Descriptor files #89
Descriptor files #89
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The goal is to create descriptor files from a data csv file. Each line corresponds to a different descriptor file
The goal is to create descriptor files from a data csv file. Each line corresponds to a different descriptor file
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@JuliaSprenger new PR ! i think i did a mistake with the version so i have change it ... |
JuliaSprenger
added
the
safe to test
| @@ -81,3 +81,27 @@ def remove_columns(csv_file, compressed_file=None): | |||
| def exportCSVtoXLS(csv_file, compressed_file=None): | |||
| read_file = pd.read_csv(csv_file, na_filter=False, dtype='str') | |||
| read_file.to_excel(r'Path', index=None, header=True) | |||
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| def conversion_to_odml_table_descriptor(full_elabbook_csv, session_number): | |||
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Can you add a keyword argument to automatically save this to a csv file if a filename is provided?
redcap_bridge/utils.py
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| df_melted = df_melted.rename(columns={'variable': 'Property name'}) | ||
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| print(df_melted.to_string()) |
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There is a set of mandatory columns for odmltables csv files. Can you check that all of them are present after the conversion and have values that are accepted by odmltables? E.g. the data type colum can only contain specific values that are understood by odmltables...
| def test_conversion_to_odml_table_descriptor(initialize_test_dir): | ||
| test_dir = test_directory / 'testfiles_redcap' / 'descriptors' | ||
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| conversion_to_odml_table_descriptor(test_dir / 'Vision4Action_DATA_2023-04-13_1110.csv', session_number=5) |
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this test is only checking if the code runs into an error so far. Could you extend this and also test the content of the converted file? Maybe you will need to add an odmltables reference test file to compare against.
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Yes, will change the test in priority
| @@ -1 +1 @@ | |||
| 0.0.2 | |||
| 0.0.3-a.1 | |||
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Yes, this change should not be part of this PR.
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Updating from the latest master should fix this.
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Comment: the goal of this PR is to create a new descriptor file so that it can be integrated in the V4A pipeline in the future... The BIDS-ification of the V4A pipeline will then follow... |
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The goal is to be compatible with:odmltables |
This is the new version of the PR for the creation of descriptor files.