--- a/data_manager/data_manager.py	Fri Mar 19 21:43:14 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-import argparse
-import datetime
-import json
-import os
-import shutil
-import tarfile
-import zipfile
-from urllib.request import Request, urlopen
-
-
-def url_download(url, workdir):
-    file_path = os.path.join(workdir, 'download.dat')
-    if not os.path.exists(workdir):
-        os.makedirs(workdir)
-    src = None
-    dst = None
-    try:
-        req = Request(url)
-        src = urlopen(req)
-        with open(file_path, 'wb') as dst:
-            while True:
-                chunk = src.read(2**10)
-                if chunk:
-                    dst.write(chunk)
-                else:
-                    break
-    finally:
-        if src:
-            src.close()
-    if tarfile.is_tarfile(file_path):
-        fh = tarfile.open(file_path, 'r:*')
-    elif zipfile.is_zipfile(file_path):
-        fh = zipfile.ZipFile(file_path, 'r')
-    else:
-        return
-    fh.extractall(workdir)
-    os.remove(file_path)
-
-
-def download_name_maps(url, workdir, partial):
-
-    if partial:
-        map_files = [
-            'pdb.accession2taxid.gz',
-        ]
-    else:
-        map_files = [
-            'dead_nucl.accession2taxid.gz',
-            'dead_prot.accession2taxid.gz',
-            'dead_wgs.accession2taxid.gz',
-            'nucl_gb.accession2taxid.gz',
-            'nucl_wgs.accession2taxid.gz',
-            'pdb.accession2taxid.gz',
-            'prot.accession2taxid.gz',
-            'prot.accession2taxid.FULL.gz'
-        ]
-
-    if not os.path.exists(workdir):
-        os.makedirs(workdir)
-
-    for map in map_files:
-        src = "{}{}".format(url, map)
-        dest = os.path.join(workdir, map)
-
-        print("Downloading taxonomy accession2taxid file from {} to {}".format(src, dest))
-
-        try:
-            req = Request(src)
-            src = urlopen(req)
-            with open(dest, 'wb') as dst:
-                while True:
-                    chunk = src.read(2**10)
-                    if chunk:
-                        dst.write(chunk)
-                    else:
-                        break
-        finally:
-            if src:
-                src.close()
-
-
-def move_files_to_final_dir(workdir, target_directory, copy=False):
-    for filename in os.listdir(workdir):
-        if copy:
-            shutil.copy(os.path.join(workdir, filename), target_directory)
-        else:
-            shutil.move(os.path.join(workdir, filename), target_directory)
-
-
-def main(args):
-    workdir = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
-    url_download(args.url, workdir)
-
-    data_manager_entry = {}
-    data_manager_entry['value'] = args.name.lower()
-    data_manager_entry['name'] = args.name
-    data_manager_entry['path'] = '.'
-    data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry))
-
-    with open(args.output) as fh:
-        params = json.load(fh)
-
-    if args.name_maps:
-        workdir_a2t = os.path.join(os.getcwd(), 'accession2taxid')
-        download_name_maps("ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/", workdir_a2t, args.partial)
-
-        target_directory_a2t = os.path.join(params['output_data'][0]['extra_files_path'], "accession2taxid")
-        os.makedirs(target_directory_a2t)
-        move_files_to_final_dir(workdir_a2t, target_directory_a2t)
-
-        # Also copy taxonomy data to accession2taxid dir
-        move_files_to_final_dir(workdir, target_directory_a2t, copy=True)
-
-        data_manager_json['data_tables']['ncbi_accession2taxid'] = data_manager_entry
-
-    target_directory_tax = os.path.join(params['output_data'][0]['extra_files_path'], "taxonomy")
-    os.makedirs(target_directory_tax)
-
-    move_files_to_final_dir(workdir, target_directory_tax)
-
-    with open(args.output, 'w') as fh:
-        json.dump(data_manager_json, fh, sort_keys=True)
-
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Create data manager json.')
-    parser.add_argument('--out', dest='output', action='store', help='JSON filename')
-    parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID')
-    parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL')
-    parser.add_argument('--name-maps', dest='name_maps', action='store_true', help='')
-    parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
-    args = parser.parse_args()
-
-    main(args)