Commit 57834f7e authored by Rudel Fankep's avatar Rudel Fankep
Browse files

upload without tar

parent da57157a
#!/bin/bash
REMOTE_FILE=$1
LOCAL_DATABASE_DIRECTORY=$2
cd $LOCAL_DATABASE_DIRECTORY
s3cmd get $REMOTE_FILE
cd -
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[] [{"name": "swissprot", "tool": "blast", "version": "2019_06", "created": "2019-07-29"}]
\ No newline at end of file \ No newline at end of file
...@@ -12,7 +12,7 @@ import json ...@@ -12,7 +12,7 @@ import json
def myparser(): def myparser():
parser = argparse.ArgumentParser(description='Download, convert and share the data to working computer', prog='PSOT_database_maker') parser = argparse.ArgumentParser(description='Download, convert and share databases to working computer', prog='Database Manager')
subparsers = parser.add_subparsers(title='Subcommands', description='Authorized Subcommands', help='Additional help') subparsers = parser.add_subparsers(title='Subcommands', description='Authorized Subcommands', help='Additional help')
...@@ -196,7 +196,7 @@ def get_path_local_json(args): ...@@ -196,7 +196,7 @@ def get_path_local_json(args):
def get_path_remote_json(args): def get_path_remote_json(args):
return path_maker(get_remote_databases_directory(args), 'dbman_remote_metadata.json.tar.gz') return path_maker(get_remote_databases_directory(args), 'dbman_remote_metadata.json')
def get_local_metadata(args): def get_local_metadata(args):
...@@ -217,7 +217,7 @@ def save_local_metadata(args, metaliste): ...@@ -217,7 +217,7 @@ def save_local_metadata(args, metaliste):
def get_remote_metadata(args): def get_remote_metadata(args):
if get_path_remote_json(args) in get_remote_files(): if get_path_remote_json(args) in get_remote_files():
subprocess.run(['./download_db.sh', get_path_remote_json(args), get_local_databases_directory(args), 'dbman_remote_metadata.json.tar.gz']) subprocess.run(['./download_json.sh', get_path_remote_json(args), get_local_databases_directory(args)])
with open(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json')) as f: with open(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json')) as f:
metadata = json.load(f) metadata = json.load(f)
os.remove(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json')) os.remove(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json'))
...@@ -227,10 +227,10 @@ def get_remote_metadata(args): ...@@ -227,10 +227,10 @@ def get_remote_metadata(args):
def save_remote_metadata(args, metaliste): def save_remote_metadata(args, metaliste):
with open('dbman_remote_metadata.json', 'w') as f: with open(path_maker(get_local_databases_directory(args),'dbman_remote_metadata.json'), 'w') as f:
json.dump(metaliste, f) json.dump(metaliste, f)
subprocess.run(['./upload_db.sh', './', 'dbman_remote_metadata.json.tar.gz', 'dbman_remote_metadata.json', get_remote_databases_directory(args)]) subprocess.run(['./upload_json.sh', get_local_databases_directory(args), 'dbman_remote_metadata.json', get_remote_databases_directory(args)])
os.remove('dbman_remote_metadata.json') os.remove(path_maker(get_local_databases_directory(args),'dbman_remote_metadata.json'))
def get_remote_filename(args, version): def get_remote_filename(args, version):
......
#!/bin/bash
LOCAL_DATABASE_DIRECTORY=$1
LOCAL_FILE=$2
REMOTE_DATABASE_DIRECTORY=$3
cd $LOCAL_DATABASE_DIRECTORY
s3cmd put $LOCAL_FILE $REMOTE_DATABASE_DIRECTORY
cd -
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