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navigating-stories / orange-story-navigator

Add-on to the Orange3 data mining toolkit with text processing widgets from the project Navigating Stories
https://research-software-directory.org/projects/navigating-stories
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`IndexError` on Actor Analysis #37

Closed f-hafner closed 2 weeks ago

f-hafner commented 4 months ago
Story Navigator version

0.0.18 (commit 8732988)

Orange version

3.36.2

Expected behavior

Can run actor analysis without error.

Actual behavior

get the following error


Exception:
IndexError: index 38 is out of bounds for axis 0 with size 38
Module:
Orange.data.table:96
Widget Name:
Actors
Widget Module:
storynavigation.widgets.OWSNActorAnalysis:591
Widget Scheme:
<?xml version='1.0' encoding='utf-8'?> <scheme version="2.0" title="" description=""> <nodes> <node id="0" name="Import Documents" qualified_name="orangecontrib.text.widgets.owimportdocuments.OWImportDocuments" project_name="Orange3-Text" version="" title="Import Documents" position="(188.0, 253.0)" /> <node id="1" name="File" qualified_name="Orange.widgets.data.owfile.OWFile" project_name="Orange3" version="" title="File" position="(162.0, 603.0)" /> <node id="2" name="Elements" qualified_name="storynavigation.widgets.OWSNTagger.OWSNTagger" project_name="storynavigator" version="" title="Elements" position="(337.0, 599.0)" /> <node id="3" name="Data Table" qualified_name="Orange.widgets.data.owtable.OWTable" project_name="Orange3" version="" title="Data Table" position="(555.0, 611.0)" /> <node id="4" name="Actors" qualified_name="storynavigation.widgets.OWSNActorAnalysis.OWSNActorAnalysis" project_name="storynavigator" version="" title="Actors" position="(858.0, 217.0)" /> <node id="5" name="Data Table" qualified_name="Orange.widgets.data.owtable.OWTable" project_name="Orange3" version="" title="Data Table (1)" position="(979.0, 127.0)" /> <node id="6" name="Actions" qualified_name="storynavigation.widgets.OWSNActionAnalysis.OWSNActionAnalysis" project_name="storynavigator" version="" title="Actions" position="(850.0, 617.0)" /> <node id="7" name="Select Rows" qualified_name="Orange.widgets.data.owselectrows.OWSelectRows" project_name="Orange3" version="" title="Select Rows" position="(1151.0, 130.0)" /> <node id="8" name="Bar Plot" qualified_name="Orange.widgets.visualize.owbarplot.OWBarPlot" project_name="Orange3" version="" title="Bar Plot" position="(1276.0, 136.0)" /> <node id="9" name="Data Table" qualified_name="Orange.widgets.data.owtable.OWTable" project_name="Orange3" version="" title="Data Table (2)" position="(1079.0, 447.0)" /> </nodes> <links> <link id="0" source_node_id="0" sink_node_id="2" source_channel="Corpus" sink_channel="Stories" enabled="true" source_channel_id="data" sink_channel_id="stories" /> <link id="1" source_node_id="1" sink_node_id="2" source_channel="Data" sink_channel="Custom tags" enabled="true" source_channel_id="data" sink_channel_id="custom_tag_dict" /> <link id="2" source_node_id="2" sink_node_id="3" source_channel="Story elements" sink_channel="Data" enabled="true" source_channel_id="dataset_level_data" sink_channel_id="data" /> <link id="3" source_node_id="3" sink_node_id="4" source_channel="Data" sink_channel="Story elements" enabled="true" source_channel_id="annotated_data" sink_channel_id="story_elements" /> <link id="4" source_node_id="4" sink_node_id="5" source_channel="Actor stats: all" sink_channel="Data" enabled="true" source_channel_id="story_collection_results" sink_channel_id="data" /> <link id="5" source_node_id="3" sink_node_id="6" source_channel="Data" sink_channel="Story elements" enabled="true" source_channel_id="annotated_data" sink_channel_id="story_elements" /> <link id="6" 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'__version__': 1}</properties> </node_properties> <session_state> <window_groups /> </session_state> </scheme> 
Version:
3.36.2
Environment:
Python 3.9.13 on Linux 5.15.0-100-generic #110~20.04.1-Ubuntu SMP Tue Feb 13 14:25:03 UTC 2024 x86_64
Installed Packages:
