Mercurial > repos > iuc > data_manager_mothur_toolsuite
diff data_manager/fetch_mothur_reference_data.py @ 0:ab7a7e798c34 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
| author | iuc |
|---|---|
| date | Mon, 06 Nov 2017 06:21:50 -0500 |
| parents | |
| children | aec831b54a5b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/fetch_mothur_reference_data.py Mon Nov 06 06:21:50 2017 -0500 @@ -0,0 +1,560 @@ +#!/usr/bin/env python +# +# Data manager for reference data for the 'mothur_toolsuite' Galaxy tools +import json +import optparse +import os +import shutil +import sys +import tarfile +import tempfile +import urllib2 +import zipfile + +# When extracting files from archives, skip names that +# start with the following strings +IGNORE_PATHS = ('.', '__MACOSX/', '__') + +# Map file extensions to data table names +MOTHUR_FILE_TYPES = {".map": "map", + ".fasta": "aligndb", + ".align": "aligndb", + ".pat": "lookup", + ".tax": "taxonomy"} + +# Reference data URLs +MOTHUR_REFERENCE_DATA = { + # Look up data + # http://www.mothur.org/wiki/Lookup_files + "lookup_titanium": { + "GS FLX Titanium": ["http://www.mothur.org/w/images/9/96/LookUp_Titanium.zip", ] + }, + "lookup_gsflx": { + "GSFLX": ["http://www.mothur.org/w/images/8/84/LookUp_GSFLX.zip", ] + }, + "lookup_gs20": { + "GS20": ["http://www.mothur.org/w/images/7/7b/LookUp_GS20.zip", ] + }, + # RDP reference files + # http://www.mothur.org/wiki/RDP_reference_files + "RDP_v16": { + "16S rRNA RDP training set 16": + ["https://mothur.org/w/images/d/dc/Trainset16_022016.rdp.tgz", ], + "16S rRNA PDS training set 16": + ["https://mothur.org/w/images/c/c3/Trainset16_022016.pds.tgz", ], + }, + "RDP_v14": { + "16S rRNA RDP training set 14": + ["https://mothur.org/w/images/6/6c/Trainset14_032015.rdp.tgz", ], + "16S rRNA PDS training set 14": + ["https://mothur.org/w/images/8/88/Trainset14_032015.pds.tgz", ], + }, + "RDP_v10": { + "16S rRNA RDP training set 10": + ["http://www.mothur.org/w/images/b/b5/Trainset10_082014.rdp.tgz", ], + "16S rRNA PDS training set 10": + ["http://www.mothur.org/w/images/2/24/Trainset10_082014.pds.tgz", ], + }, + "RDP_v9": { + "16S rRNA RDP training set 9": + ["http://www.mothur.org/w/images/7/72/Trainset9_032012.rdp.zip", ], + "16S rRNA PDS training set 9": + ["http://www.mothur.org/w/images/5/59/Trainset9_032012.pds.zip", ], + }, + "RDP_v7": { + "16S rRNA RDP training set 7": + ["http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip", ], + "16S rRNA PDS training set 7": + ["http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip", ], + "8S rRNA Fungi training set 7": + ["http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip", ], + }, + "RDP_v6": { + "RDP training set 6": + ["http://www.mothur.org/w/images/4/49/RDPTrainingSet.zip", ], + }, + # Silva reference files + # http://www.mothur.org/wiki/Silva_reference_files + "silva_release_128": { + "SILVA release 128": + ["https://mothur.org/w/images/b/b4/Silva.nr_v128.tgz", + "https://mothur.org/w/images/a/a4/Silva.seed_v128.tgz", ], + }, + "silva_release_123": { + "SILVA release 123": + ["https://mothur.org/w/images/b/be/Silva.nr_v123.tgz", + "https://mothur.org/w/images/1/15/Silva.seed_v123.tgz", ], + }, + "silva_release_119": { + "SILVA release 119": + ["http://www.mothur.org/w/images/2/27/Silva.nr_v119.tgz", + "http://www.mothur.org/w/images/5/56/Silva.seed_v119.tgz", ], + }, + "silva_release_102": { + "SILVA release 102": + ["http://www.mothur.org/w/images/9/98/Silva.bacteria.zip", + "http://www.mothur.org/w/images/3/3c/Silva.archaea.zip", + "http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip", ], + }, + "silva_gold_bacteria": { + "SILVA gold": + ["http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip", ], + }, + # Greengenes + # http://www.mothur.org/wiki/Greengenes-formatted_databases + "greengenes_August2013": { + "Greengenes August 2013": + ["http://www.mothur.org/w/images/1/19/Gg_13_8_99.refalign.tgz", + "http://www.mothur.org/w/images/6/68/Gg_13_8_99.taxonomy.tgz", ], + }, + "greengenes_May2013": { + "Greengenes May 2013": + ["http://www.mothur.org/w/images/c/cd/Gg_13_5_99.refalign.tgz", + "http://www.mothur.org/w/images/9/9d/Gg_13_5_99.taxonomy.tgz", ], + }, + "greengenes_old": { + "Greengenes pre-May 2013": + ["http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip", + "http://www.mothur.org/w/images/1/16/Greengenes.tax.tgz", ], + }, + "greengenes_gold_alignment": { + "Greengenes