Merge pull request #319 from ales-erjavec/geo-datasets-init

[ENH] GEO Datasets: Move GDSInfo initialization in a worker thread

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
 - repo: https://github.com/psf/black
- rev: 23.7.0
+ rev: 24.3.0
  hooks:
  - id: black
  language_version: python3
 
 - repo: https://github.com/timothycrosley/isort
- rev: 5.12.0
+ rev: 5.13.2
  hooks:
  - id: isort
  language_version: python3
 
 - repo: https://github.com/pycqa/flake8
- rev: 6.1.0
+ rev: 7.0.0
  hooks:
  - id: flake8
  language_version: python3

orangecontrib/bioinformatics/tests/widgets/test_OWGEODatasets.py

@@ -13,6 +13,8 @@ def setUp(self):
  self.test_sample = 'GDS1001'
  self.test_organism = '10090'
  self.widget = self.create_widget(OWGEODatasets)
+ self.wait_until_finished(self.widget)
+ self.process_events()
 
  def test_minimum_size(self):
  pass

orangecontrib/bioinformatics/widgets/OWGEODatasets.py

@@ -1,12 +1,13 @@
 """ Gene Expression Omnibus datasets widget """
+
 import sys
 from types import SimpleNamespace
-from typing import Any, Optional, DefaultDict
+from typing import Any, Union, Optional, DefaultDict
 from collections import defaultdict
 
 import requests
 
-from AnyQt.QtCore import Qt
+from AnyQt.QtCore import Qt, QTimer
 from AnyQt.QtWidgets import (
  QSplitter,
  QTreeWidget,
@@ -63,6 +64,8 @@ def callback():
  nonlocal current_iter
  current_iter += 1
  state.set_progress_value(100 * (current_iter / max_iter))
+ if state.is_interruption_requested():
+ raise KeyboardInterrupt
 
  state.set_status("Downloading...")
  res.gds_dataset = dataset_download(
@@ -71,6 +74,16 @@ def callback():
  return res
 
 
+class GDSInfoResult(SimpleNamespace):
+ gds_info: Optional[GDSInfo]
+
+
+def run_gds_info_task(state: TaskState):
+ state.set_status("Fetching index...")
+ gds_info = GDSInfo()
+ return GDSInfoResult(gds_info=gds_info)
+
+
 class GEODatasetsModel(TableModel):
  (
  indicator_col,
@@ -108,9 +121,9 @@ def render_pubmed_url(row):
  TableModel.Column(
  title(""),
  {
- Qt.DisplayRole: lambda row: " "
- if is_cached(items[row]["name"])
- else "",
+ Qt.DisplayRole: lambda row: (
+  " " if is_cached(items[row]["name"]) else ""
+ ),
  Qt.UserRole: lambda row: items[row],
  },
  ),
@@ -211,6 +224,7 @@ class Warning(OWWidget.Warning):
 
  class Error(OWWidget.Error):
  no_connection = Msg("Widget can't connect to serverfiles.")
+ error = Msg("{}")
 
  class Outputs:
  gds_data = Output("Expression Data", Table)
@@ -232,14 +246,7 @@ class Outputs:
  def __init__(self):
  OWWidget.__init__(self)
  ConcurrentWidgetMixin.__init__(self)
-
- try:
- self.gds_info: Optional[GDSInfo] = GDSInfo()
- except requests.exceptions.ConnectionError:
- self.gds_info = {}
- self.Error.no_connection()
- return
-
+ self.gds_info: Optional[GDSInfo] = None
  self.gds_data: Optional[Table] = None
  self.__updating_filter = False
 
@@ -291,7 +298,7 @@ def __init__(self):
  self.table_view.verticalHeader().setVisible(False)
  self.table_view.viewport().setMouseTracking(True)
 
- self.table_model = GEODatasetsModel(self.gds_info)
+ self.table_model = GEODatasetsModel({})
  self.proxy_model = FilterProxyModel()
  self.proxy_model.setSourceModel(self.table_model)
  self.table_view.setModel(self.proxy_model)
@@ -343,7 +350,7 @@ def __init__(self):
  )
  self._apply_filter()
 
- self.commit()
+ self.start(run_gds_info_task)
 
  def _splitter_moved(self, *args):
  self.splitter_settings = [bytes(sp.saveState()) for sp in self.splitters]
@@ -452,7 +459,7 @@ def current_changed():
 
  def _run(self):
  self.Warning.using_local_files.clear()
- if self.selected_gds is not None:
+ if self.gds_info and self.selected_gds is not None:
  self.gds_data = None
  self.start(
  run_download_task,
@@ -541,16 +548,28 @@ def commit(self):
  self._run()
 
  def on_exception(self, ex: Exception):
- self.Warning.using_local_files()
-
- def on_done(self, result: Result):
- assert isinstance(result.gds_dataset, Table)
- self.gds_data = result.gds_dataset
-
- if self.gds_info:
- self.table_model.update_cache_indicator()
-
- self.Outputs.gds_data.send(self.gds_data)
+ if isinstance(ex, requests.exceptions.ConnectionError):
+ self.Warning.using_local_files()
+ else:
+ self.Error.error("", exc_info=ex)
+
+ def on_done(self, result: Union[GDSInfoResult, Result]):
+ self.Error.error.clear()
+ if isinstance(result, GDSInfoResult):
+ self.gds_info = result.gds_info
+ self.table_model = GEODatasetsModel(result.gds_info)
+ self.proxy_model.setSourceModel(self.table_model)
+ self.table_view.resizeColumnsToContents()
+ self._set_selection()
+ QTimer.singleShot(0, lambda: self.unconditional_commit())
+ else:
+ assert isinstance(result.gds_dataset, Table)
+ self.gds_data = result.gds_dataset
+
+ if self.gds_info:
+ self.table_model.update_cache_indicator()
+
+ self.Outputs.gds_data.send(self.gds_data)
 
  def on_partial_result(self, result: Any) -> None:
  pass