def do_slow_split( cls, input_datasets, subdir_generator_function, split_params):
# count the sequences so we can split
# TODO: if metadata is present, take the number of lines / 4
if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences is not None:
total_sequences = input_datasets[0].metadata.sequences
else:
input_file = input_datasets[0].file_name
compress = is_gzip(input_file)
if compress:
# gzip is really slow before python 2.7!
in_file = gzip.GzipFile(input_file, 'r')
else:
# TODO
# if a file is not compressed, seek locations can be calculated and stored
# ideally, this would be done in metadata
# TODO
# Add BufferedReader if python 2.7?
in_file = open(input_file, 'rt')
total_sequences = long(0)
for i, line in enumerate(in_file):
total_sequences += 1
in_file.close()
total_sequences /= 4
sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
return cls.write_split_files(input_datasets, None, subdir_generator_function, sequences_per_file)
def get_headers( fname, sep, count=60, is_multi_byte=False ):
"""
Returns a list with the first 'count' lines split by 'sep'
>>> fname = get_test_fname('complete.bed')
>>> get_headers(fname,'\\t')
[['chr7', '127475281', '127491632', 'NM_000230', '0', '+', '127486022', '127488767', '0', '3', '29,172,3225,', '0,10713,13126,'], ['chr7', '127486011', '127488900', 'D49487', '0', '+', '127486022', '127488767', '0', '2', '155,490,', '0,2399']]
"""
headers = []
compressed_gzip = is_gzip(fname)
compressed_bzip2 = is_bz2(fname)
try:
if compressed_gzip:
in_file = gzip.GzipFile(fname, 'r')
elif compressed_bzip2:
in_file = bz2.BZ2File(fname, 'r')
else:
in_file = open(fname, 'rt')
for idx, line in enumerate(in_file):
line = line.rstrip('\n\r')
if is_multi_byte:
# TODO: fix this - sep is never found in line
line = unicodify( line, 'utf-8' )
sep = sep.encode( 'utf-8' )
headers.append( line.split(sep) )
if idx == count:
break
finally:
in_file.close()
return headers
def sniff( self, filename ):
"""
Determines whether the file is in ELAND export format
A file in ELAND export format consists of lines of tab-separated data.
There is no header.
Rules for sniffing as True::
- There must be 22 columns on each line
- LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct
- We will only check that up to the first 5 alignments are correctly formatted.
"""
try:
compress = is_gzip(filename)
if compress:
fh = gzip.GzipFile(filename, 'r')
else:
fh = open( filename )
count = 0
while True:
line = fh.readline()
line = line.strip()
if not line:
break # EOF
if line:
linePieces = line.split('\t')
if len(linePieces) != 22:
return False
try:
if long(linePieces[1]) < 0:
raise Exception('Out of range')
if long(linePieces[2]) < 0:
raise Exception('Out of range')
if long(linePieces[3]) < 0:
raise Exception('Out of range')
int(linePieces[4])
int(linePieces[5])
# can get a lot more specific
except ValueError:
fh.close()
return False
count += 1
if count == 5:
break
if count > 0:
fh.close()
return True
except:
pass
fh.close()
return False
def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
"""Return the display-safe contents of a repository file for display in a browser."""
safe_str = ''
if not is_path_browsable(app, file_path, repository_id, is_admin):
log.warning('Request tries to access a file outside of the repository location. File path: %s', file_path)
return 'Invalid file path'
# Symlink targets are checked by is_path_browsable
if os.path.islink(file_path):
safe_str = 'link to: ' + basic_util.to_html_string(os.readlink(file_path))
return safe_str
elif checkers.is_gzip(file_path):
return '<br/>gzip compressed file<br/>'
elif checkers.is_bz2(file_path):
return '<br/>bz2 compressed file<br/>'
elif checkers.is_zip(file_path):
return '<br/>zip compressed file<br/>'
elif checkers.check_binary(file_path):
return '<br/>Binary file<br/>'
else:
for i, line in enumerate(open(file_path)):
safe_str = '%s%s' % (safe_str, basic_util.to_html_string(line))
