def get_available_modules():
'''Lists all available Jterator modules in the
`JtLibrary <https://github.com/TissueMAPS/JtLibrary>`_ repository.
'''
logger.info('get list of available jterator modules')
modules = AvailableModules()
return jsonify(jtmodules=modules.to_dict())
def get_available_modules():
'''Lists all available Jterator modules in the
`JtLibrary <https://github.com/TissueMAPS/JtLibrary>`_ repository.
'''
logger.info('get list of available jterator modules')
modules = AvailableModules()
return jsonify(jtmodules=modules.to_dict())
def pipeline(self):
'''List[tmlib.jterator.module.ImageAnalysisModule]:
pipeline built based on
:class`PipelineDescription <tmlib.workflow.jterator.description.PipelineDescription>` and
:class:`HandleDescriptions <tmlib.workflow.jterator.description.HandleDescriptions>`.
'''
handles = self.project.handles # only compute this once
pipeline = list()
for i, element in enumerate(self.project.pipe.description.pipeline):
if not element.active:
continue
if '/' in element.source:
logger.debug(
'assuming module `%s` resides outside the configured module path',
element.source)
source_file = os.path.expanduser(
os.path.expandvars(element.source))
if not os.path.isabs(source_file):
source_file = os.path.join(self.step_location, source_file)
else:
logger.debug(
'searching for module `%s` in configured module path %r ...',
element.source, cfg.modules_path)
source_file = AvailableModules().find_module_by_name(
element.source)
if not os.path.exists(source_file):
raise PipelineDescriptionError(
'Module source `{0}` resolved to non-existing file `{1}`'.
format(element.source, source_file))
pipeline.append(
ImageAnalysisModule(name=handles[i].name,
source_file=source_file,
handles=handles[i].description))
return pipeline
def get_module_source_code():
'''Gets the source code for a given module.'''
module_filename = request.args.get('module_filename')
logger.info('get source code of module file "%s"', module_filename)
modules = AvailableModules()
files = [
f for i, f in enumerate(modules.module_files)
if os.path.basename(f) == module_filename
]
return send_file(files[0])
def get_module_source_code():
'''Gets the source code for a given module.'''
name = request.args.get('module_name')
logger.info('get source code of module "%s"', name)
try:
modules = AvailableModules()
# XXX: this code relies on the fact that `.module_names` and
# `.module_files` return corresponding items at the same
# position in the list! The `AvailableModules` class should
# be changed to provide a map name=>List[files] instead.
idx = modules.module_names.index(name)
return send_file(modules.module_files[idx])
except ValueError:
logger.error("Could not find module `%s` in available modules %r",
name, modules.module_names)
raise