Add Notes to dataset export #1220

fanse · 2022-09-12T15:34:12Z

fanse
Sep 12, 2022

First of all, thanks for creating asreview. It is a really great tool and the usability is awesome.

In my review, I created notes to justify and trace my decision later on, but I realized that the notes are not exported when I export the database. My co-author would instead review my choices in excel than in asreview. Is it possible to also export the note related to the dataset item?

Rensvandeschoot · 2022-09-13T07:10:42Z

Rensvandeschoot
Sep 13, 2022
Maintainer

There are two options:

Ask your colleague to install ASReview and send this person your exported .asreview file. Your colleague should then import the file and open the history panel. Your colleague can now use the filter to select the records containing notes.
You can add the notes from the .asreview project file to the . csv file via theASReview Python API.

0 replies

fanse · 2022-09-13T07:28:54Z

fanse
Sep 13, 2022
Author

Hey Rens,
thanks for your fast answer.

Unfortunately, Option 1 is not feasible since my colleague cannot search for specific references in the history panel. If he/she wants to access the note of a specific reference because, for example, I noted there why I think a reference is relevant or irrelevant, he/she cannot do this. And I cannot really ask them to scroll through thousands of references.

1 reply

Rensvandeschoot Sep 13, 2022
Maintainer

I understand! So, option 2 it is :-)

elisebvd · 2022-12-05T12:41:21Z

elisebvd
Dec 5, 2022

I have the same question. Unfortunately but I'm not a python user, so I have no clue how to do this. Would you be able to provide a step-by-step guide for dummies? That would be great. And it would be even greater if this could be build into ASReview lab, so it would just always include the notes in the export.

2 replies

rohitgarud Jan 18, 2023

Hi.. were you able to figure it out? Were you able to use Python API to get notes? Thank you.

elisebvd Jan 19, 2023

Hi, yes, in the end I managed to get the notes with Python API instructions, but it was quite a puzzle.

Rensvandeschoot · 2023-01-19T08:18:13Z

Rensvandeschoot
Jan 19, 2023
Maintainer

Great to hear!!! If you can share the steps you have taken, we can create this tutorial together for on the blog: https://asreview.nl/blog/

1 reply

rohitgarud Jan 19, 2023

Actually, after going through same issue, I have created extension for ASReview which can be installed using pip. @Rensvandeschoot sir, please review it at asreview-notes-export give me suggestions to improve it. Thank you very much.

j0sien · 2023-01-30T08:17:51Z

j0sien
Jan 30, 2023

Great @rohitgarud it worked out for me for the first screening round using the default settings.
However, when trying to export after the second screening round (using the exported decisions with notes from the first round as import), I get error messages:

C:\Users\HU\Documents>asreview notes_export ScreeningRound2.asreview
Traceback (most recent call last):
File "C:\Python310\lib\runpy.py", line 196, in _run_module_as_main
return run_code(code, main_globals, None,
File "C:\Python310\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "C:\Python310\Scripts\asreview.exe_main.py", line 7, in
File "C:\Users\HU\AppData\Roaming\Python\Python310\site-packages\asreview_main.py", line 78, in main
entry.load()().execute(sys.argv[2:])
File "C:\Python310\lib\site-packages\asreviewcontrib\notes_export\entrypoint.py", line 63, in execute
export_notes(
File "C:\Python310\lib\site-packages\asreviewcontrib\notes_export\notes_export.py", line 36, in export_notes
dataset_with_results = dataset.df.join(df.set_index('record_id')[['labeling_order','label','exported_notes']], on='record_id')
File "C:\Python310\lib\site-packages\pandas\core\frame.py", line 9260, in join
return self._join_compat(
File "C:\Python310\lib\site-packages\pandas\core\frame.py", line 9291, in _join_compat
return merge(
File "C:\Python310\lib\site-packages\pandas\core\reshape\merge.py", line 122, in merge
return op.get_result()
File "C:\Python310\lib\site-packages\pandas\core\reshape\merge.py", line 718, in get_result
llabels, rlabels = _items_overlap_with_suffix(
File "C:\Python310\lib\site-packages\pandas\core\reshape\merge.py", line 2317, in _items_overlap_with_suffix
raise ValueError(f"columns overlap but no suffix specified: {to_rename}")
ValueError: columns overlap but no suffix specified: Index(['labeling_order', 'exported_notes'], dtype='object')

