README.rst

+Database Manager
+================
+
+This tool provide the preparation of Databases for several bioinformaticians tools.
+The preparated databases can be used on the working computer or can be saved on the cloud Server(Amazon Web Service S3)
+so that other computer can be able to download the data from there. It's also possible to delete some undesirable 
+databases on the working computer and/or in the Cloud.
+
+Supported Databases with associated tools:
+
+* Uniprot-Swissprot [Blast, Ghostx]
+* CARD [Blast, Ghostx]
+* Pfam [hmmer]
+
+Installation
+------------
+
+Prerequisites:
+
+* Python (Version >= 3.7)
+* Git
+
+Install for user::
+
+    pip install git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git
+
+Install for developer::
+
+    #checkout repository
+    git clone git+https://git.computational.bio.uni-giessen.de/cfankep/psotdb.git
+
+    #install
+    pip3 install -e .
+
+
+Using Database Manager
+----------------------
+
+For the general help use::
+
+    dbman --help
+
+Checkout which databases are available::
+
+    # in the S3 directory
+    dbman list_remote_databases
+
+    # in the local directory
+    dbman list_local_databases 
+
+Checkout which databases with associated transformations are available::
+
+    dbman list_recipes
+
+Prepare databases::
+
+    # check the available optional parameters
+    dbman prepare -h
+
+    # run the standard preparation
+    dbman prepare example/database exemple/tool
+
+Transfer databases from the working computer to s3 Cloud::
+
+    # check the available optional parameters
+    dbman upload -h
+
+    # run the standard transfer
+    dbman upload example/database exemple/tool*
+
+Transfer databases from s3 Cloud to working computer::
+
+    # check the available optional parameters
+    dbman download -h
+
+    # run the standard download
+    dbman download example/database exemple/tool*
+
+Delete undesirable databases::
+
+    # from the local directory
+    dbman delete example/database example/tool* local
+
+    # from the s3 cloud directory
+    dbman delete example/database example/tool* s3
+
+remplace the standard directory to save the data::
+
+    # change local directory with the environment variable
+    export DBMAN_DBDIR = example/path
+
+    # change remote directory with the environment variable
+    export DBMAN_S3DIR = example/path
+
+The standard directories(local and remote) can also be change with optional parameters. 
+
+
+
+(*) For upload, download and delete of the raw databank instead of 'example/tool' enter 'raw'.   

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
+requirements.txt
+setup.cfg
+setup.py
+test.py
+testfile.txt
+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
+dbman/scripts/blast_db.sh
+dbman/scripts/delete_remote_file.sh
+dbman/scripts/download_db.sh
+dbman/scripts/download_json.sh
+dbman/scripts/ghostx_db.sh
+dbman/scripts/hmmer_pfam.sh
+dbman/scripts/prepare_card.sh
+dbman/scripts/prepare_pfam.sh
+dbman/scripts/prepare_swissprot.sh
+dbman/scripts/upload_db.sh
+dbman/scripts/upload_json.sh
+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": "2b012ee", "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 the data to working computer', prog='PSOT_database_maker')
+
+    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):
@@ -75,8 +85,8 @@ def get_remote_databases_directory(args):
     web_dir = 's3://db_storage'
     if args.store:
         web_dir = args.store
-    elif 'S3_DBDIR' in os.environ:
-        web_dir = os.environ['S3_DBDIR']
+    elif 'DBMAN_S3DIR' in os.environ:
+        web_dir = os.environ['DBMAN_S3DIR']
     return web_dir
 
 
@@ -196,7 +206,7 @@ def get_path_local_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):
@@ -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_db.sh', get_path_remote_json(args), get_local_databases_directory(args), 'dbman_remote_metadata.json.tar.gz'])
+        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'))
@@ -227,10 +237,10 @@ def get_remote_metadata(args):
 
 
 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)
-    subprocess.run(['./upload_db.sh', './', 'dbman_remote_metadata.json.tar.gz', 'dbman_remote_metadata.json', get_remote_databases_directory(args)])
-    os.remove('dbman_remote_metadata.json')
+    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'))
 
 
 def get_remote_filename(args, version):
@@ -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:
@@ -337,36 +347,40 @@ def download(args):
 def delete(args):
     if args.database in data.keys():
         if args.tool in data[args.database]['tool'].keys() or args.tool == "raw":
-            if args.place == 'local':
-                version = get_local_json_version(args)
-                dbman_dir = get_local_databases_directory(args)
-                directory_to_delete = path_maker(dbman_dir, get_tool_directory_name(args, version))
-                if os.path.isdir(directory_to_delete):
-                    shutil.rmtree(directory_to_delete)
-                    metadata = get_local_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:
-                            del metadata[position]
-                            break
-                    save_local_metadata(args, metadata)
-                    print("The {} files were successfully delete from: ".format(get_tool_directory_name(args, version)) + os.path.abspath(dbman_dir))
-                else:
-                    print("The {} files aren't existing in: ".format(get_tool_directory_name(args, version)) + os.path.abspath(dbman_dir))
-            elif args.place == 's3':
-                version = get_remote_json_version(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])
-                    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:
-                            del metadata[position]
-                            break
-                    save_remote_metadata(args, metadata)
-                    print("The {} files were successfully delete from: ".format(get_tool_directory_name(args, version)) + web_store)
-                else:
-                    print("The {} files aren't existing in: ".format(get_tool_directory_name(args, version)) + web_store)
+            frage = input('Do you want to continue (Y/N)? ')
+            if frage.lower() == 'y':
+                if args.place == 'local':
+                    version = get_local_json_version(args)
+                    dbman_dir = get_local_databases_directory(args)
+                    directory_to_delete = path_maker(dbman_dir, get_tool_directory_name(args, version))
+                    if os.path.isdir(directory_to_delete):
+                        shutil.rmtree(directory_to_delete)
+                        metadata = get_local_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:
+                                del metadata[position]
+                                break
+                        save_local_metadata(args, metadata)
+                        print("The {} files were successfully delete from: ".format(get_tool_directory_name(args, version)) + os.path.abspath(dbman_dir))
+                    else:
+                        print("The {} files aren't existing in: ".format(get_tool_directory_name(args, version)) + os.path.abspath(dbman_dir))
+                elif args.place == 's3':
+                    version = get_remote_json_version(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([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:
+                                del metadata[position]
+                                break
+                        save_remote_metadata(args, metadata)
+                        print("The {} files were successfully delete from: ".format(get_tool_directory_name(args, version)) + web_store)
+                    else:
+                        print("The {} files aren't existing in: ".format(get_tool_directory_name(args, version)) + web_store)
+            else:
+                print('delete canceled')
         else:
             print('Tool error. There are following possibility: {}'.format([tool for tool in data[args.database]['tool'].keys()]))
     else:
@@ -390,18 +404,18 @@ 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'},
+            'pfam': {'prepare': pkg_resources.resource_filename(__name__, "scripts/prepare_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
                     }

dbman/scripts/download_json.sh

+#!/bin/bash
+REMOTE_FILE=$1
+LOCAL_DATABASE_DIRECTORY=$2
+
+cd $LOCAL_DATABASE_DIRECTORY
+s3cmd get $REMOTE_FILE 
+cd -
\ No newline at end of file