# Stop reading after string is larger than MAX_CONTENT_SIZE.
if len(safe_str) > MAX_CONTENT_SIZE:
large_str = \
'<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \
util.nice_size(MAX_CONTENT_SIZE)
safe_str = '%s%s' % (safe_str, large_str)
break
if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
# Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
# This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
join_by_str = \
"<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \
util.nice_size(basic_util.MAX_DISPLAY_SIZE)
safe_str = util.shrink_string_by_size(safe_str,
basic_util.MAX_DISPLAY_SIZE,
join_by=join_by_str,
left_larger=True,
beginning_on_size_error=True)
return safe_str
def process_split_file(data):
"""
This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine)
to create the input files for the Task. The parameters:
data - a dict containing the contents of the split file
"""
args = data['args']
input_name = data['input_name']
output_name = data['output_name']
start_sequence = long(args['start_sequence'])
sequence_count = long(args['num_sequences'])
if 'toc_file' in args:
toc_file = json.load(open(args['toc_file'], 'r'))
commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count)
else:
commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count)
for cmd in commands:
if 0 != os.system(cmd):
raise Exception("Executing '%s' failed" % cmd)
return True
def looks_like_xml(path, regex=TOOL_REGEX):
full_path = os.path.abspath(path)
if not full_path.endswith(".xml"):
return False
if not os.path.getsize(full_path):
return False
if(checkers.check_binary(full_path) or
checkers.check_image(full_path) or
checkers.is_gzip(full_path) or
checkers.is_bz2(full_path) or
checkers.is_zip(full_path)):
return False
with open(path, "r") as f:
start_contents = f.read(5 * 1024)
if regex.search(start_contents):
return True
return False
def main():
"""
The format of the file is JSON::
{ "sections" : [
{ "start" : "x", "end" : "y", "sequences" : "z" },
...
]}
This works only for UNCOMPRESSED fastq files. The Python GzipFile does not provide seekable
offsets via tell(), so clients just have to split the slow way
"""
input_fname = sys.argv[1]
if is_gzip(input_fname):
print('Conversion is only possible for uncompressed files')
sys.exit(1)
out_file = open(sys.argv[2], 'w')
current_line = 0
sequences = 1000000
lines_per_chunk = 4 * sequences
chunk_begin = 0
in_file = open(input_fname)
out_file.write('{"sections" : [')
for line in in_file:
current_line += 1
if 0 == current_line % lines_per_chunk:
chunk_end = in_file.tell()
out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences))
chunk_begin = chunk_end
chunk_end = in_file.tell()
out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4))
out_file.write(']}\n')
def looks_like_a_tool_xml(path):
"""Quick check to see if a file looks like it may be a Galaxy XML tool file."""
full_path = os.path.abspath(path)
if not full_path.endswith(".xml"):
return False
if not os.path.getsize(full_path):
return False
if(checkers.check_binary(full_path) or
checkers.check_image(full_path) or
checkers.is_gzip(full_path) or
checkers.is_bz2(full_path) or
checkers.is_zip(full_path)):
return False
with open(path, "r") as f:
start_contents = f.read(5 * 1024)
if TOOL_REGEX.search(start_contents):
return True
return False
def is_data_index_sample_file( file_path ):
"""
Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when
a tool shed repository is being installed into a Galaxy instance.
