| Previous changeset 3:3e73c97f025d (2023-06-23) Next changeset 5:baceff842902 (2024-06-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e |
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modified:
data_manager/bakta_build_database.py data_manager/macro.xml test-data/bakta_test.loc test-data/bakta_test_data_manager1.json test-data/bakta_test_data_manager2.json test-data/bakta_test_data_manager3.json |
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| diff -r 3e73c97f025d -r d74850cf4e42 data_manager/bakta_build_database.py --- a/data_manager/bakta_build_database.py Fri Jun 23 21:37:05 2023 +0000 +++ b/data_manager/bakta_build_database.py Fri Aug 25 23:34:04 2023 +0000 |
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| @@ -3,6 +3,7 @@ import json import os import re +import shutil import sys import tarfile from datetime import datetime @@ -20,17 +21,16 @@ def __init__( self, data_table_name="bakta_database", - db_name=Path.cwd().joinpath("db"), db_version="latest", tarball_name="db.tar.gz", test_mode=False, ): self.bakta_table_list = None self.db_url = None + self.db_name = "bakta-db" self.db_type = "" self.data_table_entry = None self.data_table_name = data_table_name - self.db_name = db_name self.tar_name = tarball_name self.db_version = db_version self.DB_VERSIONS_URL = "https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json" @@ -103,7 +103,7 @@ value=bakta_name, dbkey=bakta_database_info["record"], bakta_version=tool_version, - path="db", + path=self.db_name, ) self.bakta_table_list["data_tables"][self.data_table_name] = [data_info] return self.bakta_table_list @@ -117,7 +117,11 @@ """ def __init__( - self, db_dir=Path.cwd(), db_name="bakta", db_version="latest", test_mode=False + self, + db_dir=Path.cwd(), + db_name="bakta-db", + db_version="latest", + test_mode=False ): super().__init__() self.md5 = None @@ -129,7 +133,6 @@ self.get_database_type() def download(self): - self.db_name = f"{self.db_name}_{self.db_version}{self.db_type}" bakta_path = Path(self.db_dir).joinpath(self.tar_name) try: with bakta_path.open("wb") as fh_out, requests.get( @@ -150,16 +153,31 @@ ) def untar(self): - db_path = Path(self.db_dir).as_posix() + db_path = Path(self.db_dir).joinpath(self.db_name) try: with self.tarball_path.open("rb") as fh_in, tarfile.open( fileobj=fh_in, mode="r:gz" ) as tar_file: tar_file.extractall(path=db_path) print(f"Untar the database in {db_path}") - return db_path + + if not self.test_mode: + self.moove_files(db_path=db_path) + except OSError: - sys.exit(f"ERROR: Could not extract {self.tar_name} " f"to {self.db_name}") + sys.exit(f"ERROR: Could not extract {self.tar_name} " f"to {db_path}") + + def moove_files(self, db_path): + if os.path.isdir(db_path.joinpath("db-light")): + input_dir = db_path.joinpath("db-light") + elif os.path.isdir(db_path.joinpath("db")): + input_dir = db_path.joinpath("db") + file_list = os.listdir(input_dir) + output_dir = db_path + for file in file_list: + input = input_dir.joinpath(file) + output = output_dir.joinpath(file) + shutil.move(input, output) def calc_md5_sum(self, buffer_size=1048576): tarball_path = Path(self.db_dir).joinpath(self.tar_name) |
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| diff -r 3e73c97f025d -r d74850cf4e42 data_manager/macro.xml --- a/data_manager/macro.xml Fri Jun 23 21:37:05 2023 +0000 +++ b/data_manager/macro.xml Fri Aug 25 23:34:04 2023 +0000 |
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| @@ -2,7 +2,7 @@ <token name="@TOOL_VERSION@">1.8.1</token> <token name="@REQUESTS_VERSION@">2.27.1</token> <token name="@PYTHON_VERSION@">3.8</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">21.05</token> <xml name="requirements"> <requirements> |
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| diff -r 3e73c97f025d -r d74850cf4e42 test-data/bakta_test.loc --- a/test-data/bakta_test.loc Fri Jun 23 21:37:05 2023 +0000 +++ b/test-data/bakta_test.loc Fri Aug 25 23:34:04 2023 +0000 |
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| @@ -1,6 +1,3 @@ -V1.0_2022-10-12 7197299 1.4 /tmp/tmpq5t7s3c5/galaxy-dev/tool-data/bakta_database/7197299 -V5.0_2023-06-08 8021027 1.8 /tmp/tmpq5t7s3c5/galaxy-dev/tool-data/bakta_database/8021027 -V5.0light_2023-06-08 8021027 1.8 /tmp/tmpq5t7s3c5/galaxy-dev/tool-data/bakta_database/8021027 -V1.0_2022-10-12 7197299 1.4 /tmp/tmpydhjlpxl/galaxy-dev/tool-data/bakta_database/7197299 -V5.0_2023-06-08 8021027 1.8 /tmp/tmpydhjlpxl/galaxy-dev/tool-data/bakta_database/8021027 -V5.0light_2023-06-08 8021027 1.8 /tmp/tmpydhjlpxl/galaxy-dev/tool-data/bakta_database/8021027 +V1.0_2022-10-12 7197299 1.4 bakta-db +V5.0_2023-06-08 8021027 1.8 bakta-db +V5.0light_2023-06-08 8021027 1.8 bakta-db |
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| diff -r 3e73c97f025d -r d74850cf4e42 test-data/bakta_test_data_manager1.json --- a/test-data/bakta_test_data_manager1.json Fri Jun 23 21:37:05 2023 +0000 +++ b/test-data/bakta_test_data_manager1.json Fri Aug 25 23:34:04 2023 +0000 |
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| @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "7197299", "path": "db", "value": "V1.0_2022-10-12"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.4", "dbkey": "7197299", "path": "bakta-db", "value": "V1.0_2022-10-12"}]}} \ No newline at end of file |
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| diff -r 3e73c97f025d -r d74850cf4e42 test-data/bakta_test_data_manager2.json --- a/test-data/bakta_test_data_manager2.json Fri Jun 23 21:37:05 2023 +0000 +++ b/test-data/bakta_test_data_manager2.json Fri Aug 25 23:34:04 2023 +0000 |
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| @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.8", "dbkey": "8021027", "path": "db", "value": "V5.0_2023-06-08"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.8", "dbkey": "8021027", "path": "bakta-db", "value": "V5.0_2023-06-08"}]}} \ No newline at end of file |
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| diff -r 3e73c97f025d -r d74850cf4e42 test-data/bakta_test_data_manager3.json --- a/test-data/bakta_test_data_manager3.json Fri Jun 23 21:37:05 2023 +0000 +++ b/test-data/bakta_test_data_manager3.json Fri Aug 25 23:34:04 2023 +0000 |
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| @@ -1,1 +1,1 @@ -{"data_tables": {"bakta_database": [{"bakta_version": "1.8", "dbkey": "8021027", "path": "db", "value": "V5.0light_2023-06-08"}]}} \ No newline at end of file +{"data_tables": {"bakta_database": [{"bakta_version": "1.8", "dbkey": "8021027", "path": "bakta-db", "value": "V5.0light_2023-06-08"}]}} \ No newline at end of file |