# HG changeset patch
# User trinity_ctat
# Date 1531788175 14400
# Node ID a3aa3f9e17027b7f479bb35da77e5aa6d375c1fd
Uploaded
diff -r 000000000000 -r a3aa3f9e1702 data_manager/add_ctat_lncrna_annotations.py
--- /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()
diff -r 000000000000 -r a3aa3f9e1702 data_manager/add_ctat_lncrna_annotations.xml
--- /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 @@
+
+ Retrieve, and/or specify the location of CTAT lncrna annotations.
+
+
+ python
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. 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
+
+