AnyQt==0.2.0, Babel==2.14.0, Bottleneck==1.3.8, DHTMLParser3==3.0.17, Jinja2==3.1.3, MarkupSafe==2.1.5, Orange3-Network==1.9.0, Orange3-Text==1.15.0, Orange3==3.36.2, PyQt5-Qt5==5.15.2, PyQt5-sip==12.13.0, PyQt5==5.15.10, PyQt6-Qt6==6.6.2, PyQt6-sip==13.6.0, PyQt6==6.6.1, PyQtWebEngine-Qt5==5.15.2, PyQtWebEngine==5.15.6, PyYAML==6.0.1, QtPy==2.4.1, SecretStorage==3.3.3, XlsxWriter==3.2.0, alabaster==0.7.16, annotated-types==0.6.0, anyio==4.3.0, asttokens==2.4.1, attrs==23.2.0, baycomp==1.0.3, beautifulsoup4==4.12.3, biopython==1.83, blis==0.7.11, catalogue==2.0.10, catboost==1.2.3, cattrs==23.2.3, certifi==2024.2.2, cffi==1.16.0, chardet==5.2.0, charset-normalizer==3.3.2, click==8.1.7, cloudpathlib==0.16.0, comm==0.2.1, commonmark==0.9.1, confection==0.1.4, conllu==4.5.3, contourpy==1.2.0, coverage==7.4.3, cryptography==42.0.5, cycler==0.12.1, cymem==2.0.8, debugpy==1.8.1, decorator==5.1.1, defusedxml==0.7.1, dictdiffer==0.9.0, docutils==0.20.1, docx2txt==0.8, et-xmlfile==1.1.0, exceptiongroup==1.2.0, executing==2.0.1, filelock==3.13.1, fonttools==4.49.0, fsspec==2024.2.0, gensim==4.3.2, graphviz==0.20.1, h11==0.14.0, httpcore==1.0.4, httpx==0.27.0, huggingface-hub==0.21.3, idna==3.6, imagesize==1.4.1, importlib-metadata==7.0.1, importlib-resources==6.1.2, ipykernel==6.29.3, ipython==8.18.1, jaraco.classes==3.3.1, jedi==0.19.1, jeepney==0.8.0, jellyfish==1.0.3, joblib==1.3.2, jupyter-client==8.6.0, jupyter-core==5.7.1, keyring==24.3.1, keyrings.alt==5.0.0, kiwisolver==1.4.5, langcodes==3.3.0, langdetect==1.0.9, lemmagen3==3.5.1, matplotlib-inline==0.1.6, matplotlib==3.8.3, more-itertools==10.2.0, mpmath==1.3.0, murmurhash==1.0.10, nest-asyncio==1.6.0, networkx==3.2.1, nl-core-news-sm==3.7.0, nltk==3.8.1, numpy==1.26.4, nvidia-cublas-cu12==12.1.3.1, nvidia-cuda-cupti-cu12==12.1.105, nvidia-cuda-nvrtc-cu12==12.1.105, nvidia-cuda-runtime-cu12==12.1.105, nvidia-cudnn-cu12==8.9.2.26, nvidia-cufft-cu12==11.0.2.54, nvidia-curand-cu12==10.3.2.106, nvidia-cusolver-cu12==11.4.5.107, nvidia-cusparse-cu12==12.1.0.106, nvidia-nccl-cu12==2.19.3, nvidia-nvjitlink-cu12==12.3.101, nvidia-nvtx-cu12==12.1.105, oauthlib==3.2.2, odfpy==1.4.1, openTSNE==1.0.1, openpyxl==3.1.2, orange-canvas-core==0.1.35, orange-widget-base==4.22.0, owlready2==0.45, packaging==23.2, pandas==2.2.1, parso==0.8.3, pexpect==4.9.0, pillow==10.2.0, pip==22.0.4, platformdirs==4.2.0, plotly==5.19.0, preshed==3.0.9, prompt-toolkit==3.0.43, psutil==5.9.8, ptyprocess==0.7.0, pure-eval==0.2.2, pybind11==2.11.1, pycparser==2.21, pydantic-core==2.16.3, pydantic==2.6.3, pydot==2.0.0, pygments==2.17.2, pyparsing==3.1.1, pypdf==4.1.0, pyqtgraph==0.13.3, python-dateutil==2.9.0.post0, python-louvain==0.16, pytz==2024.1, pyzmq==25.1.2, qasync==0.27.1, qtconsole==5.5.1, rapidfuzz==3.6.1, recommonmark==0.7.1, regex==2023.12.25, requests-cache==1.2.0, requests-oauthlib==1.3.1, requests==2.31.0, safetensors==0.4.2, scikit-learn==1.3.2, scipy==1.12.0, segtok==1.5.11, serverfiles==0.3.1, setuptools==58.1.0, shapely==2.0.3, simhash==2.1.2, six==1.16.0, smart-open==6.4.0, sniffio==1.3.1, snowballstemmer==2.2.0, soupsieve==2.5, spacy-legacy==3.0.12, spacy-loggers==1.0.5, spacy==3.7.4, sphinx==7.2.6, sphinxcontrib-applehelp==1.0.8, sphinxcontrib-devhelp==1.0.6, sphinxcontrib-htmlhelp==2.0.5, sphinxcontrib-jsmath==1.0.1, sphinxcontrib-qthelp==1.0.7, sphinxcontrib-serializinghtml==1.1.10, srsly==2.4.8, stack-data==0.6.3, storynavigator==0.0.11, sympy==1.12, tabulate==0.9.0, tenacity==8.2.3, textblob-nl==0.0.1, textblob==0.18.0.post0, thefuzz==0.22.1, thinc==8.2.3, threadpoolctl==3.3.0, tokenizers==0.15.2, torch==2.2.1, tornado==6.4, tqdm==4.66.2, traitlets==5.14.1, transformers==4.38.2, trimesh==4.1.7, triton==2.2.0, tweepy==4.14.0, typer==0.9.0, typing-extensions==4.10.0, tzdata==2024.1, ufal.udpipe==1.3.1.1, url-normalize==1.4.3, urllib3==2.2.1, wasabi==1.1.2, wcwidth==0.2.13, weasel==0.3.4, wikipedia==1.4.0, xgboost==2.0.3, xlrd==2.0.1, yake==0.4.8, zipp==3.17.0
Machine ID:
aa7e8c73-d204-4802-a437-067c75a3dffd
Stack Trace:
Traceback (most recent call last):
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/.venv/lib/python3.9/site-packages/Orange/widgets/utils/concurrent.py", line 591, in _on_task_done
    super()._on_task_done(future)
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/.venv/lib/python3.9/site-packages/Orange/widgets/utils/concurrent.py", line 547, in _on_task_done
    self.on_exception(ex)
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/orangecontrib/storynavigation/widgets/OWSNActorAnalysis.py", line 937, in on_exception
    raise ex
  File "/home/flavio/.pyenv/versions/3.9.13/lib/python3.9/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/orangecontrib/storynavigation/widgets/OWSNActorAnalysis.py", line 612, in run
    self.valid_stories.append(self.stories[int(storyid)])
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/.venv/lib/python3.9/site-packages/orangecontrib/text/corpus.py", line 549, in __getitem__
    c = super().__getitem__(key)
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/.venv/lib/python3.9/site-packages/Orange/data/table.py", line 1168, in __getitem__
    return RowInstance(self, key)
  File "/home/flavio/repositories/projects/navigating-stories/orange-story-navigator/.venv/lib/python3.9/site-packages/Orange/data/table.py", line 96, in __init__
    self.id = table.ids[row_index]
IndexError: index 38 is out of bounds for axis 0 with size 38
Steps to reproduce the behavior

