# HG changeset patch
# User trinity_ctat
# Date 1531787226 14400
# Node ID b4d4f0d76e94c86fdb6abe97d59f77722e56139b
Uploaded
diff -r 000000000000 -r b4d4f0d76e94 data_manager/add_ctat_centrifuge_index.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_centrifuge_index.py Mon Jul 16 20:27:06 2018 -0400
@@ -0,0 +1,354 @@
+#!/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 allows downloading of a centrifuge index, or specification of its disk location.
+# This index is one of the input paramters needed by the ctat_metagenomics tool.
+# At the moment only one index is supported by the ctat_metagenomics tool:
+# ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
+
+import argparse
+import os
+#import tarfile
+#import urllib
+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_CentrifugeIndexPage_URL = 'https://ccb.jhu.edu/software/centrifuge/'
+_CTAT_CentrifugeDownload_URL = 'ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz'
+_CTAT_CentrifugeIndexTableName = 'ctat_centrifuge_indexes'
+_CTAT_CentrifugeDir_Name = 'p_compressed+h+v'
+_CTAT_Centrifuge_DisplayNamePrefix = 'CTAT_CentrifugeIndex_'
+_CentrifugeIndexFileExtension = 'cf'
+_NumBytesNeededForIndex = 7400130287 # 6.9 GB
+#_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_centrifuge_index_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_CentrifugeIndexPage_URL)
+ theHTML = resource.read()
+ filelist_parser = FileListParser()
+ filelist_parser.feed(theHTML)
+ # This is what was returned on 2018-04-23
+ # ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed_2018_4_15.tar.gz
+ # ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/nt_2018_3_3.tar.gz
+ # ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
+ # ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p+h+v.tar.gz
+ # Which could be hard coded:
+ # options.append(("p_compressed+h+v", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz", True))
+ # options.append(("p+h+v", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p+h+v.tar.gz", False))
+ # options.append(("nt_2018_3_3", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/nt_2018_3_3.tar.gz", False))
+ # options.append(("p_compressed_2018_4_15", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed_2018_4_15.tar.gz", False))
+ # but only returning the one we want, which for now is assumed to be present.
+ # For now, I am printing the list, just so I can see what was returned,
+ # print "FYI: The URL's that were found on Centrifuge's page are:"
+ # print "\t" + "\n\t".join(filelist_parser.filenames)
+ # For now instead of sending back the list of found URL's, send back the one URL we want.
+ # Currently, only one of the options is supported.
+ options.append((_CTAT_CentrifugeDir_Name, _CTAT_CentrifugeDownload_URL, True))
+ print "The list of items being returned for the option menu is:"
+ print str(options)
+ return options
+
+# The following was used by the example program to get input parameters through the json.
+# Just leaving here for reference.
+# We are getting all of our parameter values through command line arguments.
+#def get_reference_id_name(params):
+# genome_id = params['param_dict']['genome_id']
+# genome_name = params['param_dict']['genome_name']
+# return genome_id, genome_name
+#
+#def get_url(params):
+# trained_url = params['param_dict']['trained_url']
+# return trained_url
+
+def download_index(src_location, destination, force_download):
+ # We do not know if the index has been downloaded already.
+ # This function returns whether or not the index actually gets downloaded.
+ index_was_downloaded = False
+ # Get the root filename of the Genome Directory.
+ # The part after the last '/' and before the first '.'
+ root_index_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_index_dirname:
+ cannonical_destination += "/" + root_index_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 index.
+ statvfs = os.statvfs(cannonical_destination)
+ # fs_size = statvfs.f_frsize * statvfs.f_blocks # Size of filesystem in bytes
+ # num_free_bytes = statvfs.f_frsize * statvfs.f_bfree # Actual number of free bytes
+ 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 < _NumBytesNeededForIndex):
+ raise OSError("There is insufficient space ({:s} bytes)".format(str(num_avail_bytes)) + \
+ " on the device of the destination directory: " + \
+ "{:s}".format(cannonical_destination))
+
+ #Previous code to download and untar. Not using anymore.
+ #full_filepath = os.path.join(destination, src_filename)
+ #
+ #Download ref: https://dzone.com/articles/how-download-file-python
+ #f = urllib2.urlopen(ctat_resource_lib_url)
+ #data = f.read()
+ #with open(full_filepath, 'wb') as code:
+ # code.write(data)
+ #
+ #Another way to download:
+ #try:
+ # urllib.urlretrieve(url=ctat_resource_lib_url, filename=full_filepath)
+ #
+ #Then untar the file.
+ #try:
+ # tarfile.open(full_filepath, mode='r:*').extractall()
+
+ 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}".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:
+ index_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 -lad {: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 index files.
+ # The download files' names should start with the root_index_dirname
+ # print "Is root: {:s} in file: {:s}".format(root_index_dirname, filename)
+ if root_index_dirname in filename:
+ found_filenames.add(filename)
+ # print "The found_filenames are:\n\t{:s}".format(str(found_filenames))
+ if (len(found_filenames) >= 3):
+ # 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 index files found are:\n\t{:s}".format(str(found_filenames))
+ raise ValueError("ERROR: Could not find the extracted index files " + \
+ "in the destination directory:\n\t{:s}".format(cannonical_destination))
+
+ return (cannonical_destination, root_index_dirname, index_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 centrifuge index.')
+ parser.add_argument('-n', '--display_name', default="", \
+ help='Is used as the selector text for the entry of this Centrifuge Index in the data table.')
