# Contains objects for using external display applications
import logging
from copy import deepcopy
from urllib.parse import quote_plus
from galaxy.util import (
parse_xml,
string_as_bool,
)
from galaxy.util.template import fill_template
from .parameters import (
DEFAULT_DATASET_NAME,
DisplayApplicationDataParameter,
DisplayApplicationParameter,
)
from .util import encode_dataset_user
log = logging.getLogger(__name__)
[docs]def quote_plus_string(value, **kwds):
# Simple helper to make sure value is a string when trying to quote
# Object passed in might not be a bare string/bytes, if is e.g., a template result
# Prevents e.g. issue of "quote_from_bytes() expected bytes"
return quote_plus(str(value), **kwds)
[docs]class DisplayApplicationLink:
[docs] @classmethod
def from_elem(cls, elem, display_application, other_values=None):
rval = DisplayApplicationLink(display_application)
rval.id = elem.get("id", None)
assert rval.id, "Link elements require a id."
rval.name = elem.get("name", rval.id)
rval.url = elem.find("url")
assert rval.url is not None, "A url element must be provided for link elements."
rval.other_values = other_values
rval.filters = elem.findall("filter")
for param_elem in elem.findall("param"):
param = DisplayApplicationParameter.from_elem(param_elem, rval)
assert param, f"Unable to load parameter from element: {param_elem}"
rval.parameters[param.name] = param
rval.url_param_name_map[param.url] = param.name
return rval
[docs] def __init__(self, display_application):
self.display_application = display_application
self.parameters = {}
self.url_param_name_map = {}
self.url = None
self.id = None
self.name = None
[docs] def get_display_url(self, data, trans):
dataset_hash, user_hash = encode_dataset_user(trans, data, None)
return trans.app.url_for(
controller="dataset",
action="display_application",
dataset_id=dataset_hash,
user_id=user_hash,
app_name=quote_plus(self.display_application.id),
link_name=quote_plus(self.id),
app_action=None,
)
[docs] def get_inital_values(self, data, trans):
if self.other_values:
rval = dict(self.other_values)
else:
rval = {}
rval.update(
{"BASE_URL": trans.request.base, "APP": trans.app}
) # trans automatically appears as a response, need to add properties of trans that we want here
BASE_PARAMS = {"qp": quote_plus_string, "url_for": trans.app.url_for}
for key, value in BASE_PARAMS.items(): # add helper functions/variables
rval[key] = value
rval[DEFAULT_DATASET_NAME] = data # always have the display dataset name available
return rval
[docs] def build_parameter_dict(self, data, dataset_hash, user_hash, trans, app_kwds):
other_values = self.get_inital_values(data, trans)
other_values["DATASET_HASH"] = dataset_hash
other_values["USER_HASH"] = user_hash
ready = True
for name, param in self.parameters.items():
assert name not in other_values, f"The display parameter '{name}' has been defined more than once."
if param.ready(other_values):
if name in app_kwds and param.allow_override:
other_values[name] = app_kwds[name]
else:
other_values[name] = param.get_value(
other_values, dataset_hash, user_hash, trans
) # subsequent params can rely on this value
else:
ready = False
other_values[name] = param.get_value(
other_values, dataset_hash, user_hash, trans
) # subsequent params can rely on this value
if other_values[name] is None:
# Need to stop here, next params may need this value to determine its own value
return False, other_values
return ready, other_values
[docs] def filter_by_dataset(self, data, trans):
context = self.get_inital_values(data, trans)
for filter_elem in self.filters:
if fill_template(filter_elem.text, context=context) != filter_elem.get("value", "True"):
return False
return True
[docs]class DynamicDisplayApplicationBuilder:
[docs] def __init__(self, elem, display_application, build_sites):
filename = None
data_table = None
if elem.get("site_type", None) is not None:
filename = build_sites.get(elem.get("site_type"))
else:
filename = elem.get("from_file", None)
if filename is None:
data_table_name = elem.get("from_data_table", None)
if data_table_name:
data_table = display_application.app.tool_data_tables.get(data_table_name, None)
assert data_table is not None, f'Unable to find data table named "{data_table_name}".'
