--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sortmerna_download.py	Wed May 31 14:53:00 2017 -0400
@@ -0,0 +1,215 @@
+#!/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
+        command = "indexdb_rna --ref %s,%s" % (
+            output_filepath,
+            os.path.splitext(output_filepath)[0])
+        process = subprocess.call(command, shell=True )
+        # 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.")

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sortmerna_download.xml	Wed May 31 14:53:00 2017 -0400
@@ -0,0 +1,33 @@
+<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.0" tool_type="manage_data">
+    <description>reference databases</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">sortmerna</requirement>
+        <requirement type="package" version="2.13.0">requests</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <command><![CDATA[
+        python '$__tool_directory__/data_manager_sortmerna_download.py'
+            --version @VERSION@
+            --jsonfile '$out_file'
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+This tool downloads the reference databases for SortMeRNA and index it
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts611</citation>
+        <yield />
+    </citations>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml	Wed May 31 14:53:00 2017 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0" ?>
+<macros>
+    <token name="@VERSION@">2.1b</token>
+</macros>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Wed May 31 14:53:00 2017 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/data_manager_sortmerna_download.xml" id="data_manager_sortmerna_download" >
+        <data_table name="rRNA_databases">  <!-- Defines a Data Table to be modified. -->
+            <output> <!-- Handle the output of the Data Manager Tool -->
+                <column name="value" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="path" output_ref="out_file" >
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${dbkey}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${dbkey}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rRNA_databases.loc.sample	Wed May 31 14:53:00 2017 -0400
@@ -0,0 +1,2 @@
+#<unique_id>  <database_caption>  <name>  <fasta_file_path>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed May 31 14:53:00 2017 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="rRNA_databases" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/rRNA_databases.loc" />
+    </table>
+</tables>
\ No newline at end of file