+ parser.add_argument('-p', '--destination_path', \
+ help='Full path of the Centrifuge Index 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 the Centrifuge Index, even if previously downloaded. ' + \
+ 'Requires download_location to be set in order to work.', action="store_true")
+ args = parser.parse_args()
+
+ # All of the input parameters are written by default to the output file prior to
+ # this program being called.
+ # But I do not get input values from the json file, but rather from command line.
+ # Just leaving the following code as a comment, in case it might be useful to someone later.
+ # params = from_json_string(open(filename).read())
+ # target_directory = params['output_data'][0]['extra_files_path']
+ # os.mkdir(target_directory)
+
+ # print "Arguments are parsed."
+ print "\ndownload_location is {:s}".format(str(args.download_location))
+ print "display_name is {:s}".format(str(args.display_name))
+ print "destination_path is {:s}\n".format(str(args.destination_path))
+ root_index_dirname = None
+ # FIX - Prob don't need index_was_downloaded. Not doing anything with it.
+ # But it indicates success downloading the index, so maybe should be checking it.
+ index_was_downloaded = False
+ if (args.download_location != ""):
+ index_directory, root_index_dirname, index_was_downloaded = \
+ download_index(src_location=args.download_location, \
+ destination=args.destination_path, \
+ force_download=args.force_download)
+ else:
+ cannonical_destination = os.path.realpath(args.destination_path)
+ if not os.path.exists(cannonical_destination):
+ raise ValueError("Cannot find the Centrifuge Index.\n" + \
+ "The directory does not exist:\n\t{:s}".format(index_directory))
+ # If args.destination_path is a directory containing
+ # a subdirectory that contains the index files,
+ # then we need to set the index_directory to be that subdirectory.
+ files_in_destination_path = os.listdir(cannonical_destination)
+ if (len(files_in_destination_path) == 1):
+ path_to_file = "{:s}/{:s}".format(cannonical_destination, files_in_destination_path[0])
+ if os.path.isdir(path_to_file):
+ index_directory = path_to_file
+ else:
+ index_directory = cannonical_destination
+ else:
+ index_directory = cannonical_destination
+ # Get the root_index_dirname of the index from the index_directory name.
+ root_index_dirname = index_directory.split("/")[-1].split(".")[0]
+
+ # Check if there is an actual Centrifuge Index file in the index_directory.
+ print "\nThe location of the Centrifuge Index is {:s}.\n".format(index_directory)
+ files_in_index_directory = set(os.listdir(index_directory))
+ index_file_found = False
+ index_file_path = index_directory
+ for filename in files_in_index_directory:
+ # The current index is split into 3 files.
+ # filenames are in the form: index_root_name.#.cf,
+ # where # is a numeral (1, 2, or 3)
+ # indicating the order of the files.
+ if filename.split(".")[-1] == _CentrifugeIndexFileExtension:
+ index_file_found = True
+ # The centrifuge program wants the root name of the files to be final part of the path.
+ index_file_path = "{:s}/{:s}".format(index_directory, filename.split(".")[0])
+ if not index_file_found:
+ raise ValueError("Cannot find any Centrifuge Index files.\n" + \
+ "The contents of the directory {:s} are:\n\t".format(index_directory) + \
+ "\n\t".join(files_in_index_directory))
+
+ # Set the display_name
+ if (args.display_name is None) or (args.display_name == ""):
+ # Use the root_index_dirname.
+ if (root_index_dirname != None) and (root_index_dirname != ""):
+ display_name = _CTAT_Centrifuge_DisplayNamePrefix + root_index_dirname
+ else:
+ display_name = _CTAT_Centrifuge_DisplayNamePrefix + _CTAT_CentrifugeDir_Name
+ print "WARNING: Did not set the display name. Using the default: {:s}".format(display_name_value)
+ else:
+ display_name = _CTAT_Centrifuge_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_index_dirname != None) and (root_index_dirname != ""):
+ unique_id = root_index_dirname + datetime_stamp
+ else:
+ unique_id = _CTAT_CentrifugeDir_Name + datetime_stamp
+
+ print "The Index's display_name will be set to: {:s}\n".format(display_name)
+ print "Its unique_id will be set to: {:s}\n".format(unique_id)
+ print "Its dir_path will be set to: {:s}\n".format(index_file_path)
+
+ data_manager_dict = {}
+ data_manager_dict['data_tables'] = {}
+ data_manager_dict['data_tables'][_CTAT_CentrifugeIndexTableName] = []
+ data_table_entry = dict(value=unique_id, name=display_name, path=index_file_path)
+ data_manager_dict['data_tables'][_CTAT_CentrifugeIndexTableName].append(data_table_entry)
+
+ # 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 b4d4f0d76e94 data_manager/add_ctat_centrifuge_index.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_centrifuge_index.xml Mon Jul 16 20:27:06 2018 -0400
@@ -0,0 +1,89 @@
+
+ Retrieve, and/or specify the location of, a CTAT Centrifuge Index.
+
+
+ python
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+Retrieve, and/or specify the location of, a CTAT Centrifuge Index.
+When download is true, Centrifuge index on this FTP link_ will be downloaded.
+
+Currently that is the only supported index.
+
+.. class:: infomark
+
+Specify the Full Path of the destination where the CTAT Reference Library should be placed.
+If you already have the index, 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.
+
+.. _link: ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
+
+