assert filename is not None or data_table is not None, "Filename or data Table is required for dynamic_links."
skip_startswith = elem.get("skip_startswith", None)
separator = elem.get("separator", "\t")
id_col = elem.get("id", None)
try:
id_col = int(id_col)
except (TypeError, ValueError):
if data_table:
if id_col is None:
id_col = data_table.columns.get("id", None)
if id_col is None:
id_col = data_table.columns.get("value", None)
try:
id_col = int(id_col)
except (TypeError, ValueError):
# id is set to a string or None, use column by that name if available
id_col = data_table.columns.get(id_col, None)
id_col = int(id_col)
name_col = elem.get("name", None)
try:
name_col = int(name_col)
except (TypeError, ValueError):
if data_table:
if name_col is None:
name_col = data_table.columns.get("name", None)
else:
name_col = data_table.columns.get(name_col, None)
else:
name_col = None
if name_col is None:
name_col = id_col
max_col = max(id_col, name_col)
dynamic_params = {}
if data_table is not None:
max_col = max([max_col] + list(data_table.columns.values()))
for key, value in data_table.columns.items():
dynamic_params[key] = {"column": value, "split": False, "separator": ","}
for dynamic_param in elem.findall("dynamic_param"):
name = dynamic_param.get("name")
value = int(dynamic_param.get("value"))
split = string_as_bool(dynamic_param.get("split", False))
param_separator = dynamic_param.get("separator", ",")
max_col = max(max_col, value)
dynamic_params[name] = {"column": value, "split": split, "separator": param_separator}
if filename:
data_iter = open(filename)
elif data_table:
version, data_iter = data_table.get_version_fields()
display_application.add_data_table_watch(data_table.name, version)
links = []
for line in data_iter:
if isinstance(line, str):
if not skip_startswith or not line.startswith(skip_startswith):
line = line.rstrip("\n\r")
if not line:
continue
fields = line.split(separator)
else:
continue
else:
fields = line
if len(fields) > max_col:
new_elem = deepcopy(elem)
new_elem.set("id", fields[id_col])
new_elem.set("name", fields[name_col])
dynamic_values = {}
for key, attributes in dynamic_params.items():
value = fields[attributes["column"]]
if attributes["split"]:
value = value.split(attributes["separator"])
dynamic_values[key] = value
# now populate
links.append(
DisplayApplicationLink.from_elem(new_elem, display_application, other_values=dynamic_values)
)
else:
log.warning(f'Invalid dynamic display application link specified in {filename}: "{line}"')
self.links = links
def __iter__(self):
return iter(self.links)
[docs]class PopulatedDisplayApplicationLink:
[docs] def __init__(self, display_application_link, data, dataset_hash, user_hash, trans, app_kwds):
self.link = display_application_link
self.data = data
self.dataset_hash = dataset_hash
self.user_hash = user_hash
self.trans = trans
self.ready, self.parameters = self.link.build_parameter_dict(
self.data, self.dataset_hash, self.user_hash, trans, app_kwds
)
[docs] def display_ready(self):
return self.ready
[docs] def get_param_value(self, name):
value = None
if self.ready:
value = self.parameters.get(name, None)
assert value, "Unknown parameter requested"
return value
[docs] def preparing_display(self):
if not self.ready:
return self.link.parameters[list(self.parameters.keys())[-1]].is_preparing(self.parameters)
return False
[docs] def prepare_display(self):
rval = []
found_last = False
if not self.ready and not self.preparing_display():
other_values = self.parameters
for name, param in self.link.parameters.items():
if found_last or list(other_values.keys())[-1] == name: # found last parameter to be populated
found_last = True
value = param.prepare(other_values, self.dataset_hash, self.user_hash, self.trans)
rval.append({"name": name, "value": value, "param": param})
other_values[name] = value
if value is None:
# We can go no further until we have a value for this parameter
return rval
return rval
[docs] def get_prepare_steps(self, datasets_only=True):
rval = []
for name, param in self.link.parameters.items():