following widgets:

Additional info (worksheets, data, screenshots, ...)

image

f-hafner commented 4 months ago

I just tried to run it again and it worked this time...

f-hafner commented 4 months ago

So it seems to be a problem when changing the number of segments per story and then rerunning the workflow.

For instance, run the workflow above with extracting 10 story segments, then change it to 5, extract story elements again. then, the error should be raised on the Actors widget

f-hafner commented 4 months ago

And I get the same error when changing the language in the setting widget from nl to en and re-running the workflow.

image

f-hafner commented 4 months ago

It also happens when I remove the custom tags from an existing workflow and re-run the entire workflow.

image

kodymoodley commented 3 months ago

@f-hafner can you help me reproduce this error? I cannot seem to on my installation.

f-hafner commented 3 months ago

It's a bit specific to the dataset. I can share with you input data and workflow to reproduce. Because it's occurring when the analysis is rerun, it could be related to #44

kodymoodley commented 2 months ago

Confirmed will be fixed when #44 is fixed. I tested when re-running workflow (refreshing). Duplicate stories get added to the document window and these do not have corresponding story ids that have entries in the id - story dictionary.

ThijsVroegh commented 3 weeks ago

44 is fixed and indeed as @kodymoodley mentioned in the last comment, i could not reproduce the above-mentioned errors anymore. #37 will therefore be closed together with #44

eriktks commented 2 weeks ago

See PR #71