Mercurial > repos > trinity_ctat > ctat_lncrna_annotations_data_manager
view data_manager/add_ctat_lncrna_annotations.py @ 0:a3aa3f9e1702 draft default tip
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author | trinity_ctat |
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date | Mon, 16 Jul 2018 20:42:55 -0400 |
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#!/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()