# HG changeset patch
# User trinity_ctat
# Date 1525181478 14400
# Node ID bf41e354f3594e37532843c7d3bbd5c2be39d1b8
# Parent 9f99eb3aebfb6c0e13b6c53fa934bf8d5f151612
Uploaded
diff -r 9f99eb3aebfb -r bf41e354f359 data_manager/add_ctat_centrifuge_index.py
--- a/data_manager/add_ctat_centrifuge_index.py Fri Apr 27 07:24:29 2018 -0400
+++ b/data_manager/add_ctat_centrifuge_index.py Tue May 01 09:31:18 2018 -0400
@@ -14,6 +14,9 @@
#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:
@@ -30,8 +33,10 @@
_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'
@@ -58,36 +63,36 @@
# 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)
- # return a tuple of the filenames
- # return tuple(filelist_parser.filenames)
- # For now, I am printing the list, just so I can see what was returned,
# 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:
+ # vals.append(("p_compressed+h+v", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz", True))
+ # vals.append(("p+h+v", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p+h+v.tar.gz", False))
+ # vals.append(("nt_2018_3_3", "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/nt_2018_3_3.tar.gz", False))
+ # vals.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)
- # Instead of sending back the list of found URL's, send back the one URL we want.
- # But the selection interface chokes on a single value, so send two of the same item.
- #vals=set()
- #vals.add("one")
- #vals.add("two")
- # vals.add(_CTAT_CentrifugeDownload_URL)
- # vals = ("one", "onemore", "/path/to/one")
- vals = [dict(name="one", value="onemore", path="/path/to/one")]
+ # 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.
+ vals.append((_CTAT_CentrifugeDir_Name, _CTAT_CentrifugeDownload_URL, True))
print "The items in vals are:"
print str(vals)
- return vals # works kind of, but nothing is printed in the pull down list.
- # return tuple(vals)
- # return tuple(filelist_parser.filenames)
- # return ("one","two") # only prints 'o' and 't'.
+ return vals
# The following was used by the example program to get input parameters through the json.
# Just leaving here for reference.
@@ -186,7 +191,8 @@
# 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.
- command = "curl {:s} | tar -xzvf - -C {:s}".format(src_location, cannonical_destination)
+ # 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
@@ -232,7 +238,7 @@
def main():
#Parse Command Line
- print "At start before parsing arguments."
+ # 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.')
@@ -255,12 +261,13 @@
# target_directory = params['output_data'][0]['extra_files_path']
# os.mkdir(target_directory)
- print "Arguments are parsed."
- print "download location is {:s}".format(str(args.download_location))
+ # 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}".format(str(args.destination_path))
+ 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 = \
@@ -268,14 +275,45 @@
destination=args.destination_path, \
force_download=args.force_download)
else:
- index_directory = args.destination_path
- if not os.path.exists(index_directory):
- raise ValueError("Cannot find the Centrifuge Index. " + \
+ 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))
- # FIX - Check if there is an actual Centrifuge Index in there.
+ # 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 != ""):
@@ -284,20 +322,25 @@
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 = args.display_name
+ 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
+ unique_id = root_index_dirname + datetime_stamp
else:
- unique_id = _CTAT_CentrifugeDir_Name
+ 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_directory)
+ 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_centrifuge_index'] = []
- data_table_entry = dict(value=unique_id, name=display_name, path=index_directory)
- data_manager_dict['data_tables']['ctat_centrifuge_index'].append(data_table_entry)
+ 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))
diff -r 9f99eb3aebfb -r bf41e354f359 data_manager/add_ctat_centrifuge_index.xml
--- a/data_manager/add_ctat_centrifuge_index.xml Fri Apr 27 07:24:29 2018 -0400
+++ b/data_manager/add_ctat_centrifuge_index.xml Tue May 01 09:31:18 2018 -0400
@@ -43,13 +43,18 @@
However, I have not been able to figure out how to send information back correctly
from the function and there is no documentation that I have found showing how to do it.
- -->
+ dynamic_options="get_ctat_centrifuge_index_locations()"
+ help="Select a Centrifuge Index to Download." />
+ Hard coded version.
+ -->
+