--- a/env/lib/python3.7/site-packages/ephemeris/setup_data_libraries.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,218 +0,0 @@
-#!/usr/bin/env python
-'''Tool to setup data libraries on a galaxy instance'''
-import argparse
-import logging as log
-import sys
-import time
-
-import yaml
-from bioblend import galaxy
-
-from .common_parser import get_common_args
-
-
-def create_legacy(gi, desc):
-    destination = desc["destination"]
-    if destination["type"] != "library":
-        raise Exception("Only libraries may be created with pre-18.05 Galaxies using this script.")
-    library_name = destination.get("name")
-    library_description = destination.get("description")
-    library_synopsis = destination.get("synopsis")
-
-    # Check to see if the library already exists. If it does, do not recreate it. If it doesn't, create it.
-    lib_id = None
-    print("Library name: " + str(library_name))
-    rmt_lib_list = gi.libraries.get_libraries(name=library_name, deleted=False)
-    # Now we need to check if the library has been deleted since deleted=False still returns the deleted libraries!
-    not_deleted_rmt_lib_list = []
-    folder_id = None
-
-    if rmt_lib_list:
-        for x in rmt_lib_list:
-            if not x['deleted']:
-                not_deleted_rmt_lib_list.append(x)
-    if not_deleted_rmt_lib_list:
-        lib_id = not_deleted_rmt_lib_list[0]['id']
-        print("Library already exists! id: " + str(lib_id))
-        folder_id = gi.libraries.show_library(lib_id)['root_folder_id']
-    else:
-        lib = gi.libraries.create_library(library_name, library_description, library_synopsis)
-        lib_id = lib['id']
-        folder_id = lib['root_folder_id']
-
-    def populate_items(base_folder_id, has_items):
-        if "items" in has_items:
-            name = has_items.get("name")
-            description = has_items.get("description")
-            folder_id = base_folder_id
-            if name:
-                # Check to see if the folder already exists, if it doesn't create it.
-                rmt_folder_list = []
-                folder = gi.libraries.get_folders(lib_id, folder_id)
-                new_folder_name = "/" + name
-                if folder and not folder[0]['name'] == "/":
-                    new_folder_name = folder[0]['name'] + "/" + name
-                rmt_folder_list = gi.libraries.get_folders(lib_id, name=new_folder_name)
-                if rmt_folder_list:
-                    folder_id = rmt_folder_list[0]['id']
-                else:
-                    folder = gi.libraries.create_folder(lib_id, name, description, base_folder_id=base_folder_id)
-                    folder_id = folder[0]["id"]
-            for item in has_items["items"]:
-                populate_items(folder_id, item)
-        else:
-            src = has_items["src"]
-            if src != "url":
-                raise Exception("For pre-18.05 Galaxies only support URLs src items are supported.")
-            rmt_library_files = gi.folders.show_folder(base_folder_id, contents=True)['folder_contents']
-            file_names = []
-            for item in rmt_library_files:
-                if item['type'] == 'file':
-                    file_names.append(item['name'])
-            if has_items['url'] not in file_names:
-                try:
-                    gi.libraries.upload_file_from_url(
-                        lib_id,
-                        has_items['url'],
-                        folder_id=base_folder_id,
-                        file_type=has_items['ext']
-                    )
-                except Exception:
-                    log.exception("Could not upload %s to %s/%s", has_items['url'], lib_id, base_folder_id)
-        return None
-
-    populate_items(folder_id, desc)
-    return []
-
-
-def create_batch_api(gi, desc):
-    hc = galaxy.histories.HistoryClient(gi)
-    tc = galaxy.tools.ToolClient(gi)
-
-    history = hc.create_history()
-    url = "%s/tools/fetch" % gi.url
-    payload = {
-        'targets': [desc],
-        'history_id': history["id"]
-    }
-    yield tc._post(payload=payload, url=url)
-
-
-def setup_data_libraries(gi, data, training=False, legacy=False):
-    """
-    Load files into a Galaxy data library.
