def persist_uploads(params):
"""
Turn any uploads in the submitted form to persisted files.
"""
if 'files' in params:
new_files = []
for upload_dataset in params['files']:
f = upload_dataset['file_data']
if isinstance(f, FieldStorage):
assert not isinstance(f.file, StringIO.StringIO)
assert f.file.name != '<fdopen>'
local_filename = util.mkstemp_ln(f.file.name,
'upload_file_data_')
f.file.close()
upload_dataset['file_data'] = dict(
filename=f.filename, local_filename=local_filename)
elif type(f) == dict and 'local_filename' not in f:
raise Exception(
'Uploaded file was encoded in a way not understood by Galaxy.'
)
if upload_dataset[
'url_paste'] and upload_dataset['url_paste'].strip() != '':
upload_dataset[
'url_paste'], is_multi_byte = datatypes.sniff.stream_to_file(
StringIO.StringIO(upload_dataset['url_paste']),
prefix="strio_url_paste_")
else:
upload_dataset['url_paste'] = None
new_files.append(upload_dataset)
params['files'] = new_files
return params
def persist_uploads(params, trans):
"""
Turn any uploads in the submitted form to persisted files.
"""
if 'files' in params:
new_files = []
for upload_dataset in params['files']:
f = upload_dataset['file_data']
if isinstance(f, cgi_FieldStorage):
assert not isinstance(f.file, StringIO)
assert f.file.name != '<fdopen>'
local_filename = util.mkstemp_ln(f.file.name, 'upload_file_data_')
f.file.close()
upload_dataset['file_data'] = dict(filename=f.filename,
local_filename=local_filename)
elif type(f) == dict and 'local_filename' not in f:
raise Exception('Uploaded file was encoded in a way not understood by Galaxy.')
if 'url_paste' in upload_dataset and upload_dataset['url_paste'] and upload_dataset['url_paste'].strip() != '':
upload_dataset['url_paste'] = datatypes.sniff.stream_to_file(
StringIO(validate_url(upload_dataset['url_paste'], trans.app.config.fetch_url_whitelist_ips)),
prefix="strio_url_paste_"
)
else:
upload_dataset['url_paste'] = None
new_files.append(upload_dataset)
params['files'] = new_files
return params
def persist_uploads(params):
"""
Turn any uploads in the submitted form to persisted files.
"""
if "files" in params:
new_files = []
for upload_dataset in params["files"]:
f = upload_dataset["file_data"]
if isinstance(f, FieldStorage):
assert not isinstance(f.file, StringIO.StringIO)
assert f.file.name != "<fdopen>"
local_filename = util.mkstemp_ln(f.file.name, "upload_file_data_")
f.file.close()
upload_dataset["file_data"] = dict(filename=f.filename, local_filename=local_filename)
elif type(f) == dict and "local_filename" not in f:
raise Exception("Uploaded file was encoded in a way not understood by Galaxy.")
if upload_dataset["url_paste"] and upload_dataset["url_paste"].strip() != "":
upload_dataset["url_paste"], is_multi_byte = datatypes.sniff.stream_to_file(
StringIO.StringIO(upload_dataset["url_paste"]), prefix="strio_url_paste_"
)
else:
upload_dataset["url_paste"] = None
new_files.append(upload_dataset)
params["files"] = new_files
return params
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 )
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 not ok:
return {
"err_msg": message,
"content_alert": content_alert_str
}
else:
return {
"message": message,
"content_alert": content_alert_str
}
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)
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 not ok:
return {"err_msg": message, "content_alert": content_alert_str}
else:
return {"message": message, "content_alert": content_alert_str}