if datasets_only and not isinstance(param, DisplayApplicationDataParameter):
continue
value = self.parameters.get(name, None)
rval.append({"name": name, "value": value, "param": param, "ready": param.ready(self.parameters)})
return rval
[docs] def display_url(self):
assert self.display_ready(), "Display is not yet ready, cannot generate display link"
return fill_template(self.link.url.text, context=self.parameters)
[docs] def get_param_name_by_url(self, url):
for name, parameter in self.link.parameters.items():
if parameter.build_url(self.parameters) == url:
return name
raise ValueError(f"Unknown URL parameter name provided: {url}")
@property
def allow_cors(self):
return self.link.allow_cors
[docs]class DisplayApplication:
[docs] @classmethod
def from_file(cls, filename, app):
return cls.from_elem(parse_xml(filename).getroot(), app, filename=filename)
[docs] @classmethod
def from_elem(cls, elem, app, filename=None):
att_dict = cls._get_attributes_from_elem(elem)
rval = DisplayApplication(
att_dict["id"], att_dict["name"], app, att_dict["version"], filename=filename, elem=elem
)
rval._load_links_from_elem(elem)
return rval
@classmethod
def _get_attributes_from_elem(cls, elem):
display_id = elem.get("id", None)
assert display_id, "ID tag is required for a Display Application"
name = elem.get("name", display_id)
version = elem.get("version", None)
return dict(id=display_id, name=name, version=version)
[docs] def __init__(self, display_id, name, app, version=None, filename=None, elem=None):
self.id = display_id
self.name = name
self.app = app
if version is None:
version = "1.0.0"
self.version = version
self.links = {}
self._filename = filename
self._elem = elem
self._data_table_versions = {}
def _load_links_from_elem(self, elem):
for link_elem in elem.findall("link"):
link = DisplayApplicationLink.from_elem(link_elem, self)
if link:
self.links[link.id] = link
try:
for dynamic_links in elem.findall("dynamic_links"):
for link in DynamicDisplayApplicationBuilder(
dynamic_links, self, self.app.datatypes_registry.build_sites
):
self.links[link.id] = link
except Exception as e:
log.error("Error loading a set of Dynamic Display Application links: %s", e)
[docs] def get_link(self, link_name, data, dataset_hash, user_hash, trans, app_kwds):
# returns a link object with data knowledge to generate links
self._check_and_reload()
return PopulatedDisplayApplicationLink(self.links[link_name], data, dataset_hash, user_hash, trans, app_kwds)
[docs] def filter_by_dataset(self, data, trans):
self._check_and_reload()
filtered = DisplayApplication(self.id, self.name, self.app, version=self.version)
for link_name, link_value in self.links.items():
if link_value.filter_by_dataset(data, trans):
filtered.links[link_name] = link_value
return filtered
[docs] def reload(self):
if self._filename:
elem = parse_xml(self._filename).getroot()
elif self._elem:
elem = self._elem
else:
raise Exception(f"Unable to reload DisplayApplication {self.name}.")
# All toolshed-specific attributes added by e.g the registry will remain
attr_dict = self._get_attributes_from_elem(elem)
# We will not allow changing the id at this time (we'll need to fix several mappings upstream to handle this case)
assert attr_dict.get("id") == self.id, ValueError(
"You cannot reload a Display application where the ID has changed. You will need to restart the server instead."
)
# clear old links
self.links = {}
# clear data table versions:
self._data_table_versions = {}
# Set new attributes
for key, value in attr_dict.items():
setattr(self, key, value)
# Load new links
self._load_links_from_elem(elem)
return self
[docs] def add_data_table_watch(self, table_name, version=None):
self._data_table_versions[table_name] = version
def _requires_reload(self):
for key, value in self._data_table_versions.items():
table = self.app.tool_data_tables.get(key, None)
if table and not table.is_current_version(value):
return True
return False
def _check_and_reload(self):
if self._requires_reload():
self.reload()