"""
# Currently most data index files are tabular, so check that first. We'll assume that
# if the file is tabular, it's ok to copy.
if is_column_based( file_path ):
return True
# If the file is any of the following, don't copy it.
if checkers.check_html( file_path ):
return False
if checkers.check_image( file_path ):
return False
if checkers.check_binary( name=file_path ):
return False
if checkers.is_bz2( file_path ):
return False
if checkers.is_gzip( file_path ):
return False
if checkers.check_zip( file_path ):
return False
# Default to copying the file if none of the above are true.
return True
def set_meta( self, dataset, overwrite=True, skip=None, max_data_lines=5, **kwd ):
if dataset.has_data():
compress = is_gzip(dataset.file_name)
if compress:
dataset_fh = gzip.GzipFile(dataset.file_name, 'r')
else:
dataset_fh = open( dataset.file_name )
lanes = {}
tiles = {}
barcodes = {}
reads = {}
# Should always read the entire file (until we devise a more clever way to pass metadata on)
# if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
# If the dataset is larger than optional_metadata, just count comment lines.
# dataset.metadata.data_lines = None
# else:
# Otherwise, read the whole thing and set num data lines.
for i, line in enumerate(dataset_fh):
if line:
linePieces = line.split('\t')
if len(linePieces) != 22:
raise Exception('%s:%d:Corrupt line!' % (dataset.file_name, i))
lanes[linePieces[2]] = 1
tiles[linePieces[3]] = 1
barcodes[linePieces[6]] = 1
reads[linePieces[7]] = 1
pass
dataset.metadata.data_lines = i + 1
dataset_fh.close()
dataset.metadata.comment_lines = 0
dataset.metadata.columns = 21
dataset.metadata.column_types = ['str', 'int', 'int', 'int', 'int', 'int', 'str', 'int', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str']
dataset.metadata.lanes = lanes.keys()
dataset.metadata.tiles = ["%04d" % int(t) for t in tiles.keys()]
dataset.metadata.barcodes = filter(lambda x: x != '0', barcodes.keys()) + ['NoIndex' for x in barcodes.keys() if x == '0']
dataset.metadata.reads = reads.keys()
def create_changeset_revision( self, trans, id, payload, **kwd ):
"""
POST /api/repositories/{encoded_repository_id}/changeset_revision
Create a new tool shed repository commit - leaving PUT on parent
resource open for updating meta-attributes of the repository (and
Galaxy doesn't allow PUT multipart data anyway
https://trello.com/c/CQwmCeG6).
:param id: the encoded id of the Repository object
The following parameters may be included in the payload.
:param commit_message: hg commit message for update.
"""
# Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False )
tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False )
repository = suc.get_repository_in_tool_shed( trans.app, id )
if not ( trans.user_is_admin() or
trans.app.security_agent.user_can_administer_repository( trans.user, repository ) or
trans.app.security_agent.can_push( trans.app, trans.user, repository ) ):
trans.response.status = 400
return {
"err_msg": "You do not have permission to update this repository.",
}
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
upload_point = commit_util.get_upload_point( repository, **kwd )
tip = repository.tip( trans.app )
file_data = payload.get('file')
# Code stolen from gx's upload_common.py
if isinstance( file_data, FieldStorage ):
assert not isinstance( file_data.file, StringIO.StringIO )
assert file_data.file.name != '<fdopen>'
local_filename = util.mkstemp_ln( file_data.file.name, 'upload_file_data_' )
file_data.file.close()
file_data = dict( filename=file_data.filename,
local_filename=local_filename )
elif type( file_data ) == dict and 'local_filename' not in file_data:
raise Exception( 'Uploaded file was encoded in a way not understood.' )
commit_message = kwd.get( 'commit_message', 'Uploaded' )
uploaded_file = open(file_data['local_filename'], 'rb')
uploaded_file_name = file_data['local_filename']
isgzip = False
isbz2 = False
isgzip = checkers.is_gzip( uploaded_file_name )
if not isgzip:
isbz2 = checkers.is_bz2( uploaded_file_name )
if ( isgzip or isbz2 ):
# Open for reading with transparent compression.
tar = tarfile.open( uploaded_file_name, 'r:*' )
else:
tar = tarfile.open( uploaded_file_name )
new_repo_alert = False
remove_repo_files_not_in_tar = True
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
repository_content_util.upload_tar(
trans,
rdah,
tdah,
repository,
tar,
uploaded_file,
upload_point,
remove_repo_files_not_in_tar,
commit_message,
new_repo_alert
)
if ok:
# Update the repository files for browsing.
hg_util.update_repository( repo )
# Get the new repository tip.
if tip == repository.tip( trans.app ):
trans.response.status = 400
message = 'No changes to repository.'
