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Introduce spreadsheet-based sample registration #813

Merged
merged 111 commits into from
Oct 15, 2024
Merged

Introduce spreadsheet-based sample registration #813

merged 111 commits into from
Oct 15, 2024

Commits on Aug 29, 2024

  1. Provide docs for the process

    @sven1103
    sven1103 committed Aug 29, 2024
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  2. Provide readme

    @sven1103
    sven1103 committed Aug 29, 2024
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Commits on Sep 3, 2024

  1. Merge branch 'development' into feature/#680-move-from-the-spreadshee… 

    …t-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 authored Sep 3, 2024
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  2. Save work

    @sven1103
    sven1103 committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Checkin progress

    @sven1103
    sven1103 committed Sep 4, 2024
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  2. Merge branch 'feature/#680-move-from-the-spreadsheet-component-for-sa… 

    …mple-batch-registration-to-xlsx-upload' of github.com:qbicsoftware/data-manager-app into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Sep 4, 2024
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Commits on Sep 5, 2024

  1. Finish registration template

    @sven1103
    sven1103 committed Sep 5, 2024
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  2. Checkin spreadsheet update feature

    @sven1103
    sven1103 committed Sep 5, 2024
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  3. Introduce constant for max row

    @sven1103
    sven1103 committed Sep 5, 2024
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  4. Add JDs

    @sven1103
    sven1103 committed Sep 5, 2024
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Commits on Sep 6, 2024

  1. Checkin Progress

    @sven1103
    sven1103 committed Sep 6, 2024
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  2. Merge remote-tracking branch 'origin/development' into feature/#680-m… 

    …ove-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Sep 6, 2024
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  3. Validation for new samples

    @sven1103
    sven1103 committed Sep 6, 2024
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  4. Merge branch 'development' into feature/#680-move-from-the-spreadshee… 

    …t-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Sep 6, 2024
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Commits on Sep 17, 2024

  1. use the FileRemovedListener

    @KochTobi
    KochTobi committed Sep 17, 2024
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  2. use the power of enums

    @KochTobi
    KochTobi committed Sep 17, 2024
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Commits on Sep 23, 2024

  1. Provide async service methods

    @sven1103
    sven1103 committed Sep 23, 2024
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  2. Update process diagram

    @sven1103
    sven1103 committed Sep 23, 2024
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  3. Provide registration API

    @sven1103
    sven1103 committed Sep 23, 2024
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  4. Improve registration api

    @sven1103
    sven1103 committed Sep 23, 2024
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  5. Update API

    @sven1103
    sven1103 committed Sep 23, 2024
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  6. Remove gibberish code line

    @sven1103
    sven1103 committed Sep 23, 2024
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  7. Add registration exception

    @sven1103
    sven1103 committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. Provide validation result with payload

    @sven1103
    sven1103 committed Sep 24, 2024
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  2. Fix broken class import

    @sven1103
    sven1103 committed Sep 24, 2024
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  3. Update registration service

    @sven1103
    sven1103 committed Sep 24, 2024
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  4. Update registration service implementation

    @sven1103
    sven1103 committed Sep 24, 2024
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  5. Update service method name

    @sven1103
    sven1103 committed Sep 24, 2024
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  6. Merge branch 'development' into feature/#680-move-from-the-spreadshee… 

    …t-component-for-sample-batch-registration-to-xlsx-upload

# Conflicts:
#	user-interface/src/main/bundles/dev.bundle
    @KochTobi
    KochTobi committed Sep 24, 2024
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  7. Update sample registration

    @sven1103
    sven1103 committed Sep 24, 2024
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  8. Merge branch 'feature/#680-move-from-the-spreadsheet-component-for-sa… 

    …mple-batch-registration-to-xlsx-upload' of github.com:qbicsoftware/data-manager-app into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Sep 24, 2024
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  9. fix method signature

    @KochTobi
    KochTobi committed Sep 24, 2024
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  10. make accessing parsing result values easier

    @KochTobi
    KochTobi committed Sep 24, 2024
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  11. make the option headers bold

    @KochTobi
    KochTobi committed Sep 24, 2024
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  12. fix indexing

    @KochTobi
    KochTobi committed Sep 24, 2024
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  13. move methods to helper class

    @KochTobi
    KochTobi committed Sep 24, 2024
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  14. move measurement templates

    @KochTobi
    KochTobi committed Sep 24, 2024
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  15. split sample registration tempaltes

