--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_lncrna_annotations.py	Mon Jul 16 20:42:55 2018 -0400
@@ -0,0 +1,323 @@
+#!/usr/bin/env python
+# ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
+
+# Rewritten by H.E. Cicada Brokaw Dennis from a source downloaded from the toolshed and
+# other example code on the web.
+# This file downloads annotations for lncrna (slncky tool)
+
+import argparse
+import os
+import subprocess
+
+# The following is used to generate a unique_id value
+from datetime import *
+
+# Remove the following line when testing without galaxy package:
+from galaxy.util.json import to_json_string
+# Am not using the following:
+# from galaxy.util.json import from_json_string
+
+# The FileListParser is used by get_ctat_genome_filenames(),
+# which is called by the Data Manager interface (.xml file) to get
+# the filenames that are available online at broadinstitute.org
+# Not sure best way to do it. 
+# This object uses HTMLParser to look through the html 
+# searching for the filenames within anchor tags.
+import urllib2
+from HTMLParser import HTMLParser
+
+#_CTAT_lncrnaIndexPage_URL = 'https://data.broadinstitute.org/Trinity/CTAT/lncrna/annotations.tar.gz'
+_CTAT_lncrnaDownload_URL = 'https://data.broadinstitute.org/Trinity/CTAT/lncrna/annotations.tar.gz'
+_CTAT_lncrnaTableName = 'ctat_lncrna_annotations'
+_CTAT_lncrnaDir_Name = 'annotations'
+_CTAT_lncrna_DisplayNamePrefix = 'CTAT_lncrna_annotations_'
+_lncrnaFileExtension = 'lc'
+_NumBytesNeededForAnnotations = 2147483648 # Number of bytes
+#_DownloadFileSize = 5790678746 # 5.4 Gigabytes.
+_Download_TestFile = 'write_testfile.txt'
+_DownloadSuccessFile = 'download_succeeded.txt'
+
+'''
+class FileListParser(HTMLParser):
+    def __init__(self):
+        # Have to use direct call to super class rather than using super():
+        # super(FileListParser, self).__init__()
+        # because HTMLParser is an "old style" class and its inheritance chain does not include object.
+        HTMLParser.__init__(self)
+        self.filenames = set()
+    def handle_starttag(self, tag, attrs):
+        # Look for filename references in anchor tags and add them to filenames.
+        if tag == "a":
+            # The tag is an anchor tag.
+            for attribute in attrs:
+                # print "Checking: {:s}".format(str(attribute))
+                if attribute[0] == "href":
+                    # Does the href have a tar.gz in it?
+                    if ("tar.gz" in attribute[1]) and ("md5" not in attribute[1]):
+                        # Add the value to filenames.
+                        self.filenames.add(attribute[1])            
+# End of class FileListParser
+'''
+
+
+def get_ctat_lncrna_annotations_locations():
+    # For dynamic options need to return an interable with contents that are tuples with 3 items.
+    # Item one is a string that is the display name put into the option list.
+    # Item two is the value that is put into the parameter associated with the option list.
+    # Item three is a True or False value, indicating whether the item is selected.
+    options = []
+    # open the url and retrieve the filenames of the files in the directory.
+    # resource = urllib2.urlopen(_CTAT_lncrnaIndexPage_URL)
+    # theHTML = resource.read()
+    # filelist_parser = FileListParser()
+    # filelist_parser.feed(theHTML)
+    options.append((_CTAT_lncrnaDir_Name, _CTAT_lncrnaDownload_URL, True))
+    print "The list of items being returned for the option menu is:"
+    print str(options)
+    return options 
+
+def download_annotations(src_location, destination, force_download):
+    # We do not know if the annotations has been downloaded already.
+    # This function returns whether or not the annotations actually gets downloaded.
+    annotations_was_downloaded = False
+    # Get the root filename of the Genome Directory. 
+    # The part after the last '/' and before the first '.'
+    root_annotations_dirname = src_location.split("/")[-1].split(".")[0]
+
+    # We want to make sure that destination is absolute fully specified path.