ok = False
else:
rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
user=trans.user,
repository=repository )
status, error_message = \
rmm.set_repository_metadata_due_to_new_tip( trans.request.host,
content_alert_str=content_alert_str,
**kwd )
if error_message:
ok = False
trans.response.status = 500
message = error_message
else:
trans.response.status = 500
if os.path.exists( uploaded_file_name ):
os.remove( uploaded_file_name )
if not ok:
return {
"err_msg": message,
"content_alert": content_alert_str
}
else:
return {
"message": message,
"content_alert": content_alert_str
}
def upload(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
commit_message = escape(kwd.get('commit_message', 'Uploaded'))
repository_id = kwd.get('repository_id', '')
repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
repo_dir = repository.repo_path(trans.app)
repo = hg_util.get_repo_for_repository(trans.app, repository=None, repo_path=repo_dir, create=False)
uncompress_file = util.string_as_bool(kwd.get('uncompress_file', 'true'))
remove_repo_files_not_in_tar = util.string_as_bool(kwd.get('remove_repo_files_not_in_tar', 'true'))
uploaded_file = None
upload_point = commit_util.get_upload_point(repository, **kwd)
tip = repository.tip(trans.app)
file_data = kwd.get('file_data', '')
url = kwd.get('url', '')
# Part of the upload process is sending email notification to those that have registered to
# receive them. One scenario occurs when the first change set is produced for the repository.
# See the suc.handle_email_alerts() method for the definition of the scenarios.
new_repo_alert = repository.is_new(trans.app)
uploaded_directory = None
if kwd.get('upload_button', False):
if file_data == '' and url == '':
message = 'No files were entered on the upload form.'
status = 'error'
uploaded_file = None
elif url and url.startswith('hg'):
# Use mercurial clone to fetch repository, contents will then be copied over.
uploaded_directory = tempfile.mkdtemp()
repo_url = 'http%s' % url[len('hg'):]
repo_url = repo_url.encode('ascii', 'replace')
try:
commands.clone(hg_util.get_configured_ui(), repo_url, uploaded_directory)
except Exception as e:
message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string(str(e))
status = 'error'
basic_util.remove_dir(uploaded_directory)
uploaded_directory = None
elif url:
valid_url = True
try:
stream = requests.get(url, stream=True)
except Exception as e:
valid_url = False
message = 'Error uploading file via http: %s' % str(e)
status = 'error'
uploaded_file = None
if valid_url:
fd, uploaded_file_name = tempfile.mkstemp()
uploaded_file = open(uploaded_file_name, 'wb')
for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
if chunk:
uploaded_file.write(chunk)
uploaded_file.flush()
uploaded_file_filename = url.split('/')[-1]
isempty = os.path.getsize(os.path.abspath(uploaded_file_name)) == 0
elif file_data not in ('', None):
uploaded_file = file_data.file
uploaded_file_name = uploaded_file.name
uploaded_file_filename = os.path.split(file_data.filename)[-1]
isempty = os.path.getsize(os.path.abspath(uploaded_file_name)) == 0
if uploaded_file or uploaded_directory:
rdah = attribute_handlers.RepositoryDependencyAttributeHandler(trans.app, unpopulate=False)
tdah = attribute_handlers.ToolDependencyAttributeHandler(trans.app, unpopulate=False)
stdtm = ShedToolDataTableManager(trans.app)
ok = True
isgzip = False
isbz2 = False
if uploaded_file:
if uncompress_file:
isgzip = checkers.is_gzip(uploaded_file_name)
if not isgzip:
isbz2 = checkers.is_bz2(uploaded_file_name)
if isempty:
tar = None
istar = False
else:
# Determine what we have - a single file or an archive
try:
if (isgzip or isbz2) and uncompress_file:
# Open for reading with transparent compression.
tar = tarfile.open(uploaded_file_name, 'r:*')
else:
tar = tarfile.open(uploaded_file_name)
istar = True
except tarfile.ReadError as e:
tar = None
istar = False
else:
# Uploaded directory
istar = False
if istar:
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
repository_content_util.upload_tar(
trans,
rdah,
tdah,
repository,
tar,
uploaded_file,
upload_point,
remove_repo_files_not_in_tar,
commit_message,
new_repo_alert
)
elif uploaded_directory:
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_directory(trans,
rdah,
tdah,
repository,
uploaded_directory,
upload_point,
remove_repo_files_not_in_tar,
commit_message,
new_repo_alert)
else:
if (isgzip or isbz2) and uncompress_file:
uploaded_file_filename = commit_util.uncompress(repository,
uploaded_file_name,
uploaded_file_filename,
isgzip=isgzip,
isbz2=isbz2)
if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION and \
uploaded_file_filename != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
ok = False
message = 'Repositories of type <b>Repository suite definition</b> can only contain a single file named '
message += '<b>repository_dependencies.xml</b>.'
elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and \
uploaded_file_filename != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
ok = False
message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named '
message += '<b>tool_dependencies.xml</b>.'
if ok:
if upload_point is not None:
full_path = os.path.abspath(os.path.join(repo_dir, upload_point, uploaded_file_filename))
else:
full_path = os.path.abspath(os.path.join(repo_dir, uploaded_file_filename))
# Move some version of the uploaded file to the load_point within the repository hierarchy.
if uploaded_file_filename in [rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME]:
# Inspect the contents of the file to see if toolshed or changeset_revision attributes
# are missing and if so, set them appropriately.
altered, root_elem, error_message = rdah.handle_tag_attributes(uploaded_file_name)
if error_message:
ok = False
message = error_message
status = 'error'
elif altered:
tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
shutil.move(tmp_filename, full_path)
else:
shutil.move(uploaded_file_name, full_path)
elif uploaded_file_filename in [rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME]:
# Inspect the contents of the file to see if changeset_revision values are
# missing and if so, set them appropriately.
altered, root_elem, error_message = tdah.handle_tag_attributes(uploaded_file_name)
if error_message:
ok = False
message = error_message
status = 'error'
if ok:
if altered:
tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
shutil.move(tmp_filename, full_path)
else:
shutil.move(uploaded_file_name, full_path)
else:
shutil.move(uploaded_file_name, full_path)
if ok:
# See if any admin users have chosen to receive email alerts when a repository is updated.
# If so, check every uploaded file to ensure content is appropriate.
check_contents = commit_util.check_file_contents_for_email_alerts(trans.app)
if check_contents and os.path.isfile(full_path):
content_alert_str = commit_util.check_file_content_for_html_and_images(full_path)
else:
content_alert_str = ''
hg_util.add_changeset(repo.ui, repo, full_path)
# Convert from unicode to prevent "TypeError: array item must be char"
full_path = full_path.encode('ascii', 'replace')
hg_util.commit_changeset(repo.ui,
repo,
full_path_to_changeset=full_path,
username=trans.user.username,
message=commit_message)
if full_path.endswith('tool_data_table_conf.xml.sample'):
# Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded
# by parsing the file and adding new entries to the in-memory trans.app.tool_data_tables
# dictionary.
error, error_message = stdtm.handle_sample_tool_data_table_conf_file(full_path, persist=False)
if error:
message = '%s<br/>%s' % (message, error_message)
# See if the content of the change set was valid.
admin_only = len(repository.downloadable_revisions) != 1
suc.handle_email_alerts(trans.app,
trans.request.host,
repository,
content_alert_str=content_alert_str,
new_repo_alert=new_repo_alert,
admin_only=admin_only)
if ok:
# Update the repository files for browsing.
hg_util.update_repository(repo)
