Comments (15)
And also I'm applying for GSOC 2021
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I have made a python script for this
Here is the Github link to the repo: https://github.com/Nishchal-007/CheckingNull
Also, there is a dummy CSV file for testing purpose
Let me know if there's anything else to be done.
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A few pointers:
- When we say missing entries, what we mean is a file:
empi, accassion
32323, 32323323232
23323,
323232, 332323
, 3232332323
In this case, the line 2 and 4 should be skipped, but the rest of the extraction should go on.
-
It is not the entire CSV that is empty or should be considered invalid and ignored. Rather, making the executions succeed, despite the missing lines.
-
Also, I recommend cloning the repository and submitting pull requests, rather than creating private repositories with stand-alone codes. The code changes will modify the https://github.com/Emory-HITI/Niffler/blob/dev/modules/cold-extraction/ColdDataRetriever.py (Please use the dev branch).
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Okay, Will do that !!
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I have forked and made changes to the cold-extraction module and added the checkCSV.py file.
Can you please check it out?
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That pull request modifies 67 files. Please resubmit a new pull request without modifying other files, also addressing other comments in the pull request.
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Yeah I checked the points in the pull request
My approach to this current issue is if there are any missing values in the file I'm just dropping them in the beginning itself
Is this approach okay or should I change this?
And regarding the file changes, I did "add all" that's why it affected all the files
But no file is modified or changed internally
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Ideally, you should drop it on the go, as otherwise, this process of reading the file will introduce an initial delay.
Also, there is no reason to create a separate python class. You can modify modules/cold-extraction/ColdDataRetriever.py.
You can use the "csv_file" variable there as it already points to the csv_file.
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Okay
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Made the necessary changes in the ColdDataRetriever.py file
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Please pay attention to the comments.
https://github.com/Emory-HITI/Niffler/pull/115/files changes files unnecessarily. Please avoid changing files that have no relevance to the pull request. Also, I believe you are modifying only the ColdDataRetriever.py and other changes (such as a sample CSV file) are not necessary.
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Only changed the ColdDataRetriever.py file
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Added some important comments in your pull request. Please attend to them and submit an updated request when you have tested the changes.
A comment that is more specific to elaborate this issue:
Please note that you should check only for the missing entry of the mandatory fields.
-
empi_date: make sure neither empi nor date is empty (there could be other fields that can be empty).
-
empi: make sure empi is not empty (there could be other fields that can be empty).
-
accession: make sure accession is not empty (there could be other fields that can be empty).
-
empi_accession: make sure neither empi nor accession is empty (there could be other fields that can be empty).
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Hey,
I made the required changes to the ColdDataRetriever.py file
Can you please check it out?
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Looks good now. Merged to dev. Thanks.
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Related Issues (20)
- A composable workflow module HOT 2
- Support for custom Non-DICOM Time attributes HOT 2
- Support extracting Private DICOM tags using the png-extraction HOT 9
- Containerize PNG Extraction module HOT 8
- MemoryError while extracting metadata using PNG Extraction Module HOT 6
- png-extractor module not working in arch linux HOT 3
- Random PNG Extraction Errors HOT 2
- Enable the feature to extract only a certain DICOM headers in png-extraction HOT 6
- Niffler commit workflows are faling. HOT 20
- In png-extraction module, this configuration "PublicHeadersOnly" is not working during the extraction of private tags. After adding configuration "SpecificHeadersOnly".
- If there are large no. of mapping or metadata files - concatenating or merging them leads to a Memory Error. HOT 1
- CommonHeadersOnly is not working as expected. HOT 7
- Packaging Niffler with pip HOT 3
- Containerizing Niffler HOT 11
- file column is nan for certain images.
- Running ImageExtractor.py is not finding .dcm files in target directory HOT 8
- Anaconda reinstallation HOT 1
- macOS_install.sh script for quick installation of dependancies for MacOS HOT 1
- syntax error in the ImageExtractorNifti.py, line 206 HOT 1
- PNG-Extraction bugs: Missing Imports and Undeclared Variable Errors
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