--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/ephemeris/setup_data_libraries.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,218 @@
+#!/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()