+    cannonical_destination = os.path.realpath(destination) 
+    if cannonical_destination.split("/")[-1] != root_annotations_dirname:
+        cannonical_destination += "/" + root_annotations_dirname
+    if os.path.exists(cannonical_destination):
+        if not os.path.isdir(cannonical_destination):
+            raise ValueError("The destination is not a directory: " + \
+                             "{:s}".format(cannonical_destination))
+        # else all is good. It is a directory.
+    else:
+        # We need to create it.
+        try:
+            os.makedirs(cannonical_destination)
+        except os.error:
+            print "ERROR: Trying to create the following directory path:"
+            print "\t{:s}".format(cannonical_destination)
+            raise
+
+    # Make sure the directory now exists and we can write to it.
+    if not os.path.exists(cannonical_destination):
+        # It should have been created, but if it doesn't exist at this point
+        # in the code, something is wrong. Raise an error.
+        raise OSError("The destination directory could not be created: " + \
+                      "{:s}".format(cannonical_destination))
+    test_writing_file = "{:s}/{:s}".format(cannonical_destination, _Download_TestFile)
+    try:
+        filehandle = open(test_writing_file, "w")
+        filehandle.write("Testing writing to this file.")
+        filehandle.close()
+        os.remove(test_writing_file)
+    except IOError:
+        print "The destination directory could not be written into: " + \
+                      "{:s}".format(cannonical_destination)
+        raise
+    
+    # Get the list of files in the directory,
+    # We use it to check for a previous download or extraction among other things.
+    orig_files_in_destdir = set(os.listdir(cannonical_destination))
+    # See whether the file has been downloaded already.
+    download_success_file_path = "{:s}/{:s}".format(cannonical_destination, _DownloadSuccessFile)
+    if (_DownloadSuccessFile not in orig_files_in_destdir) or force_download:
+        # Check whether there is enough space on the device for the annotations.
+        statvfs = os.statvfs(cannonical_destination)
+        num_avail_bytes = statvfs.f_frsize * statvfs.f_bavail    # Number of free bytes that ordinary users
+                                                                 # are allowed to use (excl. reserved space)
+        if (num_avail_bytes < _NumBytesNeededForAnnotations):
+            raise OSError("There is insufficient space ({:s} bytes)".format(str(num_avail_bytes)) + \
+                          " on the device of the destination directory: " + \
+                          "{:s}".format(cannonical_destination))
+    
+        
+        if (_DownloadSuccessFile in orig_files_in_destdir):
+            # Since we are redoing the download, 
+            # the success file needs to be removed
+            # until the download has succeeded.
+            os.remove(download_success_file_path)
+        # We want to transfer and untar the file without storing the tar file, because that
+        # adds all that much more space to the needed amount of free space on the disk.
+        # Use subprocess to pipe the output of curl into tar.
+        # Make curl silent so progress is not printed to stderr.
+        command = "curl --silent {:s} | tar -xzf - -C {:s} --strip 1".format(src_location, cannonical_destination) 
+        try: # to send the command that downloads and extracts the file.
+            command_output = subprocess.check_output(command, shell=True)
+            # FIX - not sure check_output is what we want to use. If we want to have an error raised on
+            # any problem, maybe we should not be checking output.
+        except subprocess.CalledProcessError:
+            print "ERROR: Trying to run the following command:\n\t{:s}".format(command)
+            raise
+        else:
+            annotations_was_downloaded = True
+
+    # Some code to help us if errors occur.
+    print "\n*******************************\nFinished download and extraction."
+    if os.path.exists(cannonical_destination) and os.path.isdir(cannonical_destination):
+        subprocess.check_call("ls -la {:s} 2>&1".format(cannonical_destination), shell=True)
+    
+    files_in_destdir = set(os.listdir(cannonical_destination))
+    found_filenames = set()
+    for filename in files_in_destdir:
+        # There should be three files, but some OS's might have created
+        # other files in the directory, or maybe the user did.
+        # Look for the annotations files.