# Get the new repository tip.
if tip == repository.tip(trans.app):
message = 'No changes to repository. '
status = 'warning'
else:
if (isgzip or isbz2) and uncompress_file:
uncompress_str = ' uncompressed and '
else:
uncompress_str = ' '
if uploaded_directory:
source_type = "repository"
source = url
else:
source_type = "file"
source = uploaded_file_filename
message = "The %s <b>%s</b> has been successfully%suploaded to the repository. " % \
(source_type, escape(source), uncompress_str)
if istar and (undesirable_dirs_removed or undesirable_files_removed):
items_removed = undesirable_dirs_removed + undesirable_files_removed
message += " %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) " % items_removed
message += "were removed from the archive. "
if istar and remove_repo_files_not_in_tar and files_to_remove:
if upload_point is not None:
message += " %d files were removed from the repository relative to the selected upload point '%s'. " % \
(len(files_to_remove), upload_point)
else:
message += " %d files were removed from the repository root. " % len(files_to_remove)
rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
user=trans.user,
repository=repository)
status, error_message = \
rmm.set_repository_metadata_due_to_new_tip(trans.request.host,
content_alert_str=content_alert_str,
**kwd)
if error_message:
message = error_message
kwd['message'] = message
if repository.metadata_revisions:
# A repository's metadata revisions are order descending by update_time, so the zeroth revision
# will be the tip just after an upload.
metadata_dict = repository.metadata_revisions[0].metadata
else:
metadata_dict = {}
dd = dependency_display.DependencyDisplayer(trans.app)
if str(repository.type) not in [rt_util.REPOSITORY_SUITE_DEFINITION,
rt_util.TOOL_DEPENDENCY_DEFINITION]:
change_repository_type_message = rt_util.generate_message_for_repository_type_change(trans.app,
repository)
if change_repository_type_message:
message += change_repository_type_message
status = 'warning'
else:
# Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies
# weren't loaded due to a requirement tag mismatch or some other problem. Tool dependency
# definitions can define orphan tool dependencies (no relationship to any tools contained in the
# repository), so warning messages are important because orphans are always valid. The repository
# owner must be warned in case they did not intend to define an orphan dependency, but simply
# provided incorrect information (tool shed, name owner, changeset_revision) for the definition.
orphan_message = dd.generate_message_for_orphan_tool_dependencies(repository, metadata_dict)
if orphan_message:
message += orphan_message
status = 'warning'
# Handle messaging for invalid tool dependencies.
invalid_tool_dependencies_message = dd.generate_message_for_invalid_tool_dependencies(metadata_dict)
if invalid_tool_dependencies_message:
message += invalid_tool_dependencies_message
status = 'error'
# Handle messaging for invalid repository dependencies.
invalid_repository_dependencies_message = \
dd.generate_message_for_invalid_repository_dependencies(metadata_dict,
error_from_tuple=True)
if invalid_repository_dependencies_message:
message += invalid_repository_dependencies_message
status = 'error'
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
stdtm.reset_tool_data_tables()
if uploaded_directory:
basic_util.remove_dir(uploaded_directory)
trans.response.send_redirect(web.url_for(controller='repository',
action='browse_repository',
id=repository_id,
commit_message='Deleted selected files',
message=message,
status=status))
else:
if uploaded_directory:
basic_util.remove_dir(uploaded_directory)
status = 'error'
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
stdtm.reset_tool_data_tables()
return trans.fill_template('/webapps/tool_shed/repository/upload.mako',
repository=repository,
changeset_revision=tip,
url=url,
commit_message=commit_message,
uncompress_file=uncompress_file,
remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
message=message,
status=status)
isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
elif file_data not in ( '', None ):
uploaded_file = file_data.file
uploaded_file_name = uploaded_file.name
uploaded_file_filename = os.path.split( file_data.filename )[ -1 ]
isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
if uploaded_file or uploaded_directory:
rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False )
tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False )
tdtm = data_table_manager.ToolDataTableManager( trans.app )
ok = True
isgzip = False
isbz2 = False
if uploaded_file:
if uncompress_file:
isgzip = checkers.is_gzip( uploaded_file_name )
if not isgzip:
isbz2 = checkers.is_bz2( uploaded_file_name )
if isempty:
tar = None
istar = False
else:
# Determine what we have - a single file or an archive
try:
if ( isgzip or isbz2 ) and uncompress_file:
# Open for reading with transparent compression.
tar = tarfile.open( uploaded_file_name, 'r:*' )
else:
tar = tarfile.open( uploaded_file_name )
istar = True
except tarfile.ReadError, e:
def create_changeset_revision(self, trans, id, payload, **kwd):
"""
POST /api/repositories/{encoded_repository_id}/changeset_revision
Create a new tool shed repository commit - leaving PUT on parent
resource open for updating meta-attributes of the repository (and
Galaxy doesn't allow PUT multipart data anyway
https://trello.com/c/CQwmCeG6).
:param id: the encoded id of the Repository object
The following parameters may be included in the payload.
:param commit_message: hg commit message for update.
"""
# Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
rdah = attribute_handlers.RepositoryDependencyAttributeHandler(
trans.app, unpopulate=False)
tdah = attribute_handlers.ToolDependencyAttributeHandler(
trans.app, unpopulate=False)
repository = suc.get_repository_in_tool_shed(trans.app, id)
if not (trans.user_is_admin()
or trans.app.security_agent.user_can_administer_repository(
trans.user, repository)
or trans.app.security_agent.can_push(trans.app, trans.user,
repository)):
trans.response.status = 400
return {
"err_msg":
"You do not have permission to update this repository.",
}
repo_dir = repository.repo_path(trans.app)
repo = hg_util.get_repo_for_repository(trans.app,
repository=None,
repo_path=repo_dir,
create=False)
upload_point = commit_util.get_upload_point(repository, **kwd)
tip = repository.tip(trans.app)
file_data = payload.get('file')
# Code stolen from gx's upload_common.py
if isinstance(file_data, FieldStorage):
assert not isinstance(file_data.file, StringIO.StringIO)
assert file_data.file.name != '<fdopen>'
local_filename = util.mkstemp_ln(file_data.file.name,
'upload_file_data_')
file_data.file.close()
file_data = dict(filename=file_data.filename,
local_filename=local_filename)
elif type(file_data) == dict and 'local_filename' not in file_data:
raise Exception(
'Uploaded file was encoded in a way not understood.')
commit_message = kwd.get('commit_message', 'Uploaded')
uploaded_file = open(file_data['local_filename'], 'rb')
uploaded_file_name = file_data['local_filename']
isgzip = False
isbz2 = False
isgzip = checkers.is_gzip(uploaded_file_name)
if not isgzip:
isbz2 = checkers.is_bz2(uploaded_file_name)
if (isgzip or isbz2):
# Open for reading with transparent compression.
tar = tarfile.open(uploaded_file_name, 'r:*')
else:
tar = tarfile.open(uploaded_file_name)
new_repo_alert = False
remove_repo_files_not_in_tar = True
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
repository_content_util.upload_tar(
trans,
rdah,
tdah,
repository,
tar,
uploaded_file,
upload_point,
remove_repo_files_not_in_tar,
commit_message,
new_repo_alert
)
if ok:
# Update the repository files for browsing.
hg_util.update_repository(repo)
# Get the new repository tip.
if tip == repository.tip(trans.app):
trans.response.status = 400
message = 'No changes to repository.'
ok = False
else:
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=trans.app, user=trans.user, repository=repository)
status, error_message = \
rmm.set_repository_metadata_due_to_new_tip( trans.request.host,
content_alert_str=content_alert_str,
**kwd )
if error_message:
ok = False
trans.response.status = 500
message = error_message
else:
trans.response.status = 500
if os.path.exists(uploaded_file_name):
os.remove(uploaded_file_name)
if not ok:
return {"err_msg": message, "content_alert": content_alert_str}
else:
return {"message": message, "content_alert": content_alert_str}