gold alignment": + ["http://www.mothur.org/w/images/2/21/Greengenes.gold.alignment.zip", ], + }, + # Secondary structure maps + # http://www.mothur.org/wiki/Secondary_structure_map + "secondary_structure_maps_silva": { + "SILVA": + ["http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip", ], + }, + "secondary_structure_maps_greengenes": { + "Greengenes": + ["http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip", ], + }, + # Lane masks: not used here? + "lane_masks": { + "Greengenes-compatible": + ["http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter", + "http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter", + "http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter", ], + "SILVA-compatible": + ["http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter", ] + }, +} + + +# Utility functions for interacting with Galaxy JSON +def read_input_json(jsonfile): + """Read the JSON supplied from the data manager tool + + Returns a tuple (param_dict,extra_files_path) + + 'param_dict' is an arbitrary dictionary of parameters + input into the tool; 'extra_files_path' is the path + to a directory where output files must be put for the + receiving data manager to pick them up. + + NB the directory pointed to by 'extra_files_path' + doesn't exist initially, it is the job of the script + to create it if necessary. + + """ + params = json.loads(open(jsonfile).read()) + return (params['param_dict'], + params['output_data'][0]['extra_files_path']) + + +# Utility functions for creating data table dictionaries +# +# Example usage: +# >>> d = create_data_tables_dict() +# >>> add_data_table(d,'my_data') +# >>> add_data_table_entry(dict(dbkey='hg19',value='human')) +# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse')) +# >>> print str(json.dumps(d)) +def create_data_tables_dict(): + """Return a dictionary for storing data table information + + Returns a dictionary that can be used with 'add_data_table' + and 'add_data_table_entry' to store information about a + data table. It can be converted to JSON to be sent back to + the data manager. + + """ + d = {} + d['data_tables'] = {} + return d + + +def add_data_table(d, table): + """Add a data table to the data tables dictionary + + Creates a placeholder for a data table called 'table'. + + """ + d['data_tables'][table] = [] + + +def add_data_table_entry(d, table, entry): + """Add an entry to a data table + + Appends an entry to the data table 'table'. 'entry' + should be a dictionary where the keys are the names of + columns in the data table. + + Raises an exception if the named data table doesn't + exist. + + """ + try: + d['data_tables'][table].append(entry) + except KeyError: + raise Exception("add_data_table_entry: no table '%s'" % table) + + +# Utility functions for downloading and unpacking archive files +def download_file(url, target=None, wd=None): + """Download a file from a URL + + Fetches a file from the specified URL. + + If 'target' is specified then the file is saved to this + name; otherwise it's saved as the basename of the URL. + + If 'wd' is specified then it is used as the 'working + directory' where the file will be save on the local + system. + + Returns the name that the file is saved with. + + """ + print "Downloading %s" % url + if not target: + target = os.path.basename(url) + if wd: + target = os.path.join(wd, target) + print "Saving to %s" % target + open(target, 'wb').write(urllib2.urlopen(url).read()) + return target + + +def unpack_zip_archive(filen, wd=None): + """Extract files from a ZIP archive + + Given a ZIP archive, extract the files it contains + and return a list of the resulting file names and + paths. + + 'wd' specifies the working directory to extract + the files to, otherwise they are extracted to the + current working directory. + + Once all the files are extracted the ZIP archive + file is deleted from the file system. + + """ + if not zipfile.is_zipfile(filen): + print "%s: not ZIP formatted file" + return [filen] + file_list = [] + z = zipfile.ZipFile(filen) + for name in z.namelist(): + if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False): + print "Ignoring %s" % name + continue + if wd: + target = os.path.join(wd, name) + else: + target = name + if name.endswith('/'): + # Make directory + print "Creating dir %s" % target + try: + os.makedirs(target) + except OSError: + pass + else: + # Extract file + print "Extracting %s" % name + try: + os.makedirs(os.path.dirname(target)) + except OSError: + pass + open(target, 'wb').write(z.read(name)) + file_list.append(target) + print "Removing %s" % filen + os.remove(filen) + return file_list + + +def unpack_tar_archive(filen, wd=None): + """Extract files from a TAR archive + + Given a TAR archive (which optionally can be + compressed with either gzip or bz2), extract the + files it contains and return a list of the + resulting file names and paths. + + 'wd' specifies the working directory to extract + the files to, otherwise they are extracted to the + current working directory. + + Once all the files are extracted the TAR archive + file is deleted from the file system. + + """ + file_list = [] + if not tarfile.is_tarfile(filen): + print "%s: not TAR file" + return [filen] + t = tarfile.open(filen) + for name in t.getnames(): + # Check for unwanted files + if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False): + print "Ignoring %s" % name + continue + # Extract file + print "Extracting %s" % name + t.extract(name, wd) + if wd: + target = os.path.join(wd, name) + else: + target = name + file_list.append(target) + print "Removing %s" % filen + os.remove(filen) + return file_list + + +def unpack_archive(filen, wd=None): + """Extract files from an archive + + Wrapper function that calls the appropriate + unpacking function depending on the archive + type, and returns a list of files that have + been extracted. + + 'wd' specifies the working directory to extract + the files to, otherwise they are extracted to the + current working directory. + + """ + print "Unpack %s" % filen + ext = os.path.splitext(filen)[1] + print "Extension: %s" % ext + if ext == ".zip": + return unpack_zip_archive(filen, wd=wd) + elif ext == ".tgz": + return unpack_tar_archive(filen, wd=wd) + else: + return [filen] + + +def fetch_files(urls, wd=None, files=None): + """Download and unpack files from a list of URLs + + Given a list of URLs, download and unpack each + one, and return a list of the extracted files. + + 'wd' specifies the working directory to extract + the files to, otherwise they are extracted to the + current working directory. + + If 'files' is given then the list of extracted + files will be appended to this list before being + returned. + + """ + if files is None: + files = [] + for url in urls: + filen = download_file(url, wd=wd) + files.extend(unpack_archive(filen, wd=wd)) + return files + + +# Utility functions specific to the Mothur reference data +def identify_type(filen): + """Return the data table name based on the file name + + """ + ext = os.path.splitext(filen)[1] + try: + return MOTHUR_FILE_TYPES[ext] + except KeyError: + print "WARNING: unknown file type for " + filen + ", skipping" + return None + + +def get_name(filen): + """Generate a descriptive name based on the file name + """ + # type_ = identify_type(filen) + name = os.path.splitext(os.path.basename(filen))[0] + for delim in ('.', '_'): + name = name.replace(delim, ' ') + return name + + +def fetch_from_mothur_website(data_tables, target_dir, datasets): + """Fetch reference data from the Mothur website + + For each dataset in the list 'datasets', download (and if + necessary unpack) the related files from the Mothur website, + copy them to the data manager's target directory, and add + references to the files to the appropriate data table. + + The 'data_tables' dictionary should have been created using + the 'create_data_tables_dict' and 'add_data_table' functions. + + Arguments: + data_tables: a dictionary containing the data table info + target_dir: directory to put the downloaded files + datasets: a list of dataset names corresponding to keys in + the MOTHUR_REFERENCE_DATA dictionary + """ + # Make working dir + wd = tempfile.mkdtemp(suffix=".mothur", dir=os.getcwd()) + print "Working dir %s" % wd + # Iterate over all requested reference data URLs + for dataset in datasets: + print "Handling dataset '%s'" % dataset + for name in MOTHUR_REFERENCE_DATA[dataset]: + for f in fetch_files(MOTHUR_REFERENCE_DATA[dataset][name], wd=wd): + type_ = identify_type(f) + entry_name = "%s (%s)" % (os.path.splitext(os.path.basename(f))[0], name) + print "%s\t\'%s'\t.../%s" % (type_, entry_name, os.path.basename(f)) + if type_ is not None: + # Move to target dir + ref_data_file = os.path.basename(f) + f1 = os.path.join(target_dir, ref_data_file) + print "Moving %s to %s" % (f, f1) + os.rename(f, f1) + # Add entry to data table + table_name = "mothur_%s" % type_ + add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file)) + # Remove working dir + print "Removing %s" % wd + shutil.rmtree(wd) + + +def files_from_filesystem_paths(paths): + """Return list of file paths from arbitrary input paths + + Given a list of filesystem paths, return a list of + full paths corresponding to all files found recursively + from under those paths. + + """ + # Collect files to add + files = [] + for path in paths: + path = os.path.abspath(path) + print "Examining '%s'..." % path + if os.path.isfile(path): + # Store full path for file + files.append(path) + elif os.path.isdir(path): + # Descend into directory and collect the files + for f in os.listdir(path): + files.extend(files_from_filesystem_paths((os.path.join(path, f), ))) + else: + print "Not a file or directory, ignored" + return files + + +def import_from_server(data_tables, target_dir, paths, description, link_to_data=False): + """Import reference data from filesystem paths + + Creates references to the specified file(s) on the Galaxy + server in the appropriate data table (determined from the + file extension). + + The 'data_tables' dictionary should have been created using + the 'create_data_tables_dict' and 'add_data_table' functions. + + Arguments: + data_tables: a dictionary containing the data table info + target_dir: directory to put copy or link to the data file + paths: list of file and/or directory paths to import + description: text to associate with the files + link_to_data: boolean, if False then copy the data file + into Galaxy (default); if True then make a symlink to + the data file + + """ + # Collect list of files based on input paths + files = files_from_filesystem_paths(paths) + # Handle each file individually + for f in files: + type_ = identify_type(f) + if type_ is None: + print "%s: unrecognised type, skipped" % f + continue + ref_data_file = os.path.basename(f) + target_file = os.path.join(target_dir, ref_data_file) + entry_name = "%s" % os.path.splitext(ref_data_file)[0] + if description: + entry_name += " (%s)" % description + print "%s\t\'%s'\t.../%s" % (type_, entry_name, ref_data_file) + # Link to or copy the data + if link_to_data: + os.symlink(f, target_file) + else: + shutil.copyfile(f, target_file) + # Add entry to data table + table_name = "mothur_%s" % type_ + add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file)) + + +if __name__ == "__main__": + print "Starting..." + + # Read command line + parser = optparse.OptionParser() + parser.add_option('--source', action='store', dest='data_source') + parser.add_option('--datasets', action='store', dest='datasets', default='') + parser.add_option('--paths', action='store', dest='paths', default=[]) + parser.add_option('--description', action='store', dest='description', default='') + parser.add_option('--link', action='store_true', dest='link_to_data') + options, args = parser.parse_args() + print "options: %s" % options + print "args : %s" % args + + # Check for JSON file + if len(args) != 1: + sys.stderr.write("Need to supply JSON file name") + sys.exit(1) + + jsonfile = args[0] + + # Read the input JSON + params, target_dir = read_input_json(jsonfile) + + # Make the target directory + print "Making %s" % target_dir + os.mkdir(target_dir) + + # Set up data tables dictionary + data_tables = create_data_tables_dict() + add_data_table(data_tables, 'mothur_lookup') + add_data_table(data_tables, 'mothur_aligndb') + add_data_table(data_tables, 'mothur_map') + add_data_table(data_tables, 'mothur_taxonomy') + + # Fetch data from specified data sources + if options.data_source == 'mothur_website': + datasets = options.datasets.split(',') + fetch_from_mothur_website(data_tables, target_dir, datasets) + elif options.data_source == 'filesystem_paths': + # Check description text + description = options.description.strip() + # Get list of paths (need to remove any escapes for '\n' and '\r' + # that might have been inserted by Galaxy) + paths = options.paths.replace('__cn__', '\n').replace('__cr__', '\r').split() + import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data) + # Write output JSON + print "Outputting JSON" + print str(json.dumps(data_tables)) + open(jsonfile, 'wb').write(json.dumps(data_tables)) + print "Done."