all_failed_jobs = []
+        all_skipped_jobs = []
+
+        if not log:
+            log = logging.getLogger()
+
+        def run_jobs(jobs, skipped_jobs):
+            job_list = []
+            for skipped_job in skipped_jobs:
+                if overwrite:
+                    log.info('%s already run for %s. Entry will be overwritten.' %
+                             (skipped_job["tool_id"], skipped_job["inputs"]))
+                    jobs.append(skipped_job)
+                else:
+                    log.info('%s already run for %s. Skipping.' % (skipped_job["tool_id"], skipped_job["inputs"]))
+                    all_skipped_jobs.append(skipped_job)
+            for job in jobs:
+                started_job = self.tool_client.run_tool(history_id=None, tool_id=job["tool_id"],
+                                                        tool_inputs=job["inputs"])
+                log.info('Dispatched job %i. Running DM: "%s" with parameters: %s' %
+                         (started_job['outputs'][0]['hid'], job["tool_id"], job["inputs"]))
+                job_list.append(started_job)
+
+            successful_jobs, failed_jobs = wait(self.gi, job_list, log)
+            if failed_jobs:
+                if not ignore_errors:
+                    log.error('Not all jobs successful! aborting...')
+                    raise RuntimeError('Not all jobs successful! aborting...')
+                else:
+                    log.warning('Not all jobs successful! ignoring...')
+            all_succesful_jobs.extend(successful_jobs)
+            all_failed_jobs.extend(failed_jobs)
+
+        log.info("Running data managers that populate the following source data tables: %s" % self.source_tables)
+        run_jobs(self.fetch_jobs, self.skipped_fetch_jobs)
+        log.info("Running data managers that index sequences.")
+        run_jobs(self.index_jobs, self.skipped_index_jobs)
+
+        log.info('Finished running data managers. Results:')
+        log.info('Successful jobs: %i ' % len(all_succesful_jobs))
+        log.info('Skipped jobs: %i ' % len(all_skipped_jobs))
+        log.info('Failed jobs: %i ' % len(all_failed_jobs))
+        InstallResults = namedtuple("InstallResults", ["successful_jobs", "failed_jobs", "skipped_jobs"])
+        return InstallResults(successful_jobs=all_succesful_jobs, failed_jobs=all_failed_jobs,
+                              skipped_jobs=all_skipped_jobs)
+
+
+def _parser():
+    """returns the parser object."""
+    parent = get_common_args(log_file=True)
+
+    parser = argparse.ArgumentParser(
+        parents=[parent],
+        description='Running Galaxy data managers in a defined order with defined parameters.'
+                    "'watch_tool_data_dir' in galaxy config should be set to true.'")
+    parser.add_argument("--config", required=True,
+                        help="Path to the YAML config file with the list of data managers and data to install.")
+    parser.add_argument("--overwrite", action="store_true",
+                        help="Disables checking whether the item already exists in the tool data table.")
+    parser.add_argument("--ignore_errors", action="store_true",
+                        help="Do not stop running when jobs have failed.")
+    return parser
+
+
+def main():
+    disable_external_library_logging()
+    parser = _parser()
+    args = parser.parse_args()
+    log = setup_global_logger(name=__name__, log_file=args.log_file)
+    if args.verbose:
+        log.setLevel(logging.DEBUG)
+    else:
+        log.setLevel(logging.INFO)
+    gi = get_galaxy_connection(args, file=args.config, log=log, login_required=True)
+    config = load_yaml_file(args.config)
+    data_managers = DataManagers(gi, config)
+    data_managers.run(log, args.ignore_errors, args.overwrite)
+
+
+if __name__ == '__main__':
+    main()