# HG changeset patch
# User bebatut
# Date 1496227102 14400
# Node ID 505260412cb1550bc2def0d767c968ac98bda787
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sortmerna_database_downloader commit af5cc2acf0e97637c9a28b80455cc87caf13b79c-dirty
diff -r 000000000000 -r 505260412cb1 data_manager/data_manager_sortmerna_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sortmerna_download.py Wed May 31 06:38:22 2017 -0400
@@ -0,0 +1,216 @@
+#!/usr/bin/env python
+# Data manager for reference data for the SortMeRNA Galaxy tools
+
+import argparse
+import json
+import os
+import tarfile
+import requests
+import subprocess
+
+
+# Utility functions for interacting with Galaxy JSON
+def read_input_json(jsonfile):
+ """Read the JSON supplied from the data manager tool
+
+ Returns a tuple (param_dict,extra_files_path)
+
+ 'param_dict' is an arbitrary dictionary of parameters
+ input into the tool; 'extra_files_path' is the path
+ to a directory where output files must be put for the
+ receiving data manager to pick them up.
+
+ NB the directory pointed to by 'extra_files_path'
+ doesn't exist initially, it is the job of the script
+ to create it if necessary.
+
+ """
+ params = json.loads(open(jsonfile).read())
+ return (params['param_dict'],
+ params['output_data'][0]['extra_files_path'])
+
+
+# Utility functions for creating data table dictionaries
+#
+# Example usage:
+# >>> d = create_data_tables_dict()
+# >>> add_data_table(d,'my_data')
+# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
+# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
+# >>> print str(json.dumps(d))
+def create_data_tables_dict():
+ """Return a dictionary for storing data table information
+
+ Returns a dictionary that can be used with 'add_data_table'
+ and 'add_data_table_entry' to store information about a
+ data table. It can be converted to JSON to be sent back to
+ the data manager.
+
+ """
+ d = {}
+ d['data_tables'] = {}
+ return d
+
+
+def add_data_table(d, table):
+ """Add a data table to the data tables dictionary
+
+ Creates a placeholder for a data table called 'table'.
+
+ """
+ d['data_tables'][table] = []
+
+
+def add_data_table_entry(d, table, entry):
+ """Add an entry to a data table
+
+ Appends an entry to the data table 'table'. 'entry'
+ should be a dictionary where the keys are the names of
+ columns in the data table.
+
+ Raises an exception if the named data table doesn't
+ exist.
+
+ """
+ try:
+ d['data_tables'][table].append(entry)
+ except KeyError:
+ raise Exception("add_data_table_entry: no table '%s'" % table)
+
+
+def download_archive(version):
+ """
+
+ """
+ filepath = "%s.tar.gz" % (version)
+ url = "https://github.com/biocore/sortmerna/archive/%s.tar.gz" % (version)
+ r = requests.get(url, stream=True)
+ r.raise_for_status()
+ with open(filepath, "wb") as fd:
+ for chunk in r.iter_content(chunk_size=128):
+ fd.write(chunk)
+ return filepath
+
+
+def find_archive_content_path(archive_content_path):
+ """
+ """
+ content = os.listdir(archive_content_path)
+ archive_content = []
+ for x in content:
+ if not x.startswith(".") and not x.startswith("_"):
+ archive_content.append(x)
+ if len(archive_content) == 1:
+ archive_content_path = os.path.join(
+ archive_content_path,
+ archive_content[0])
+ return archive_content_path
+
+
+def extract_archive(filepath):
+ """
+ """
+ archive_content_path = "tmp"
+ tar = tarfile.open(filepath)
+ tar.extractall(path=archive_content_path)
+ tar.close()
+ archive_content_path = find_archive_content_path(archive_content_path)
+ return archive_content_path
+
+
+def move_index_files(archive_content_path, target_dir, data_tables, version):
+ """
+ """
+ file_dir = os.path.join(archive_content_path, "rRNA_databases")
+ for filename in os.listdir(file_dir):
+ if not filename.endswith("fasta"):
+ continue
+ input_filepath = os.path.join(file_dir, filename)
+ output_filepath = os.path.join(target_dir, filename)
+ # Move file
+ os.rename(input_filepath, output_filepath)
+ # Index the file with indexdb_rna
+ ref = "%s,%s" %(output_filepath, os.path.splitext(output_filepath)[0])
+ process = subprocess.run(
+ ["indexdb_rna", "--ref", ref],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ # Add entry in the data table
+ db_name = os.path.splitext(filename)[0]
+ add_data_table_entry(
+ data_tables,
+ "rRNA_databases",
+ dict(
+ dbkey=db_name,
+ value=version,
+ name=db_name,
+ path=output_filepath))
+
+
+def download_db(data_tables, version, target_dir):
+ """Download SortMeRNA database
+
+ Creates references to the specified file(s) on the Galaxy
+ server in the appropriate data table (determined from the
+ file extension).
+
+ The 'data_tables' dictionary should have been created using
+ the 'create_data_tables_dict' and 'add_data_table' functions.
+
+ Arguments:
+ data_tables: a dictionary containing the data table info
+ version: version of the database
+ table_name: name of the table
+ target_dir: directory to put copy or link to the data file
+ """
+ print("Download archive")
+ filepath = download_archive(version)
+
+ print("Extract archive %s" % filepath)
+ archive_content_path = extract_archive(filepath)
+
+ print("Moving fasta file from %s and index them" % archive_content_path)
+ move_index_files(
+ archive_content_path,
+ target_dir,
+ data_tables,
+ version)
+
+
+if __name__ == "__main__":
+ print("Starting...")
+
+ # Read command line
+ parser = argparse.ArgumentParser(
+ description='Download QIIME reference database')
+ parser.add_argument('--version', help="Database version")
+ parser.add_argument('--jsonfile', help="Output JSON file")
+ args = parser.parse_args()
+
+ jsonfile = args.jsonfile
+
+ # Read the input JSON
+ params, target_dir = read_input_json(jsonfile)
+
+ # Make the target directory
+ print("Making %s" % target_dir)
+ os.mkdir(target_dir)
+ os.mkdir(os.path.join(target_dir, "rRNA_databases"))
+ target_dir = os.path.join(target_dir, "rRNA_databases")
+
+ # Set up data tables dictionary
+ data_tables = create_data_tables_dict()
+ add_data_table(data_tables, "rRNA_databases")
+
+ # Fetch data from specified data sources
+ download_db(
+ data_tables,
+ args.version,
+ target_dir)
+
+ # Write output JSON
+ print("Outputting JSON")
+ print(str(json.dumps(data_tables)))
+ with open(jsonfile, 'w') as out:
+ json.dump(data_tables, out)
+ print("Done.")
diff -r 000000000000 -r 505260412cb1 data_manager/data_manager_sortmerna_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sortmerna_download.xml Wed May 31 06:38:22 2017 -0400
@@ -0,0 +1,33 @@
+
+ reference databases
+
+ macros.xml
+
+
+ sortmerna
+ requests
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/bioinformatics/bts611
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 505260412cb1 data_manager/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml Wed May 31 06:38:22 2017 -0400
@@ -0,0 +1,4 @@
+
+
+ 2.1b
+
\ No newline at end of file
diff -r 000000000000 -r 505260412cb1 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed May 31 06:38:22 2017 -0400
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 505260412cb1 tool-data/rRNA_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rRNA_databases.loc.sample Wed May 31 06:38:22 2017 -0400
@@ -0,0 +1,2 @@
+#
+
diff -r 000000000000 -r 505260412cb1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed May 31 06:38:22 2017 -0400
@@ -0,0 +1,6 @@
+
+