| Next changeset 1:9ef108e34063 (2023-02-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty |
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added:
data_manager/macro.xml data_manager/plasmidfinder_fetch_database.py data_manager/plasmidfinder_fetch_database.xml data_manager_conf.xml plasmidfinder_database.loc test-data/plasmidfinder.loc.test test-data/plasmidfinder_test_data_manager_2.1.json tool-data/plasmidfinder_database.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 8ad77a9dc91d data_manager/macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/macro.xml Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,13 @@ +<macros> + <token name="@TOOL_VERSION@">2.1.6</token> + <token name="@REQUESTS_VERSION@">2.27.1</token> + <token name="@PYTHON_VERSION@">3.8</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@PYTHON_VERSION@">python</requirement> + <requirement type="package" version="@REQUESTS_VERSION@">requests</requirement> + </requirements> + </xml> +</macros> |
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| diff -r 000000000000 -r 8ad77a9dc91d data_manager/plasmidfinder_fetch_database.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/plasmidfinder_fetch_database.py Tue Feb 14 14:25:43 2023 +0000 |
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| b'@@ -0,0 +1,212 @@\n+import argparse\n+import json\n+import os\n+import tarfile\n+from datetime import datetime\n+from pathlib import Path\n+\n+import requests\n+\n+\n+class GetPlasmidfinderDataManager:\n+ """\n+ Create the json file with database information for galaxy data manager\n+ """\n+\n+ def __init__(self,\n+ plasmidfinder_database="plasmidfinder_database",\n+ db_name="plasmidfinder-db",\n+ plasmidfinder_version="latest"):\n+ self.data_table_name = plasmidfinder_database\n+ self._db_name = db_name\n+ self._plasmidfinder_version = plasmidfinder_version\n+ self._plasmidfinder_date_version = None\n+ self.data_table_entry = None\n+ self.plasmidfinder_table_list = None\n+ self._commit_number = None\n+\n+ def get_data_table_format(self):\n+ """\n+ Skeleton of a data_table format\n+ return: a data table formatted for json output\n+ """\n+ self.data_table_entry = {\n+ "data_tables": {\n+ self.data_table_name: {}\n+ }\n+ }\n+ return self.data_table_entry\n+\n+ def get_data_manager(self):\n+ """\n+ Create the empty data table format and add all the information into\n+ Commit number is added if latest is required instead of version number\n+ return: The data table with database information\n+ """\n+ self.plasmidfinder_table_list = self.get_data_table_format()\n+ if self._plasmidfinder_version == "latest":\n+ version_value = self._commit_number\n+ else:\n+ version_value = self._plasmidfinder_version\n+ plasmidfinder_value = f"plasmidfinder_{self._commit_number}" \\\n+ f"_{self._plasmidfinder_date_version}"\n+ plasmidfinder_name = f"{version_value}" \\\n+ f"_{self._plasmidfinder_date_version}"\n+ data_info = dict(value=plasmidfinder_value,\n+ name=plasmidfinder_name,\n+ date=self._plasmidfinder_date_version,\n+ path=self._db_name)\n+ self.plasmidfinder_table_list["data_tables"][self.data_table_name] = [data_info]\n+ return self.plasmidfinder_table_list\n+\n+\n+class DownloadPlasmidfinderDatabase(GetPlasmidfinderDataManager):\n+ """\n+ Download the plasmidfinder database from the bitbucket repository.\n+ Build the data manager info for galaxy\n+ """\n+\n+ def __init__(self,\n+ output_dir=Path.cwd(),\n+ plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/get/",\n+ db_name="plasmidfinder-db",\n+ db_tmp="tmp_database",\n+ plasmidfinder_version="latest",\n+ json_file_path=None,\n+ date_version=datetime.now().strftime("%Y-%m-%d")):\n+\n+ super().__init__()\n+ self.json_file_path = json_file_path\n+ self._output_dir = output_dir\n+ self._plasmidfinder_url = plasmidfinder_url\n+ self._temporary_folder = db_tmp\n+ self._db_name = db_name\n+ self._db_name_tar = f\'{db_name}.gz\'\n+ self._plasmidfinder_version = plasmidfinder_version\n+ self._plasmidfinder_date_version = date_version\n+ self._commit_number = None\n+\n+ def extract_db_commit(self, request_header, title_name="content-disposition"):\n+ """\n+ Extract the commit if to add the information as identifier of the download\n+ @request_header: a request object obtained from requests.get()\n+ @title_name: the tag to search in the header of the requests object\n+ return: the value of the commit\n+ """\n+ db_info = request_header.headers[title_name]\n+ commit_number = db_info.split("-")[2].split(".")[0]\n+ return commit_number\n+\n+ def untar_files(self, file_path: Path, extracted_path_output: Path):\n+ """\n+ untar the download archive\n+ @file_path: i'..b' the version choosen by user.