opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Improved typing of histories.

Browse Source
This commit is contained in:
John Chilton
2021-10-29 12:05:27 -04:00
parent 5310960e8a
commit 2a9b0dcbe5
2 changed files with 31 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/managers/histories.py
+31 -21
View File
@@ -7,6 +7,8 @@ created (or copied) by users over the course of an analysis.
import logging
from typing import (
cast,
Dict,
List,
Optional,
Set,
)
@@ -28,6 +30,7 @@ from galaxy.managers import (
sharable
)
from galaxy.managers.base import (
Serializer,
SortableManager,
)
from galaxy.schema.schema import (
@@ -445,39 +448,41 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
super().add_serializers()
deletable.PurgableSerializerMixin.add_serializers(self)
self.serializers.update({
'model_class': lambda *a, **c: 'History',
'size': lambda i, k, **c: int(i.disk_size),
'nice_size': lambda i, k, **c: i.disk_nice_size,
serializers: Dict[str, Serializer] = {
'model_class': lambda item, key, **context: 'History',
'size': lambda item, key, **context: int(item.disk_size),
'nice_size': lambda item, key, **context: item.disk_nice_size,
'state': self.serialize_history_state,
'url': lambda i, k, **c: self.url_for('history', id=self.app.security.encode_id(i.id)),
'contents_url': lambda i, k, **c: self.url_for('history_contents',
history_id=self.app.security.encode_id(i.id)),
'url': lambda item, key, **context: self.url_for('history', id=self.app.security.encode_id(item.id)),
'contents_url': lambda item, key, **context: self.url_for('history_contents',
history_id=self.app.security.encode_id(item.id)),
'empty': lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0,
'count': lambda i, k, **c: len(i.datasets),
'hdas': lambda i, k, **c: [self.app.security.encode_id(hda.id) for hda in i.datasets],
'empty': lambda item, key, **context: (len(item.datasets) + len(item.dataset_collections)) <= 0,
'count': lambda item, key, **context: len(item.datasets),
'hdas': lambda item, key, **context: [self.app.security.encode_id(hda.id) for hda in item.datasets],
'state_details': self.serialize_state_counts,
'state_ids': self.serialize_state_ids,
'contents': self.serialize_contents,
'non_ready_jobs': lambda i, k, **c: [self.app.security.encode_id(job.id) for job
in self.manager.non_ready_jobs(i)],
'non_ready_jobs': lambda item, key, **context: [self.app.security.encode_id(job.id) for job
in self.manager.non_ready_jobs(item)],
'contents_states': self.serialize_contents_states,
'contents_active': self.serialize_contents_active,
# TODO: Use base manager's serialize_id for user_id (and others)
# after refactoring hierarchy here?
'user_id': lambda i, k, **c: self.app.security.encode_id(i.user_id) if i.user_id is not None else None
})
'user_id': lambda item, key, **context: self.app.security.encode_id(item.user_id) if item.user_id is not None else None
}
self.serializers.update(serializers)
# remove this
def serialize_state_ids(self, history, key, **context):
def serialize_state_ids(self, item, key, **context):
"""
Return a dictionary keyed to possible dataset states and valued with lists
containing the ids of each HDA in that state.
"""
state_ids = {}
history = item
state_ids: Dict[str, List[str]] = {}
for state in model.Dataset.states.values():
state_ids[state] = []
@@ -489,11 +494,12 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
return state_ids
# remove this
def serialize_state_counts(self, history, key, exclude_deleted=True, exclude_hidden=False, **context):
def serialize_state_counts(self, item, key, exclude_deleted=True, exclude_hidden=False, **context):
"""
Return a dictionary keyed to possible dataset states and valued with the number
of datasets in this history that have those states.
"""
history = item
# TODO: the default flags above may not make a lot of sense (T,T?)
state_counts = {}
for state in model.Dataset.states.values():
@@ -509,10 +515,11 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
return state_counts
# TODO: remove this (is state used/useful?)
def serialize_history_state(self, history, key, **context):
def serialize_history_state(self, item, key, **context):
"""
Returns the history state based on the states of the HDAs it contains.
"""
history = item
states = model.Dataset.states
# (default to ERROR)
state = states.ERROR
@@ -540,7 +547,8 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
return state
def serialize_contents(self, history, key, trans=None, user=None, **context):
def serialize_contents(self, item, key, trans=None, user=None, **context):
history = item
returned = []
for content in self.manager.contents_manager._union_of_contents_query(history).all():
serialized = self.history_contents_serializer.serialize_to_view(content,
@@ -548,16 +556,17 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
returned.append(serialized)
return returned
def serialize_contents_states(self, history, key, trans=None, **context):
def serialize_contents_states(self, item, key, trans=None, **context):
"""
Return a dictionary containing the counts of all contents in each state
keyed by the distinct states.
Note: does not include deleted/hidden contents.
"""
history = item
return self.manager.contents_manager.state_counts(history)
def serialize_contents_active(self, history, key, **context):
def serialize_contents_active(self, item, key, **context):
"""
Return a dictionary keyed with 'deleted', 'hidden', and 'active' with values
for each representing the count of contents in each state.
@@ -565,6 +574,7 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
Note: counts for deleted and hidden overlap; In other words, a dataset that's
both deleted and hidden will be added to both totals.
"""
history = item
return self.manager.contents_manager.active_counts(history)
setup.cfg
-2
View File
@@ -591,8 +591,6 @@ check_untyped_defs = False
check_untyped_defs = False
[mypy-galaxy.tool_shed.metadata.metadata_generator]
check_untyped_defs = False
[mypy-galaxy.managers.histories]
check_untyped_defs = False
[mypy-galaxy.jobs.handler]
check_untyped_defs = False
[mypy-galaxy.workflow.scheduling_manager]