    @KochTobi
    KochTobi committed Sep 24, 2024
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  16. fix imports

    @KochTobi
    KochTobi committed Sep 24, 2024
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  17. add column enums

    @KochTobi
    KochTobi committed Sep 24, 2024
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  18. fix javadoc reference

    @KochTobi
    KochTobi committed Sep 24, 2024
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  19. fix imports

    @KochTobi
    KochTobi committed Sep 24, 2024
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  20. rename enums

    @KochTobi
    KochTobi committed Sep 24, 2024
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  21. use correct enum

    @KochTobi
    KochTobi committed Sep 24, 2024
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  22. remove unused field

    @KochTobi
    KochTobi committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Use sanitizer

    @KochTobi
    KochTobi committed Sep 25, 2024
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  2. Add SampleInformationExtractor

    @KochTobi
    KochTobi committed Sep 25, 2024
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  3. remove misc address stuff 

    Co-authored-by: Sven F. <[email protected]>
    @KochTobi @sven1103
    KochTobi and sven1103 committed Sep 25, 2024
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  4. Switch to automatic push mode instead of manual

    @KochTobi
    KochTobi committed Sep 25, 2024
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Commits on Sep 27, 2024

  1. Enable async execution for sample methods

    @sven1103
    sven1103 committed Sep 27, 2024
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  2. push dialog rough forms

    @KochTobi
    KochTobi committed Sep 27, 2024
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  3. Fix search by Obo ID

    @KochTobi
    KochTobi committed Sep 27, 2024
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  4. Show user input back to the user instead of only ontology term

    @KochTobi
    KochTobi committed Sep 27, 2024
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  5. handle exceptions

    @KochTobi
    KochTobi committed Sep 27, 2024
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  6. add toString method to OntologyTerm for development log output

    @KochTobi
    KochTobi committed Sep 27, 2024
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  7. Do not swallow comments

    @KochTobi
    KochTobi committed Sep 27, 2024
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Commits on Sep 30, 2024

  1. fix sample name being ignored

    @KochTobi
    KochTobi committed Sep 30, 2024
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  2. Remove unused methods in ValidationResult

    @KochTobi
    KochTobi committed Sep 30, 2024
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  3. working but ugly dialog

    @KochTobi
    KochTobi committed Sep 30, 2024
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  4. Merge branch 'development' into feature/#680-move-from-the-spreadshee… 

    …t-component-for-sample-batch-registration-to-xlsx-upload
    @KochTobi
    KochTobi committed Sep 30, 2024
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  5. inline method again

    @KochTobi
    KochTobi committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Move functionality to register button

    @KochTobi
    KochTobi committed Oct 1, 2024
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  2. deprecate BatchRegistrationDialog.java

    @KochTobi
    KochTobi committed Oct 1, 2024
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  3. move to EditSampleBatchDialog

    @KochTobi
    KochTobi committed Oct 1, 2024
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  4. delete template service field

    @KochTobi
    KochTobi committed Oct 1, 2024
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Commits on Oct 7, 2024

  1. remove exception

    @KochTobi
    KochTobi committed Oct 7, 2024
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  2. add return

    @KochTobi
    KochTobi committed Oct 7, 2024
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  3. Throw registration exception

    @sven1103
    sven1103 committed Oct 7, 2024
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  4. add states to wizard window

    @KochTobi
    KochTobi committed Oct 7, 2024
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  5. add asterix

    @KochTobi
    KochTobi committed Oct 7, 2024
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  6. remove pilot checkbox

    @KochTobi
    KochTobi committed Oct 7, 2024
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  7. check for required batch name input

    @KochTobi
    KochTobi committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. extract constant

    @KochTobi
    KochTobi committed Oct 8, 2024
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  2. extract method

    @KochTobi
    KochTobi committed Oct 8, 2024
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  3. improve handling of the optional upload data

    @KochTobi
    KochTobi committed Oct 8, 2024
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  4. Change template name to start with project code

    @KochTobi
    KochTobi committed Oct 8, 2024
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  5. Fix TIBTerminologyServiceIntegration.java

    @KochTobi
    KochTobi committed Oct 8, 2024
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  6. Fix sample batch registration

    @KochTobi
    KochTobi committed Oct 8, 2024
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  7. Fix batch

    @sven1103
    sven1103 committed Oct 8, 2024
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  8. Merge branch 'feature/#680-move-from-the-spreadsheet-component-for-sa… 

