Mercurial > repos > iuc > data_manager_mothur_toolsuite
changeset 3:9d09724f2bf1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:51:44 +0000 |
| parents | 0e532fc0a0a6 |
| children | 0db22932bc39 |
| files | data_manager/fetch_mothur_reference_data.py |
| diffstat | 1 files changed, 47 insertions(+), 44 deletions(-) [+] |
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--- a/data_manager/fetch_mothur_reference_data.py Thu Sep 17 09:37:41 2020 +0000 +++ b/data_manager/fetch_mothur_reference_data.py Sun Nov 22 12:51:44 2020 +0000 @@ -160,7 +160,8 @@ to create it if necessary. """ - params = json.loads(open(jsonfile).read()) + with open(jsonfile) as fh: + params = json.load(fh) return (params['param_dict'], params['output_data'][0]['extra_files_path']) @@ -172,7 +173,7 @@ # >>> 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)) +# >>> print(json.dumps(d)) def create_data_tables_dict(): """Return a dictionary for storing data table information @@ -235,7 +236,8 @@ if wd: target = os.path.join(wd, target) print("Saving to %s" % target) - open(target, 'wb').write(urllib2.urlopen(url).read()) + with open(target, 'wb') as fh: + fh.write(urllib2.urlopen(url).read()) return target @@ -258,31 +260,32 @@ 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) + with zipfile.ZipFile(filen) as z: + 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 + with open(target, 'wb') as fh: + fh.write(z.read(name)) + file_list.append(target) print("Removing %s" % filen) os.remove(filen) return file_list @@ -308,20 +311,20 @@ 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) + with tarfile.open(filen) as t: + 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 @@ -556,6 +559,6 @@ import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data) # Write output JSON print("Outputting JSON") - print(json.dumps(data_tables)) - open(jsonfile, 'w').write(json.dumps(data_tables, sort_keys=True)) + with open(jsonfile, 'w') as fh: + json.dump(data_tables, fh, sort_keys=True) print("Done.")