# HG changeset patch
# User pimarin
# Date 1673619090 0
# Node ID c90380f8bbbc4768e334388b4f80b57e5bba65a9
# Parent 04bee0f935a22fc93ac0970c5887b9f3169413fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 8eb28a93e6f2688bb2f3f85aea0389e1b1148816-dirty
diff -r 04bee0f935a2 -r c90380f8bbbc data_manager/bakta_build_database.py
--- a/data_manager/bakta_build_database.py Wed Nov 09 15:49:56 2022 +0000
+++ b/data_manager/bakta_build_database.py Fri Jan 13 14:11:30 2023 +0000
@@ -3,12 +3,10 @@
import json
import os
import sys
-# import subprocess
import tarfile
from datetime import datetime
from pathlib import Path
-# implement pip as a subprocess:
-# subprocess.check_call([sys.executable, '-m', 'pip', 'install', 'requests'])
+
import requests
@@ -21,7 +19,8 @@
def __init__(self,
data_table_name="bakta_database",
db_name=Path.cwd().joinpath("db"),
- db_version="latest"):
+ db_version="latest",
+ test_mode=False):
self.bakta_table_list = None
self.db_url = None
self.data_table_entry = None
@@ -29,6 +28,8 @@
self.db_name = db_name
self.db_version = db_version
self.DB_VERSIONS_URL = 'https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json'
+ self.DB_TEST_URL = 'https://zenodo.org/record/7360542/files/db-versions.json'
+ self.test_mode = test_mode
def get_data_table_format(self):
"""
@@ -44,8 +45,10 @@
def fetch_db_versions(self, db_version="latest"):
"""
- List bakta database info depending of the db_version selected
+ List bakta database info related to the db_version selected
"""
+ if self.test_mode is True:
+ self.DB_VERSIONS_URL = self.DB_TEST_URL
try:
with requests.get(self.DB_VERSIONS_URL) as resp:
versions = json.loads(resp.content)
@@ -59,16 +62,6 @@
db_date_list.append(datetime.strptime(db_dic["date"],
'%Y-%m-%d').date())
filtered_version = max(versions, key=lambda x: x['date'])
- elif db_version == "test":
- filtered_version = {"date": "date_test",
- "major": "0",
- "minor": "0",
- "doi": "10.5281/zenodo.7197299",
- "record": "7197299",
- "md5": "8b0250c17078742fc12207d4efb0fc1a",
- "software-min": {"major": "0",
- "minor": "0"}
- }
else:
filtered_version = None
for item in versions:
@@ -83,15 +76,15 @@
self.db_version = db_version
return filtered_version
- def get_data_manager(self, bakta_database_info, output_path):
+ def get_data_manager(self, bakta_database_info):
self.bakta_table_list = self.get_data_table_format()
bakta_value = f"V{bakta_database_info['major']}." \
f"{bakta_database_info['minor']}_" \
f"{bakta_database_info['date']}"
tool_version = str(f"{bakta_database_info['software-min']['major']}."
f"{bakta_database_info['software-min']['minor']}")
- data_info = dict(value=bakta_database_info['record'],
- dbkey=bakta_value,
+ data_info = dict(value=bakta_value,
+ dbkey=bakta_database_info['record'],
bakta_version=tool_version,
path="db")
self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
@@ -108,13 +101,15 @@
def __init__(self,
db_dir=Path.cwd(),
db_name="bakta",
- tarball_name="db.tar.gz"):
+ tarball_name="db.tar.gz",
+ test_mode=False):
super().__init__()
self.md5 = None
self.db_dir = db_dir
self.db_name = db_name
self.tarball_name = tarball_name
self.tarball_path = None
+ self.test_mode = test_mode
def download(self):
self.db_name = f'{self.db_name}_{self.db_version}'
@@ -212,20 +207,13 @@
def main():
all_args = parse_arguments()
-
with open(all_args.data_manager_json) as fh:
params = json.load(fh)
target_dir = params['output_data'][0]['extra_files_path']
os.makedirs(target_dir)
# init the class to download bakta db
- bakta_upload = InstallBaktaDatabase()