+        # The download files' names should start with the root_annotations_dirname
+        # print "Is root: {:s} in file: {:s}".format(root_annotations_dirname, filename)
+        if root_annotations_dirname in filename:
+            found_filenames.add(filename)
+    # print "The found_filenames are:\n\t{:s}".format(str(found_filenames))
+    ## Changed from found_filenames 
+    if (len(files_in_destdir) >= 4):
+        # FIX - we could md5 the files to make sure they are correct.
+        # Or at least check their sizes, to see if the download completed ok.
+        # Also we could check the names of the files.
+        try:
+            # Create a file to indicate that the download succeeded.
+            subprocess.check_call("touch {:s}".format(download_success_file_path), shell=True)
+        except IOError:
+            print "The download_success file could not be created: " + \
+                      "{:s}".format(download_success_file_path)
+            raise
+    else:
+        print "After download, the potential annotations files found are:\n\t{:s}".format(str(found_filenames))
+        raise ValueError("ERROR: Could not find the extracted annotations files " + \
+                         "in the destination directory:\n\t{:s}".format(cannonical_destination))
+
+    return (cannonical_destination, root_annotations_dirname, annotations_was_downloaded)
+        
+def main():
+    #Parse Command Line
+    # print "At start before parsing arguments."
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-d', '--download_location', default="", \
+        help='This is the download location of the lncrna annotations.')
+    parser.add_argument('-n', '--display_name', default="", \
+        help='Is used as the selector text for the entry of this lncrna annotations in the data table.')
+    parser.add_argument('-p', '--destination_path', \
+        help='Full path of the lncrna annotations location or destination, either where it is, or where it will be placed.')
+    parser.add_argument('-o', '--output_filename', \
+        help='Name of the output file, where the json dictionary will be written.')
+    parser.add_argument('-f', '--force_download', 
+        help='Forces download of lncrna annotations, even if previously downloaded. ' + \
+             'Requires download_location to be set in order to work.', action="store_true")
+    args = parser.parse_args()
+
+    # print "Arguments are parsed."
+    print "\ndownload_location is {:s}".format(str(_CTAT_lncrnaDownload_URL))
+    print "display_name is {:s}".format(str(args.display_name))
+    print "destination_path is {:s}\n".format(str(args.destination_path))
+    root_annotations_dirname = None
+    # FIX - Prob don't need annotations_was_downloaded. Not doing anything with it.
+    # But it indicates success downloading the annotations, so maybe should be checking it.
+    annotations_was_downloaded = False
+    if (_CTAT_lncrnaDownload_URL != ""):
+        annotations_directory, root_annotations_dirname, annotations_was_downloaded = \
+            download_annotations(src_location=_CTAT_lncrnaDownload_URL, \
+                           destination=args.destination_path, \
+                           force_download=args.force_download)
+    else:
+        cannonical_destination = os.path.realpath(args.destination_path)
+        # If args.destination_path is a directory containing 
+        # a subdirectory that contains the annotations files,
+        # then we need to set the annotations_directory to be that subdirectory.
+        if not os.path.exists(cannonical_destination):
+           raise ValueError("Cannot find the Lncrna annotations.\n" + \
+               "The directory does not exist:\n\t{:s}".format(cannonical_destination))
+        files_in_destination_path = os.listdir(cannonical_destination)
+        if (len(files_in_destination_path) == 4):
+            #path_to_file = "{:s}/{:s}".format(cannonical_destination, files_in_destination_path[0])
+            #if os.path.isdir(path_to_file):
+            #    annotations_directory = path_to_file
+            #else:
+            annotations_directory = cannonical_destination
+        else:
+            raise ValueError("Contents of destination directory not equal to expected - 4")
+            #annotations_directory = cannonical_destination
+        # Get the root_annotations_dirname of the annotations from the annotations_directory name.
+        root_annotations_dirname = annotations_directory.split("/")[-1].split(".")[0]
+
+    # Check if there is an actual Lncrna annotations file in the annotations_directory.