\n+ This method could be upgraded simply by adding the new versions\n+ """\n+ if self._plasmidfinder_version == "latest":\n+ self._plasmidfinder_url = f"{self._plasmidfinder_url}master.gz"\n+ elif self._plasmidfinder_version == "2.1":\n+ self._plasmidfinder_url = f"{self._plasmidfinder_url}1307168.gz"\n+\n+ def download_database(self):\n+ """\n+ Download the plasmidfinder database using requests lib\n+ Make the directory and temporary directory for download\n+ Untar the download files\n+ """\n+ self._output_dir = Path(self._output_dir)\n+ self.choose_db_version()\n+ try:\n+ request_info = requests.get(self._plasmidfinder_url)\n+ request_info.raise_for_status()\n+ self._commit_number = self.extract_db_commit(request_info)\n+ output_tar_path = self._output_dir.joinpath(self._temporary_folder)\n+ output_tar_path_file = output_tar_path.joinpath(self._db_name_tar)\n+ output_path = self._output_dir.joinpath(self._db_name)\n+ os.makedirs(output_tar_path)\n+ os.makedirs(output_path)\n+ with open(output_tar_path_file, \'wb\') as output_dir:\n+ output_dir.write(request_info.content)\n+ untar_output = self.untar_files(file_path=output_tar_path_file, extracted_path_output=output_tar_path.joinpath(self._db_name))\n+\n+ self.moove_download_files(older_path=untar_output, new_path=output_path)\n+ except requests.exceptions.HTTPError as http_error:\n+ print(f"Requests Error: {http_error}")\n+ print(f"Fail to import Plasmidfinder database from {self._plasmidfinder_url}")\n+\n+ def moove_download_files(self, older_path, new_path, expression_search="*fsa"):\n+ """\n+ Clean downloaded data by mooving fasta files in the final folder\n+ @older_path: previous path where the files are located\n+ @new_path: final path where files will be mooved\n+ @expression_search: keep only file with this expression\n+ """\n+ fasta_files = Path(older_path).rglob(expression_search)\n+ file_list_paths = [file for file in fasta_files if file.is_file()]\n+ [self.keep_filename(pathname=path, output_path=new_path) for path in file_list_paths]\n+\n+ def keep_filename(self, pathname, output_path):\n+ """\n+ Moove files\n+ @pathname: previous path\n+ @output_path: final path\n+ """\n+ Path.replace(pathname, output_path.joinpath(pathname.name))\n+\n+ def read_json_input_file(self):\n+ """\n+ Import the json file\n+ """\n+ with open(self.json_file_path) as fh:\n+ params = json.load(fh)\n+ target_dir = params[\'output_data\'][0][\'extra_files_path\']\n+ os.makedirs(target_dir)\n+ self._output_dir = target_dir\n+\n+ def write_json_infos(self):\n+ """\n+ Write in the imported json file\n+ """\n+ with open(self.json_file_path, \'w\') as fh:\n+ json.dump(self.get_data_manager(), fh, sort_keys=True)\n+\n+\n+def parse_arguments():\n+ """\n+ List of arguments provided by the user\n+ return: parsed arguments\n+ """\n+ # parse options and arguments\n+ arg_parser = argparse.ArgumentParser()\n+ arg_parser.add_argument("data_manager_json",\n+ help="json file from galaxy")\n+ arg_parser.add_argument("-v", "--db_version",\n+ help="version of the plasmidfinder (latest or 2.1)")\n+ return arg_parser.parse_args()\n+\n+\n+def main():\n+ all_args = parse_arguments()\n+ plasmidfinder_download = DownloadPlasmidfinderDatabase(json_file_path=all_args.data_manager_json, plasmidfinder_version=all_args.db_version)\n+ plasmidfinder_download.read_json_input_file()\n+ plasmidfinder_download.download_database()\n+ plasmidfinder_download.write_json_infos()\n+\n+\n+if __name__ == \'__main__\':\n+ main()\n' |
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| diff -r 000000000000 -r 8ad77a9dc91d data_manager/plasmidfinder_fetch_database.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/plasmidfinder_fetch_database.xml Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,48 @@ +<tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>plasmidfinder database builder</description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/plasmidfinder_fetch_database.py' + --db_version '$database_select' + '$output_file' + ]]></command> + <inputs> + <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)"> + <option value="latest" selected="true">Latest available version</option> + <option value="2.1">V2.1_2019-08-28</option> + </param>param> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json"/> + </outputs> + <tests> + <!-- Test_1 DB latest --> + <test expect_num_outputs="1"> + <param name="database_select" value="latest"/> + <output name="output_file" value="plasmidfinder_test_data_manager_latest.json"> + <assert_contents> + <has_text_matching expression='{"data_tables": {"plasmidfinder_database": [{"date": "\d\d\d\d-\d\d-\d\d", "name": "b1c9ddac0e61_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_b1c9ddac0e61_\d\d\d\d-\d\d-\d\d"' /> + </assert_contents> + </output> + </test> + <!