Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.visualization.plugins.resource_parser

"""
Deserialize Galaxy resources (hdas, ldas, datasets, genomes, etc.) from
a dictionary of string data/ids (often from a query string).
"""
import json
import logging
import weakref
from typing import (
    Callable,
    Dict,
    Optional,
    Union,
)

import galaxy.exceptions
import galaxy.util
from galaxy.managers import (
    hdas as hda_manager,
    visualizations as visualization_manager,
)
from galaxy.model import (
    HistoryDatasetAssociation,
    LibraryDatasetDatasetAssociation,
    Visualization,
)
from galaxy.util import bunch

log = logging.getLogger(__name__)


ParameterPrimitiveType = Union[int, float, str]
ParameterType = Union[
    ParameterPrimitiveType, HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, Visualization
]


[docs]class ResourceParser: """ Given a parameter dictionary (often a converted query string) and a configuration dictionary (curr. only VisualizationsRegistry uses this), convert the entries in the parameter dictionary into resources (Galaxy models, primitive types, lists of either, etc.) and return in a new dictionary. The keys used to store the new values can optionally be re-mapped to new keys (e.g. dataset_id="NNN" -> hda=<HistoryDatasetAssociation>). """ primitive_parsers: Dict[str, Callable[[str], ParameterPrimitiveType]] = { "str": lambda param: galaxy.util.sanitize_html.sanitize_html(param), "bool": lambda param: galaxy.util.string_as_bool(param), "int": int, "float": float, # 'date' : lambda param: , "json": (lambda param: json.loads(galaxy.util.sanitize_html.sanitize_html(param))), }
[docs] def __init__(self, app, *args, **kwargs): self.app = weakref.ref(app) self.managers = self._init_managers(app)
def _init_managers(self, app): return bunch.Bunch( visualization=app[visualization_manager.VisualizationManager], hda=app[hda_manager.HDAManager], )
[docs] def parse_parameter_dictionary(self, trans, param_config_dict, query_params, param_modifiers=None): """ Parse all expected params from the query dictionary `query_params`. If param is required and not present, raises a `KeyError`. """ # log.debug( 'parse_parameter_dictionary, query_params:\n%s', query_params ) # parse the modifiers first since they modify the params coming next # TODO: this is all really for hda_ldda - which we could replace with model polymorphism params_that_modify_other_params = self.parse_parameter_modifiers(trans, param_modifiers, query_params) resources = {} for param_name, param_config in param_config_dict.items(): # optionally rename the variable returned, defaulting to the original name var_name_in_template = param_config.get("var_name_in_template", param_name) # if the param is present, get its value, any param modifiers for that param, and parse it into a resource # use try catch here and not caller to fall back on the default value or re-raise if required resource = None query_val = query_params.get(param_name, None) if query_val is not None: try: target_param_modifiers = params_that_modify_other_params.get(param_name, None) resource = self.parse_parameter( trans, param_config, query_val, param_modifiers=target_param_modifiers ) except Exception as exception: if trans.debug: raise else: log.warning( "Exception parsing visualization param from query: %s, %s, (%s) %s", param_name, query_val, str(type(exception)), str(exception), ) resource = None # here - we've either had no value in the query_params or there was a failure to parse # so: error if required, otherwise get a default (which itself defaults to None) if resource is None: if param_config["required"]: raise KeyError(f"required param {param_name} not found in URL") resource = self.parse_parameter_default(trans, param_config) resources[var_name_in_template] = resource return resources
[docs] def parse_config(self, trans, param_config_dict, query_params): """ Return `query_params` dict parsing only JSON serializable params. Complex params such as models, etc. are left as the original query value. Keys in `query_params` not found in the `param_config_dict` will not be returned. """ # log.debug( 'parse_config, query_params:\n%s', query_params ) config = {} for param_name, param_config in param_config_dict.items(): config_val = query_params.get(param_name, None) if config_val is not None and param_config["type"] in self.primitive_parsers: try: config_val = self.parse_parameter(trans, param_config, config_val) except Exception as exception: log.warning( "Exception parsing visualization param from query: %s, %s, (%s) %s", param_name, config_val, type(exception), exception, ) config_val = None # here - we've either had no value in the query_params or there was a failure to parse # so: if there's a default and it's not None, add it to the config if config_val is None: if param_config.get("default", None) is None: continue config_val = self.parse_parameter_default(trans, param_config) config[param_name] = config_val return config
# TODO: I would LOVE to rip modifiers out completely
[docs] def parse_parameter_modifiers( self, trans, param_modifiers, query_params ) -> Dict[str, Dict[str, Optional[ParameterType]]]: """ Parse and return parameters that are meant to modify other parameters, be grouped with them, or are needed to successfully parse other parameters. """ # only one level of modification - down that road lies madness # parse the modifiers out of query_params first since they modify the other params coming next parsed_modifiers: Dict[str, Dict[str, Optional[ParameterType]]] = {} if not param_modifiers: return parsed_modifiers # precondition: expects a two level dictionary # { target_param_name -> { param_modifier_name -> { param_modifier_data }}} for target_param_name, modifier_dict in param_modifiers.items(): target_modifiers: Dict[str, Optional[ParameterType]] = {} parsed_modifiers[target_param_name] = target_modifiers for modifier_name, modifier_config in modifier_dict.items(): query_val = query_params.get(modifier_name, None) if query_val is not None: modifier = self.parse_parameter(trans, modifier_config, query_val) target_modifiers[modifier_name] = modifier else: # TODO: required attr? target_modifiers[modifier_name] = self.parse_parameter_default(trans, modifier_config) return parsed_modifiers
[docs] def parse_parameter_default(self, trans, param_config) -> Optional[ParameterType]: """ Parse any default values for the given param, defaulting the default to `None`. """ # currently, *default* default is None, so this is quaranteed to be part of the dictionary default = param_config["default"] # if default is None, do not attempt to parse it if default is None: return default # otherwise, parse (currently param_config['default'] is a string just like query param and needs to be parsed) # this saves us the trouble of parsing the default when the config file is read # (and adding this code to the xml parser) return self.parse_parameter(trans, param_config, default)
[docs] def parse_parameter(self, trans, expected_param_data, query_param, recurse=True, param_modifiers=None): """ Use data in `expected_param_data` to parse `query_param` from a string into a resource usable directly by a template. """ param_type = expected_param_data.get("type") parsed_param: Optional[ParameterType] = None if param_type in self.primitive_parsers: # TODO: what about param modifiers on primitives? parsed_param = self.primitive_parsers[param_type](query_param) # TODO: constrain_to: this gets complicated - remove? # db models elif param_type == "visualization": # ?: is this even used anymore/anywhere? decoded_visualization_id = trans.security.decode_id(query_param, object_name=param_type) parsed_param = self.managers.visualization.get_accessible(decoded_visualization_id, trans.user) elif param_type == "dataset": decoded_dataset_id = trans.security.decode_id(query_param, object_name=param_type) parsed_param = self.managers.hda.get_accessible(decoded_dataset_id, trans.user) elif param_type == "hda_or_ldda": encoded_dataset_id = query_param # needs info from another param... hda_ldda = param_modifiers.get("hda_ldda") if hda_ldda == "hda": decoded_dataset_id = trans.security.decode_id(query_param, object_name="dataset") parsed_param = self.managers.hda.get_accessible(decoded_dataset_id, trans.user) else: parsed_param = self.managers.ldda.get(trans, encoded_dataset_id) # TODO: ideally this would check v. a list of valid dbkeys elif param_type == "dbkey": dbkey = query_param parsed_param = galaxy.util.sanitize_html.sanitize_html(dbkey) return parsed_param