-    By default all test-data tools from all installed tools
-    will be linked into a data library.
-    """
-
-    log.info("Importing data libraries.")
-    jc = galaxy.jobs.JobsClient(gi)
-    config = galaxy.config.ConfigClient(gi)
-    version = config.get_version()
-
-    if legacy:
-        create_func = create_legacy
-    else:
-        version_major = version.get("version_major", "16.01")
-        create_func = create_batch_api if version_major >= "18.05" else create_legacy
-
-    library_def = yaml.safe_load(data)
-
-    def normalize_items(has_items):
-        # Synchronize Galaxy batch format with older training material style.
-        if "files" in has_items:
-            items = has_items.pop("files")
-            has_items["items"] = items
-
-        items = has_items.get("items", [])
-        for item in items:
-            normalize_items(item)
-            src = item.get("src")
-            url = item.get("url")
-            if src is None and url:
-                item["src"] = "url"
-            if "file_type" in item:
-                ext = item.pop("file_type")
-                item["ext"] = ext
-
-    # Normalize library definitions to allow older ephemeris style and native Galaxy batch
-    # upload formats.
-    if "libraries" in library_def:
-        # File contains multiple definitions.
-        library_def["items"] = library_def.pop("libraries")
-
-    if "destination" not in library_def:
-        library_def["destination"] = {"type": "library"}
-    destination = library_def["destination"]
-
-    if training:
-        destination["name"] = destination.get("name", 'Training Data')
-        destination["description"] = destination.get("description", 'Data pulled from online archives.')
-    else:
-        destination["name"] = destination.get("name", 'New Data Library')
-        destination["description"] = destination.get("description", '')
-
-    normalize_items(library_def)
-
-    if library_def:
-        jobs = list(create_func(gi, library_def))
-
-        job_ids = []
-        if legacy:
-            for job in jc.get_jobs():
-                # Fetch all upload job IDs, ignoring complete ones.
-                if job['tool_id'] == 'upload1' and job['state'] not in ('ok', 'error'):
-                    job_ids.append(job['id'])
-
-            # Just have to check that all upload1 jobs are termianl.
-        else:
-            # Otherwise get back an actual list of jobs
-            for job in jobs:
-                if 'jobs' in job:
-                    for subjob in job['jobs']:
-                        job_ids.append(subjob['id'])
-
-        while True:
-            job_states = [jc.get_state(job) in ('ok', 'error', 'deleted') for job in job_ids]
-            log.debug('Job states: %s' % ','.join([
-                '%s=%s' % (job_id, job_state) for (job_id, job_state) in zip(job_ids, job_states)]))
-
-            if all(job_states):
-                break
-            time.sleep(3)
-
-        log.info("Finished importing test data.")
-
-
-def _parser():
-    '''Constructs the parser object'''
-    parent = get_common_args()
-    parser = argparse.ArgumentParser(
-        parents=[parent],
-        description='Populate the Galaxy data library with data.'
-    )
-    parser.add_argument('-i', '--infile', required=True, type=argparse.FileType('r'))
-    parser.add_argument('--training', default=False, action="store_true",
-                        help="Set defaults that make sense for training data.")
-    parser.add_argument('--legacy', default=False, action="store_true",
-                        help="Use legacy APIs even for newer Galaxies that should have a batch upload API enabled.")
-    return parser
-
-
-def main():
-    args = _parser().parse_args()
-    if args.user and args.password:
-        gi = galaxy.GalaxyInstance(url=args.galaxy, email=args.user, password=args.password)
-    elif args.api_key:
-        gi = galaxy.GalaxyInstance(url=args.galaxy, key=args.api_key)
-    else:
-        sys.exit('Please specify either a valid Galaxy username/password or an API key.')
-
-    if args.verbose:
-        log.basicConfig(level=log.DEBUG)
-
-    setup_data_libraries(gi, args.infile, training=args.training, legacy=args.legacy)
-
-
-if __name__ == '__main__':
-    main()