C:\Users\HU\Documents>asreview notes_export ScreeningRound2.asreview ScreeningRound2.csv
Traceback (most recent call last):
File "C:\Python310\lib\runpy.py", line 196, in _run_module_as_main
return run_code(code, main_globals, None,
File "C:\Python310\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "C:\Python310\Scripts\asreview.exe_main.py", line 7, in
File "C:\Users\HU\AppData\Roaming\Python\Python310\site-packages\asreview_main.py", line 78, in main
entry.load()().execute(sys.argv[2:])
File "C:\Python310\lib\site-packages\asreviewcontrib\notes_export\entrypoint.py", line 47, in execute
raise ValueError("Exporting notes from multiple project files"
ValueError: Exporting notes from multiple project files via the CLI is not supported yet.

7 replies

rohitgarud Jan 31, 2023

Hi.. @j0sien .. I have updated the asreview-notes-export after addressing the issue you faced.. please check and let me know if it works as expected.. you can run pip install --upgrade asreview-notes-export to get the updated version.. Thank you again for your feedback.

j0sien Jan 31, 2023

Thanks @rohitgarud . Unfortunately I still get an error after updating:

C:\Users\josien.boetje\OneDrive - Stichting Hogeschool Utrecht\PhD\Study 1 - Systematic Literature Review\d2_Results>asreview notes_export ScreeningRound2.asreview -o ScreeningRound2.csv
Traceback (most recent call last):
File "c:\program files\python38\lib\runpy.py", line 193, in run_module_as_main
return run_code(code, main_globals, None,
File "c:\program files\python38\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\Scripts\asreview.exe_main.py", line 7, in
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\site-packages\asreview_main.py", line 78, in main
entry.load()().execute(sys.argv[2:])
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\site-packages\asreviewcontrib\notes_export\entrypoint.py", line 74, in execute
export_notes(
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\site-packages\asreviewcontrib\notes_export\notes_export.py", line 47, in export_notes
screening = int(col.split("")[2])
IndexError: list index out of range

C:\Users\josien.boetje\OneDrive - Stichting Hogeschool Utrecht\PhD\Study 1 - Systematic Literature Review\d2_Results>

Also when trying from a non-cloud folder:
C:\Users\josien.boetje>asreview notes_export ScreeningRound2.asreview -o ScreeningRound2.csv
Traceback (most recent call last):
File "c:\program files\python38\lib\runpy.py", line 193, in run_module_as_main
return run_code(code, main_globals, None,
File "c:\program files\python38\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\Scripts\asreview.exe_main.py", line 7, in
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\site-packages\asreview_main.py", line 78, in main
entry.load()().execute(sys.argv[2:])
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\site-packages\asreviewcontrib\notes_export\entrypoint.py", line 74, in execute
export_notes(
File "C:\Users\josien.boetje\AppData\Roaming\Python\Python38\site-packages\asreviewcontrib\notes_export\notes_export.py", line 47, in export_notes
screening = int(col.split("")[2])
IndexError: list index out of range

C:\Users\josien.boetje>

j0sien Jan 31, 2023

I do see a folder 'tmp_data_notes_export'

rohitgarud Jan 31, 2023

Oh.. I think I missed one scenario while testing my code.. sorry for that.. will update as soon as possible and get back to you..

rohitgarud Jan 31, 2023

I have updated the version again.. I hope it works this time.. please check and let me know.. thank you.. @j0sien

cosalofa · 2023-02-23T08:42:58Z

cosalofa
Feb 23, 2023

Hi @rohitgarud, thanks for creating this extension. It worked for me the first time but I tried it again today and received an error. Please see below.

