pip_installation

dbman.egg-info/PKG-INFO

+Metadata-Version: 1.0
+Name: dbman
+Version: 0.0.1.dev14
+Summary: Download, convert and upload databases to cloud server
+Home-page: UNKNOWN
+Author: Rudel Fankep
+Author-email: Rudel.C.NKouamedjo-fankep@bio.uni-giessen.de
+License: MIT
+Project-URL: Source Code, https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git
+Description: Download, convert and upload databases to cloud server
+Keywords: tools, databases
+Platform: UNKNOWN

dbman.egg-info/SOURCES.txt

+README.rst
+blast_db.sh
+delete_remote_file.sh
+download_db.sh
+download_json.sh
+ghostx_db.sh
+hmmer_pfam.sh
+prepare_card.sh
+prepare_pfam.sh
+prepare_swissprot.sh
+setup.cfg
+setup.py
+test.py
+testfile.txt
+upload_db.sh
+upload_json.sh
+dbman/__init__.py
+dbman/main.py
+dbman.egg-info/PKG-INFO
+dbman.egg-info/SOURCES.txt
+dbman.egg-info/dependency_links.txt
+dbman.egg-info/entry_points.txt
+dbman.egg-info/not-zip-safe
+dbman.egg-info/pbr.json
+dbman.egg-info/requires.txt
+dbman.egg-info/top_level.txt
+local_databases/dbman_metadata.json
+local_databases/swissprot_2019_06_blast/uniprot_sprot.fasta.phr
+local_databases/swissprot_2019_06_blast/uniprot_sprot.fasta.pin
+local_databases/swissprot_2019_06_blast/uniprot_sprot.fasta.psq
\ No newline at end of file

dbman.egg-info/dependency_links.txt

+

dbman.egg-info/entry_points.txt

+[console_scripts]
+dbman = dbman.main:main
+

dbman.egg-info/not-zip-safe

+

dbman.egg-info/pbr.json

+{"git_version": "cfea2f1", "is_release": false}
\ No newline at end of file

dbman.egg-info/requires.txt

+wget

dbman.egg-info/top_level.txt

+dbman

main.py → dbman/main.py

@@ -9,10 +9,14 @@ import wget
 from datetime import date
 import tarfile
 import json
+import pkg_resources
 
 
 def myparser():
-    parser = argparse.ArgumentParser(description='Download, convert and share databases to working computer', prog='Database Manager')
+
+    parser = argparse.ArgumentParser(description='Download, convert and upload databases to cloud server', prog='Database Manager')
+
+    parser.set_defaults(func=help)
 
     subparsers = parser.add_subparsers(title='Subcommands', description='Authorized Subcommands', help='Additional help')
 
@@ -59,7 +63,13 @@ def myparser():
 
     list_recipes_parser = subparsers.add_parser('list_recipes', help='print databases with the possible Tool/s')
     list_recipes_parser.set_defaults(func=list_recipes)
-    return parser.parse_args()
+    args = parser.parse_args()
+    args.parser = parser
+    return args
+
+
+def help(args):
+    args.parser.print_help()
 
 
 def get_local_databases_directory(args):
@@ -217,7 +227,7 @@ def save_local_metadata(args, metaliste):
 
 def get_remote_metadata(args):
     if get_path_remote_json(args) in get_remote_files():
-        subprocess.run(['./download_json.sh', get_path_remote_json(args), get_local_databases_directory(args)])
+        subprocess.run([pkg_resources.resource_filename(__name__, "scripts/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:
             metadata = json.load(f)
         os.remove(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json'))
@@ -229,7 +239,7 @@ def get_remote_metadata(args):
 def save_remote_metadata(args, metaliste):
     with open(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json'), 'w') as f:
         json.dump(metaliste, f)
-    subprocess.run(['./upload_json.sh', get_local_databases_directory(args), 'dbman_remote_metadata.json', get_remote_databases_directory(args)])
+    subprocess.run([pkg_resources.resource_filename(__name__, "scripts/upload_json.sh"), get_local_databases_directory(args), 'dbman_remote_metadata.json', get_remote_databases_directory(args)])
     os.remove(path_maker(get_local_databases_directory(args), 'dbman_remote_metadata.json'))
 