+    print "\nThe location of the Lncrna annotations is {:s}.\n".format(annotations_directory)
+    files_in_annotations_directory = set(os.listdir(annotations_directory))
+    annotations_file_found = False
+    annotations_file_path_mm9 = annotations_directory+"/annotations.config"
+    annotations_file_path_mm10 = annotations_directory+"/annotations.config"
+    annotations_file_path_hg19 = annotations_directory+"/annotations.config"
+    annotations_file_path_hg38 = annotations_directory+"/annotations.config"
+
+    # Set the display_name
+    # if (args.display_name is None) or (args.display_name == ""):
+        # Use the root_annotations_dirname.
+        # print "display_name_ok$$$$$$$"
+    
+    if (root_annotations_dirname != None) and (root_annotations_dirname != ""):
+        print "root_annotations_ok%%%%"
+        display_name_hg19 = "hg19"
+        display_name_hg38 = "hg38"
+        display_name_mm10 = "mm10"
+        display_name_mm9 = "mm9"
+    else:
+        display_name = _CTAT_lncrna_DisplayNamePrefix + _CTAT_lncrnaDir_Name
+        print "WARNING: Did not set the display name. Using the default: {:s}".format(display_name_value)
+    #else:
+    #    display_name = _CTAT_lncrna_DisplayNamePrefix + args.display_name
+    # display_name = display_name.replace(" ","_")
+
+    # Set the unique_id
+    datetime_stamp = datetime.now().strftime("_%Y_%m_%d_%H_%M_%S_%f")
+    if (root_annotations_dirname != None) and (root_annotations_dirname != ""):
+        hg19_unique_id = "ctat_lncrna_hg19" + datetime_stamp
+        mm10_unique_id = "ctat_lncrna_mm10" + datetime_stamp
+        mm9_unique_id = "ctat_lncrna_mm9" + datetime_stamp
+        hg38_unique_id = "ctat_lncrna_hg38" + datetime_stamp
+    else:
+        unique_id = _CTAT_lncrnaDir_Name + datetime_stamp
+
+    print "The hg19 Index's display_name will be set to: {:s}\n".format(display_name_hg19)
+    print "Its hg19 unique_id will be set to: {:s}\n".format(hg19_unique_id)
+    print "Its hg19 dir_path will be set to: {:s}\n".format(annotations_file_path_hg19)
+
+
+    print "The hg38 Index's display_name will be set to: {:s}\n".format(display_name_hg38)
+    print "Its hg38 unique_id will be set to: {:s}\n".format(hg38_unique_id)
+    print "Its hg38 dir_path will be set to: {:s}\n".format(annotations_file_path_hg38)
+
+
+    print "The mm9 Index's display_name will be set to: {:s}\n".format(display_name_mm9)
+    print "Its mm9 unique_id will be set to: {:s}\n".format(mm9_unique_id)
+    print "Its mm9 dir_path will be set to: {:s}\n".format(annotations_file_path_mm9)
+
+
+    print "The mm10 Index's display_name will be set to: {:s}\n".format(display_name_mm10)
+    print "Its mm10 unique_id will be set to: {:s}\n".format(mm10_unique_id)
+    print "Its mm10 dir_path will be set to: {:s}\n".format(annotations_file_path_mm10)
+
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = {}
+    data_manager_dict['data_tables'][_CTAT_lncrnaTableName] = []
+    data_table_entry_mm9 = dict(value=display_name_mm9, name=display_name_mm9, path=annotations_file_path_mm9)
+    data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_mm9)
+
+    data_table_entry_mm10 = dict(value=display_name_mm10, name=display_name_mm10, path=annotations_file_path_mm10)
+    data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_mm10)
+
+    data_table_entry_hg19 = dict(value=display_name_hg19, name=display_name_hg19, path=annotations_file_path_hg19)
+    data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_hg19)
+
+    data_table_entry_hg38 = dict(value=display_name_hg38, name=display_name_hg38, path=annotations_file_path_hg38)
+    data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_hg38)
+
+    # Temporarily the output file's dictionary is written for debugging:
+    print "The dictionary for the output file is:\n\t{:s}".format(str(data_manager_dict))
+    # Save info to json file. This is used to transfer data from the DataManager tool, to the data manager,
+    # which then puts it into the correct .loc file (I think).