-- Test_2 DB 2.1 --> + <test expect_num_outputs="1"> + <param name="database_select" value="2.1"/> + <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json"> + <assert_contents> + <has_text_matching expression='"data_tables": \{"plasmidfinder_database": \[\{"date": "\d\d\d\\d-\d\d-\d\d", "name": "2\.1_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d"' /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Download plasmidfinder database from the bitbucket repository + ]]></help> + <citations> + <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 8ad77a9dc91d data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/plasmidfinder_fetch_database.xml" id="plasmidfinder_fetch_database" version="@TOOL_VERSION@"> + <data_table name="plasmidfinder_database"> + <output> + <column name="value" /> + <column name="name" /> + <column name="date" /> + <column name="path" output_ref="output_file"> + <move type="directory" relativize_symlinks="True"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">plasmidfinder-db/${name}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/plasmidfinder-db/${name}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r 8ad77a9dc91d plasmidfinder_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasmidfinder_database.loc Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of plasmidfinder database +# The name was obtained by merging date of download and commit number +# the columns are: +# value, name, date, path +# +# for example +#plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 plasmidfinder-db +#plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 plasmidfinder-db |
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| diff -r 000000000000 -r 8ad77a9dc91d test-data/plasmidfinder.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder.loc.test Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,12 @@ +plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 plasmidfinder-db +plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 plasmidfinder-db +plasmidfinder_c18e08c17a59_2023-01-27 c18e08c17a59_2023-01-27 2023-01-27 /tmp/tmp9g7s9mjt/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-01-27 +plasmidfinder_1307168b1ce7_2023-01-27 2.1_2023-01-27 2023-01-27 /tmp/tmp9g7s9mjt/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-01-27 +plasmidfinder_c18e08c17a59_2023-01-27 c18e08c17a59_2023-01-27 2023-01-27 /tmp/tmpdy82xyjr/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-01-27 +plasmidfinder_1307168b1ce7_2023-01-27 2.1_2023-01-27 2023-01-27 /tmp/tmpdy82xyjr/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-01-27 +plasmidfinder_c18e08c17a59_2023-01-27 c18e08c17a59_2023-01-27 2023-01-27 /tmp/tmp6_mld4pi/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-01-27 +plasmidfinder_1307168b1ce7_2023-01-27 2.1_2023-01-27 2023-01-27 /tmp/tmp6_mld4pi/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-01-27 +plasmidfinder_c18e08c17a59_2023-02-07 c18e08c17a59_2023-02-07 2023-02-07 /tmp/tmp70ecz0oo/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-07 +plasmidfinder_1307168b1ce7_2023-02-07 2.1_2023-02-07 2023-02-07 /tmp/tmp70ecz0oo/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-07 +plasmidfinder_c18e08c17a59_2023-02-14 c18e08c17a59_2023-02-14 2023-02-14 /tmp/tmpvbz0fwsy/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-14 +plasmidfinder_1307168b1ce7_2023-02-14 2.1_2023-02-14 2023-02-14 /tmp/tmpvbz0fwsy/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-14 |
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| diff -r 000000000000 -r 8ad77a9dc91d test-data/plasmidfinder_test_data_manager_2.1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder_test_data_manager_2.1.json Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"plasmidfinder_database": [{"date": "2023-01-27", "name": "2.1_2023-01-27", "path": "plasmidfinder-db", "value": "plasmidfinder_1307168b1ce7_2023-01-27"}]}} \ No newline at end of file |
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| diff -r 000000000000 -r 8ad77a9dc91d tool-data/plasmidfinder_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder_database.loc Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of plasmidfinder database +# The name was obtained by merging date of download and commit number +# the columns are: +# value, name, date, path +# +# for example +#plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 plasmidfinder-db +#plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 plasmidfinder-db |
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| diff -r 000000000000 -r 8ad77a9dc91d tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,8 @@ + +<tables> + <!-- Locations of plasmidfinder database in the required format --> + <table name="plasmidfinder_database" comment_char="#"> + <columns>value, name, date, path</columns> + <file path="tool-data/plasmidfinder.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 8ad77a9dc91d tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Feb 14 14:25:43 2023 +0000 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of plasmidfinder database in the required format --> + <table name="plasmidfinder_database" comment_char="#"> + <columns>value, name, date, path</columns> + <file path="${__HERE__}/test-data/plasmidfinder.loc.test"/> + </table> +</tables> |