 
@@ -246,7 +256,7 @@ def get_tar_filename(args, version):
 
 
 def create_tar_file_and_upload(args, version):
-    subprocess.run(['./upload_db.sh', get_local_databases_directory(args), get_tar_filename(args, version), get_tool_directory_name(args, version), get_remote_databases_directory(args)])
+    subprocess.run([pkg_resources.resource_filename(__name__, "scripts/upload_db.sh"), get_local_databases_directory(args), get_tar_filename(args, version), get_tool_directory_name(args, version), get_remote_databases_directory(args)])
 
 
 def prepare(args):
@@ -317,7 +327,7 @@ def download(args):
             if version != 'error':
                 if not os.path.isdir(get_path_tool_directory(args, version)):
                     download_file = path_maker(get_remote_databases_directory(args), get_tar_filename(args, version))
-                    subprocess.run(['./download_db.sh', download_file, get_local_databases_directory(args), get_tar_filename(args, version)])
+                    subprocess.run([pkg_resources.resource_filename(__name__, "scripts/download_db.sh"), download_file, get_local_databases_directory(args), get_tar_filename(args, version)])
                     local_metadata = get_local_metadata(args)
                     for dictionnary in get_remote_metadata(args):
                         if dictionnary['name'] == args.database and dictionnary['tool'] == args.tool and dictionnary['version'] == version:
@@ -357,7 +367,7 @@ def delete(args):
                 web_store = get_remote_databases_directory(args)
                 web_file = path_maker(web_store, get_tar_filename(args, version))
                 if web_file in get_remote_files():
-                    subprocess.run(['./delete_remote_file.sh', web_file])
+                    subprocess.run([pkg_resources.resource_filename(__name__, "scripts/delete_remote_file.sh"), web_file])
                     metadata = get_remote_metadata(args)
                     for position in range(0, len(metadata)):
                         if metadata[position]['name'] == args.database and metadata[position]['tool'] == args.tool and metadata[position]['version'] == version:
@@ -390,18 +400,18 @@ def list_remote_databases(args):
         print('\n{}[{}] Version: {} erstellt am: {}'.format(dic_fichier['name'], dic_fichier['tool'], dic_fichier['version'], dic_fichier['created']))
 
 
-data = {'swissprot': {'prepare': './prepare_swissprot.sh',
-                    'tool': {'blast': './blast_db.sh', 'ghostx': './ghostx_db.sh'},
+data = {'swissprot': {'prepare': pkg_resources.resource_filename(__name__, "scripts/prepare_swissprot.sh"),
+                    'tool': {'blast': pkg_resources.resource_filename(__name__, "scripts/blast_db.sh"), 'ghostx': pkg_resources.resource_filename(__name__, "scripts/ghostx_db.sh")},
                     'filename': 'uniprot_sprot.fasta',
                     'version': get_swissprot_version
                     },
             'pfam': {'prepare': './prepare_pfam.sh',
-                    'tool': {'hmmer': './hmmer_pfam.sh'},
+                    'tool': {'hmmer': pkg_resources.resource_filename(__name__, "scripts/hmmer_pfam.sh")},
                     'filename': 'Pfam-A.hmm',
                     'version': get_pfam_version
                     },
-            'card': {'prepare': './prepare_card.sh',
-                    'tool': {'blast': './blast_db.sh', 'ghostx': './ghostx_db.sh'},
+            'card': {'prepare': pkg_resources.resource_filename(__name__, "scripts/prepare_card.sh"),
+                    'tool': {'blast': pkg_resources.resource_filename(__name__, "scripts/blast_db.sh"), 'ghostx': pkg_resources.resource_filename(__name__, "scripts/ghostx_db.sh")},
                     'filename': 'protein_fasta_protein_homolog_model.fasta',
                     'version': get_card_version
                     }