+    # Remove the following line when testing without galaxy package.
+    open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
+
+if __name__ == "__main__":
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_lncrna_annotations.xml	Mon Jul 16 20:42:55 2018 -0400
@@ -0,0 +1,61 @@
+<tool id="ctat_lncrna_annotations_data_manager" 
+    name="CTAT lncrna annotations Data Manager" 
+    version="1.0.0" tool_type="manage_data">
+    <description>Retrieve, and/or specify the location of CTAT lncrna annotations. 
+    </description>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+    </requirements>
+    <command detect_errors="default">
+        <![CDATA[
+        python $__tool_directory__/add_ctat_lncrna_annotations.py 
+            --display_name "${display_name}" 
+            --destination_path "${destination}" 
+            --output_filename "${out_file}" 
+            #if str( $download_question.download ) == "true":
+                --download_location "\"${download_question.filename}\"" 
+                #if str( $download_question.force_download ) == "true":
+                    --force_download 
+                #end if
+            #end if
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="download_question">
+            <param name="download" type="boolean" checked="false" label="Need to Download?" />
+            <when value="true">
+                <param name="filename" type="select" label="Select File"
+                    dynamic_options="get_ctat_lncrna_annotations_locations()" 
+                    help="Select a lncrna annotations to Download." />
+                <param name="force_download" type="boolean" checked="false" label="Force New Download?" />
+            </when>
+        </conditional>
+
+        <param name="display_name" type="text" label="lncrna annotations Display Name" />
+        <param name="destination" type="text" label="Local Destination (full path)" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <help>
+.. class:: infomark
+	
+Retrieve, and/or specify the location of, a CTAT lncrna annotations.
+When download is true, the annotations from this website_ will be downloaded.
+
+Currently mm9,mm10,hg19,hg38 are supported.
+
+.. class:: infomark
+
+Specify the Full Path of the destination where the CTAT lncrna annotations should be placed.
+If you already have the annotations, specify the full path of the location where it exists and leave the download box unchecked.
+
+.. class:: infomark
+
+The display_name may be left empty if downloading. 
+The display_name will be used as the selector text of the entry in the data table.
+
+.. _website: https://data.broadinstitute.org/Trinity/CTAT/lncrna/annotations.tar.gz         
+    </help>
+    <code file="add_ctat_lncrna_annotations.py" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Mon Jul 16 20:42:55 2018 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/add_ctat_lncrna_annotations.xml" id="ctat_lncrna_annotations_data_manager"> 
+        <data_table name="ctat_lncrna_annotations">
+            <output>
+                <column name="value" />
+                    <!-- value is used to uniquely identify this entry in the table.
+                    -->
+                <column name="name" />
+                    <!-- name is used as the selector in the pull down lists for items in this table.
+                    -->
+                <column name="path" />
+                    <!-- path is the absolute path of the directory containing the lncrna annotations files.
+                    -->
+                <!-- Same as the Genome Reference Library, we create the lncrna annotations files where we want them.
+                -->
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ctat_lncrna_annotations.loc.sample	Mon Jul 16 20:42:55 2018 -0400
@@ -0,0 +1,15 @@
+# This file lists the locations of CTAT lncrna annotations
+# Usually there will only be one index, but it is concievable 
+# that there could be multiple annotations.
+# This file format is as follows
+# (white space characters are TAB characters):
+#
+#<value>    <name>  <path>
+# value is a unique id
+# name is the display name
+# path is the directory where the index files are stored
+#
+#ctat_lncrna_annotations.loc could look like:
+#
+#slncky_annotations	CTAT_lncrna_annotations	/path/to/lncrna/annotations
+#

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Jul 16 20:42:55 2018 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="ctat_lncrna_annotations" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ctat_lncrna_annotations.loc" />
+    </table>
+</tables>