C:\Users\Documents\travail_sauvegarde\Meta-analysis\ASReview>asreview notes_export biodiv-3-3.asreview -o biodiv3as.csv

Traceback (most recent call last):
File "", line 198, in run_module_as_main
File "", line 88, in run_code
File "C:\Users\AppData\Local\Programs\Python\Python311\Scripts\asreview.exe_main.py", line 7, in
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\asreview_main.py", line 78, in main
entry.load()().execute(sys.argv[2:])
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\asreviewcontrib\notes_export\entrypoint.py", line 63, in execute
export_notes(
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\asreviewcontrib\notes_export\notes_export.py", line 36, in export_notes
dataset_with_results = dataset.df.join(df.set_index('record_id')[['labeling_order','label','exported_notes']], on='record_id')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\pandas\core\frame.py", line 9976, in join
return self._join_compat(
^^^^^^^^^^^^^^^^^^
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\pandas\core\frame.py", line 10015, in _join_compat
return merge(
^^^^^^
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\pandas\core\reshape\merge.py", line 124, in merge
return op.get_result(copy=copy)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\pandas\core\reshape\merge.py", line 775, in get_result
result = self._reindex_and_concat(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\pandas\core\reshape\merge.py", line 729, in _reindex_and_concat
llabels, rlabels = _items_overlap_with_suffix(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\pandas\core\reshape\merge.py", line 2458, in _items_overlap_with_suffix
raise ValueError(f"columns overlap but no suffix specified: {to_rename}")

ValueError: columns overlap but no suffix specified: Index(['labeling_order'], dtype='object')

I think that might be getting this error because I uploaded data from a previous project with new entries to a new project. There was already a column called "labelling_order" in the uploaded file. I tried deleting that column in the temp files (C:\Users\AppData\Local\Temp\tmp71e0q6ax\data) but I still get the error.

Any help with this problem will be greatly appreciated.

3 replies

rohitgarud Feb 23, 2023

Hi @cosalofa, thank you for reporting the issue. May I know whether the exported_notes column is also present in the dataset? Can you also please check the version of asreview-notes-export using asreview notes-export --version. If it is 0.0.3, please upgrade using pip install --upgrade asreview-notes-export, if it is 0.0.5, please let me know.

cosalofa Feb 23, 2023

Thank you for your quick response @rohitgarud. I had the 0.0.3 version which I have now upgraded. I have a column entitled exported_notes1 in the dataset. I have rerun the command line and I now get a different error:

C:\Users\Documents\travail_sauvegarde\Meta-analysis\ASReview>asreview notes_export biodiv-3-3.asreview
Traceback (most recent call last):
File "", line 198, in run_module_as_main
File "", line 88, in run_code
File "C:\Users\AppData\Local\Programs\Python\Python311\Scripts\asreview.exe_main.py", line 7, in
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\asreview_main.py", line 78, in main
entry.load()().execute(sys.argv[2:])
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\asreviewcontrib\notes_export\entrypoint.py", line 74, in execute
export_notes(
File "C:\Users\AppData\Local\Programs\Python\Python311\Lib\site-packages\asreviewcontrib\notes_export\notes_export.py", line 49, in export_notes
screening = int(col.split("_")[2])
~~~~~~~~~~~~~~^^^
IndexError: list index out of range

Any idea what the issue might be?

rohitgarud Feb 23, 2023

Thank you. I think I know what is the issue. Did you manually rename the exported_notes column at some point to exported_notes1 or it was there when you exported the first time?

cosalofa · 2023-02-23T12:41:28Z

Rensvandeschoot · 2023-03-31T17:57:28Z

Rensvandeschoot
Mar 31, 2023
Maintainer

resolved in #1335

0 replies

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Add Notes to dataset export #1220

Replies: 8 comments · 17 replies

Rensvandeschoot Sep 13, 2022 Maintainer

fanse Sep 13, 2022 Author

Rensvandeschoot Sep 13, 2022 Maintainer

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Replies: 8 comments 17 replies

Rensvandeschoot
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fanse
Sep 13, 2022
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Rensvandeschoot
Jan 19, 2023
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Rensvandeschoot
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