def test_add_dir_and_commit_changeset(tmpdir):
test_init_repository(tmpdir)
path_to_add = tmpdir.mkdir('abc')
(path_to_add / 'test.txt').write('bla')
hg_util.add_changeset(str(tmpdir), str(path_to_add))
hg_util.commit_changeset(str(tmpdir), str(path_to_add), 'testuser',
'testcommit')
return path_to_add
def test_add_file_and_commmit_changeset(tmpdir):
test_init_repository(tmpdir)
path_to_add = (tmpdir / 'test.txt')
path_to_add.write('test')
hg_util.add_changeset(str(tmpdir), str(path_to_add))
hg_util.commit_changeset(str(tmpdir), str(path_to_add), 'testuser',
'testcommit')
return path_to_add
elif os.path.isfile( absolute_selected_file ):
os.remove( absolute_selected_file )
dir = os.path.split( absolute_selected_file )[0]
try:
os.rmdir( dir )
except OSError, e:
# The directory is not empty.
pass
# 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 = check_file_contents_for_email_alerts( app )
for filename_in_archive in filenames_in_archive:
# Check file content to ensure it is appropriate.
if check_contents and os.path.isfile( filename_in_archive ):
content_alert_str += check_file_content_for_html_and_images( filename_in_archive )
hg_util.add_changeset( repo.ui, repo, filename_in_archive )
if filename_in_archive.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 app.tool_data_tables
# dictionary.
tdtm = data_table_manager.ToolDataTableManager( app )
error, message = tdtm.handle_sample_tool_data_table_conf_file( filename_in_archive, persist=False )
if error:
return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
hg_util.commit_changeset( repo.ui,
repo,
full_path_to_changeset=full_path,
username=username,
message=commit_message )
admin_only = len( repository.downloadable_revisions ) != 1
suc.handle_email_alerts( app,
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)
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()
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()
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'):]
cloned_ok, error_message = hg_util.clone_repository(
repo_url, uploaded_directory)
if not cloned_ok:
message = 'Error uploading via mercurial clone: %s' % error_message
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' % util.unicodify(
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:
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_dir, full_path)
hg_util.commit_changeset(
repo_dir,
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_dir)
# Get the new repository tip.
if tip == repository.tip():
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)
def handle_directory_changes(app, host, username, repository, full_path,
filenames_in_archive,
remove_repo_files_not_in_tar, new_repo_alert,
commit_message, undesirable_dirs_removed,
undesirable_files_removed):
repo = hg_util.get_repo_for_repository(app,
repository=repository,
repo_path=None,
create=False)
content_alert_str = ''
files_to_remove = []
filenames_in_archive = [
os.path.join(full_path, name) for name in filenames_in_archive
]
if remove_repo_files_not_in_tar and not repository.is_new(app):
# We have a repository that is not new (it contains files), so discover those files that are in the
# repository, but not in the uploaded archive.
for root, dirs, files in os.walk(full_path):
if root.find('.hg') < 0 and root.find('hgrc') < 0:
for undesirable_dir in UNDESIRABLE_DIRS:
if undesirable_dir in dirs:
dirs.remove(undesirable_dir)
undesirable_dirs_removed += 1
for undesirable_file in UNDESIRABLE_FILES:
if undesirable_file in files:
files.remove(undesirable_file)
undesirable_files_removed += 1
for name in files:
full_name = os.path.join(root, name)
if full_name not in filenames_in_archive:
files_to_remove.append(full_name)
for repo_file in files_to_remove:
# Remove files in the repository (relative to the upload point) that are not in
# the uploaded archive.
try:
hg_util.remove_file(repo.ui, repo, repo_file, force=True)
except Exception as e:
log.debug(
"Error removing files using the mercurial API, so trying a different approach, the error was: %s"
% str(e))
relative_selected_file = repo_file.split(
'repo_%d' % repository.id)[1].lstrip('/')
repo.dirstate.remove(relative_selected_file)
repo.dirstate.write()
absolute_selected_file = os.path.abspath(repo_file)
if os.path.isdir(absolute_selected_file):
try:
os.rmdir(absolute_selected_file)
except OSError as e:
# The directory is not empty.
pass
elif os.path.isfile(absolute_selected_file):
os.remove(absolute_selected_file)
dir = os.path.split(absolute_selected_file)[0]
try:
os.rmdir(dir)
except OSError as e:
# The directory is not empty.
pass
# 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 = check_file_contents_for_email_alerts(app)
for filename_in_archive in filenames_in_archive:
# Check file content to ensure it is appropriate.
if check_contents and os.path.isfile(filename_in_archive):
content_alert_str += check_file_content_for_html_and_images(
filename_in_archive)
hg_util.add_changeset(repo.ui, repo, filename_in_archive)
if filename_in_archive.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 app.tool_data_tables
# dictionary.
stdtm = ShedToolDataTableManager(app)
error, message = stdtm.handle_sample_tool_data_table_conf_file(
filename_in_archive, persist=False)
if error:
return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
hg_util.commit_changeset(repo.ui,
repo,
full_path_to_changeset=full_path,
username=username,
message=commit_message)
admin_only = len(repository.downloadable_revisions) != 1
suc.handle_email_alerts(app,
host,
repository,
content_alert_str=content_alert_str,
new_repo_alert=new_repo_alert,
admin_only=admin_only)
return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
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 = tdtm.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.
os.remove(absolute_selected_file)
dir = os.path.split(absolute_selected_file)[0]
try:
os.rmdir(dir)
except OSError, e:
# The directory is not empty.
pass
# 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 = check_file_contents_for_email_alerts(app)
for filename_in_archive in filenames_in_archive:
# Check file content to ensure it is appropriate.
if check_contents and os.path.isfile(filename_in_archive):
content_alert_str += check_file_content_for_html_and_images(
filename_in_archive)
hg_util.add_changeset(repo.ui, repo, filename_in_archive)
if filename_in_archive.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 app.tool_data_tables
# dictionary.
tdtm = data_table_manager.ToolDataTableManager(app)
error, message = tdtm.handle_sample_tool_data_table_conf_file(
filename_in_archive, persist=False)
if error:
return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
hg_util.commit_changeset(repo.ui,
repo,
full_path_to_changeset=full_path,
username=username,
message=commit_message)
admin_only = len(repository.downloadable_revisions) != 1
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)
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 = tdtm.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.
def handle_directory_changes(app, host, username, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar,
new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed):
repo_path = repository.repo_path(app)
repo = hg_util.get_repo_for_repository(app, repo_path=repo_path)
content_alert_str = ''
files_to_remove = []
filenames_in_archive = [os.path.join(full_path, name) for name in filenames_in_archive]
if remove_repo_files_not_in_tar and not repository.is_new(app):
# We have a repository that is not new (it contains files), so discover those files that are in the
# repository, but not in the uploaded archive.
for root, dirs, files in os.walk(full_path):
if root.find('.hg') < 0 and root.find('hgrc') < 0:
for undesirable_dir in UNDESIRABLE_DIRS:
if undesirable_dir in dirs:
dirs.remove(undesirable_dir)
undesirable_dirs_removed += 1
for undesirable_file in UNDESIRABLE_FILES:
if undesirable_file in files:
files.remove(undesirable_file)
undesirable_files_removed += 1
for name in files:
full_name = os.path.join(root, name)
if full_name not in filenames_in_archive:
files_to_remove.append(full_name)
for repo_file in files_to_remove:
# Remove files in the repository (relative to the upload point) that are not in
# the uploaded archive.
try:
hg_util.remove_file(repo_path, repo_file, force=True)
except Exception as e:
log.debug("Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str(e))
relative_selected_file = repo_file.split('repo_%d' % repository.id)[1].lstrip('/')
repo.dirstate.remove(relative_selected_file)
repo.dirstate.write()
absolute_selected_file = os.path.abspath(repo_file)
if os.path.isdir(absolute_selected_file):
try:
os.rmdir(absolute_selected_file)
except OSError as e:
# The directory is not empty.
pass
elif os.path.isfile(absolute_selected_file):
os.remove(absolute_selected_file)
dir = os.path.split(absolute_selected_file)[0]
try:
os.rmdir(dir)
except OSError as e:
# The directory is not empty.
pass
# 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 = check_file_contents_for_email_alerts(app)
for filename_in_archive in filenames_in_archive:
# Check file content to ensure it is appropriate.
if check_contents and os.path.isfile(filename_in_archive):
content_alert_str += check_file_content_for_html_and_images(filename_in_archive)
hg_util.add_changeset(repo_path, filename_in_archive)
if filename_in_archive.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 app.tool_data_tables
# dictionary.
stdtm = ShedToolDataTableManager(app)
error, message = stdtm.handle_sample_tool_data_table_conf_file(filename_in_archive, persist=False)
if error:
return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
hg_util.commit_changeset(repo_path,
full_path_to_changeset=full_path,
username=username,
message=commit_message)
admin_only = len(repository.downloadable_revisions) != 1
suc.handle_email_alerts(app,
host,
repository,
content_alert_str=content_alert_str,
new_repo_alert=new_repo_alert,
admin_only=admin_only)
return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