- # extract the version
- if all_args.test is True:
- bakta_db = bakta_upload.fetch_db_versions(
- db_version="test")
- else:
- bakta_db = bakta_upload.fetch_db_versions(
- db_version=all_args.database_version)
+ bakta_upload = InstallBaktaDatabase(test_mode=all_args.test)
+ bakta_db = bakta_upload.fetch_db_versions(db_version=all_args.database_version)
# update the path for galaxy
bakta_upload.db_dir = target_dir
# download the database
@@ -235,7 +223,7 @@
# untar db
bakta_upload.untar()
# make the data_manager metadata
- bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=target_dir)
+ bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db)
with open(all_args.data_manager_json, 'w') as fh:
json.dump(bakta_data_manager, fh, sort_keys=True)
diff -r 04bee0f935a2 -r c90380f8bbbc data_manager/bakta_build_database.xml
--- a/data_manager/bakta_build_database.xml Wed Nov 09 15:49:56 2022 +0000
+++ b/data_manager/bakta_build_database.xml Fri Jan 13 14:11:30 2023 +0000
@@ -27,11 +27,18 @@
-
+
+
+
+
+
+
+
+
diff -r 04bee0f935a2 -r c90380f8bbbc test-data/bakta_test.loc
--- a/test-data/bakta_test.loc Wed Nov 09 15:49:56 2022 +0000
+++ b/test-data/bakta_test.loc Fri Jan 13 14:11:30 2023 +0000
@@ -5,3 +5,11 @@
#
# for example
7197299 V0.0_date_test 0.0 ${__HERE__}
+7197299 V1.0_2022-10-12 1.4 /tmp/tmpxrkfnuec/galaxy-dev/tool-data/bakta_database/7197299
+7360139 V2.0_2022-11-25 1.5 /tmp/tmpxrkfnuec/galaxy-dev/tool-data/bakta_database/7360139
+7197299 V1.0_2022-10-12 1.4 /tmp/tmpwe9n4gyg/galaxy-dev/tool-data/bakta_database/7197299
+7360139 V2.0_2022-11-25 1.5 /tmp/tmpwe9n4gyg/galaxy-dev/tool-data/bakta_database/7360139
+V1.0_2022-10-12 7197299 1.4 /tmp/tmpw5w3lbzc/galaxy-dev/tool-data/bakta_database/V1.0_2022-10-12
+V2.0_2022-11-25 7360139 1.5 /tmp/tmpw5w3lbzc/galaxy-dev/tool-data/bakta_database/V2.0_2022-11-25
+V1.0_2022-10-12 7197299 1.4 /tmp/tmpi5flu1x0/galaxy-dev/tool-data/bakta_database/V1.0_2022-10-12
+V2.0_2022-11-25 7360139 1.5 /tmp/tmpi5flu1x0/galaxy-dev/tool-data/bakta_database/V2.0_2022-11-25
diff -r 04bee0f935a2 -r c90380f8bbbc test-data/bakta_test_data_manager.json
--- a/test-data/bakta_test_data_manager.json Wed Nov 09 15:49:56 2022 +0000
+++ b/test-data/bakta_test_data_manager.json Fri Jan 13 14:11:30 2023 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"bakta_database": [{"bakta_version": "0.0", "dbkey": "V0.0_date_test", "path": "db", "value": "7197299"}]}}
\ No newline at end of file
+{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "7197299", "path": "db", "value": "V1.0_2022-10-12"}]}}
\ No newline at end of file
diff -r 04bee0f935a2 -r c90380f8bbbc test-data/bakta_test_data_manager_test2.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bakta_test_data_manager_test2.json Fri Jan 13 14:11:30 2023 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"bakta_database": [{"bakta_version": "1.5", "dbkey": "7360139", "path": "db", "value": "V2.0_2022-11-25"}]}}
\ No newline at end of file
diff -r 04bee0f935a2 -r c90380f8bbbc test-data/db-versions.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db-versions.json Fri Jan 13 14:11:30 2023 +0000
@@ -0,0 +1,26 @@
+[
+ {
+ "date": "2022-10-12",
+ "major": 1,
+ "minor": 0,
+ "doi": "10.5281/zenodo.7197299",
+ "record": "7197299",
+ "md5": "8b0250c17078742fc12207d4efb0fc1a",
+ "software-min": {
+ "major": 1,
+ "minor": 4
+ }
+ },
+ {
+ "date": "2022-11-25",
+ "major": 2,
+ "minor": 0,
+ "doi": "10.5281/zenodo.7360139",
+ "record": "7360139",
+ "md5": "ebdb799a6bd97e56ca359db781ab8bab",
+ "software-min": {
+ "major": 1,
+ "minor": 5
+ }
+ }
+]