    …mple-batch-registration-to-xlsx-upload' of github.com:qbicsoftware/data-manager-app into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Oct 8, 2024
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  9. add * to update sample headers

    @KochTobi
    KochTobi committed Oct 8, 2024
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  10. remove session scope from ClientDetailsProviderImpl

    @KochTobi
    KochTobi committed Oct 8, 2024
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  11. Handle exceptions in registration future

    @KochTobi
    KochTobi committed Oct 8, 2024
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  12. Merge remote-tracking branch 'origin/feature/#680-move-from-the-sprea… 

    …dsheet-component-for-sample-batch-registration-to-xlsx-upload' into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @KochTobi
    KochTobi committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Fix Async for SampleValidation.java 

    Previously the SampleValidation.java class was not thread safe. Now the state is wrapped by a thread local variable, solving the issues of asynchronous requests interfering with each other.
    @KochTobi
    KochTobi committed Oct 9, 2024
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  2. Simplify result aggregation 

    Simplifies the way asynchronous execution of sample validation is merged when all validation tasks completed.
    @KochTobi
    KochTobi committed Oct 9, 2024
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Commits on Oct 11, 2024

  1. Add edit functionality

    @KochTobi
    KochTobi committed Oct 11, 2024
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  2. apply css

    @KochTobi
    KochTobi committed Oct 11, 2024
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  3. show progress in edit dialog

    @KochTobi
    KochTobi committed Oct 11, 2024
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  4. make it look nicer

    @KochTobi
    KochTobi committed Oct 11, 2024
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Commits on Oct 14, 2024

  1. add css classes for headings

    @KochTobi
    KochTobi committed Oct 14, 2024
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  2. Add missing condition check

    @KochTobi
    KochTobi committed Oct 14, 2024
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  3. Add unknown condition information

    @KochTobi
    KochTobi committed Oct 14, 2024
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  4. Change heading 

    The UploadWithDisplay.java can only contain 1 file. Thus uploaded files was changed to uploaded file.
    @KochTobi
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  5. Format template columns width based on the max content

    @sven1103
    sven1103 committed Oct 14, 2024
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  6. Merge branch 'feature/#680-move-from-the-spreadsheet-component-for-sa… 

    …mple-batch-registration-to-xlsx-upload' of github.com:qbicsoftware/data-manager-app into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Oct 14, 2024
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  7. add javadoc

    @KochTobi
    KochTobi committed Oct 14, 2024
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  8. switch to analysis method

    @KochTobi
    KochTobi committed Oct 14, 2024
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  9. Fix filtering

    @KochTobi
    KochTobi committed Oct 14, 2024
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Commits on Oct 15, 2024

  1. style the steps

    @KochTobi
    KochTobi committed Oct 15, 2024
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  2. Prevent empty batch creation

    @KochTobi
    KochTobi committed Oct 15, 2024
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  3. Fix upload remove case

    @KochTobi
    KochTobi committed Oct 15, 2024
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  4. Show errors nicely

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  5. Merge branch 'development' into feature/#680-move-from-the-spreadshee… 

    …t-component-for-sample-batch-registration-to-xlsx-upload
    @KochTobi
    KochTobi authored Oct 15, 2024
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  6. Fix line breaks 

    Co-authored-by: Sven F. <[email protected]>
    @KochTobi @sven1103
    KochTobi and sven1103 committed Oct 15, 2024
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  7. Merge remote-tracking branch 'origin/feature/#680-move-from-the-sprea… 

    …dsheet-component-for-sample-batch-registration-to-xlsx-upload' into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @KochTobi
    KochTobi committed Oct 15, 2024
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  8. fix analysis method failure message

    @KochTobi
    KochTobi committed Oct 15, 2024
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  9. change failure display

    @KochTobi
    KochTobi committed Oct 15, 2024
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  10. remove parenthesis

    @KochTobi
    KochTobi committed Oct 15, 2024
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  11. Handle empty sheet case

    @sven1103
    sven1103 committed Oct 15, 2024
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  12. Merge branch 'feature/#680-move-from-the-spreadsheet-component-for-sa… 

    …mple-batch-registration-to-xlsx-upload' of github.com:qbicsoftware/data-manager-app into feature/#680-move-from-the-spreadsheet-component-for-sample-batch-registration-to-xlsx-upload
    @sven1103
    sven1103 committed Oct 15, 2024
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