Code

Metadata uploader base#1445

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deepsidhu85 merged 207 commits intodevelopmentphac-nml/irida:developmentfrom metadata-uploader-basephac-nml/irida:metadata-uploader-baseCopy head branch name to clipboardJan 27, 2023

+2,956-2,414

Commits

Commits on Aug 31, 2022

• reading file with sheetjs

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Commits on Sep 1, 2022

• persisting file contents

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Commits on Sep 8, 2022

• Merge branch 'metadata-uploader-base' into metadata-uploader-parse-file

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Commits on Sep 9, 2022

• setting sample name column

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• starting to show metadata in table on review step

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• starting to show metadata in table on review step

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Commits on Sep 12, 2022

• supplementing metadata after sample name column is selected

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Commits on Sep 13, 2022

• fixing onCell for sample name collumn

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Commits on Sep 14, 2022

• working on validating sample names

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Commits on Sep 15, 2022

• navigating to review page once setting sample name is complete

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Commits on Sep 16, 2022

• starting to create/update samples with metadata

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• displaying stats on complete page

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Commits on Sep 20, 2022

• fixing stats

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• showing errors

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Commits on Sep 21, 2022

• keeping formatted numeric cells instead of raw

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• fixing tests

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• fixing typescript errors

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• adding table pagination to review table

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Commits on Sep 22, 2022

• adding progress bar for saving samples

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Commits on Sep 23, 2022

• trying chunk uploading

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• fixing test

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Commits on Sep 27, 2022

• adding some spinners to pages to show loading

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• navigating back to beginning after upload complete

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Commits on Sep 28, 2022

• storing saving and validation details in seperate hashes instead of modifying the metadata object where twp objects are stored in memory temporarily

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• Merge branch 'metadata-uploader-base' into metadata-uploader-parse-file

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• skipping saving samples that have already been saved

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• converting SampleMetadataImportSteps.jsx to typescript

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Commits on Sep 29, 2022

• converting SampleMetadataImportUploadFile.jsx to typescript

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Commits on Oct 4, 2022

• converting SampleMetadataImportMapHeaders.jsx to typescript

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Commits on Oct 5, 2022

• converting SampleMetadataImportReview.tsx to typescript

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• converting SampleMetadataImportComplete.jsx to typescript

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• more typescript

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• getting around deadlock

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• fix test

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Commits on Oct 7, 2022

• eslinting

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Commits on Oct 11, 2022

• removing todo

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Commits on Oct 12, 2022

• starting to add restriction drop-down to map headers step

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Commits on Oct 13, 2022

• disabling restriction drop-down on sample name column selection

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• starting to save restriction level changes

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Commits on Oct 14, 2022

• starting to save metadata restrictions

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• removing redundant code

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Commits on Oct 17, 2022

• retreiving restriction drop-down list

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Commits on Oct 18, 2022

• saving state on page refresh

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• changing for loop syntax

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• making children not optional for SampleMetadataImportWizardProps

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• fixing wizard layout

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• removing file extension on DragUpload import

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• fixing DraagUpload type

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• updating colors to use css variables

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Commits on Oct 24, 2022

• Merge pull request #1362 from phac-nml/metadata-uploader-parse-file

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• Merge branch 'development' into metadata-uploader-base

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Commits on Oct 25, 2022

• Merge branch 'metadata-uploader-base' into metadata-uploader-restrictions

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• changing restriction select to radio button group

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Commits on Oct 27, 2022

• replacing table row selection with select sample name column drop down

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• changing updatedHeaders to useRef from useState

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• removing preselecting a sample name column and showing table empty on load

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• diplaying table on sample name column instead of showing table empty

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• making table scrollable

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Commits on Oct 28, 2022

• defaulting headers to existing project metadata field restrictions

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Commits on Oct 31, 2022

• reset state on completion

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Commits on Nov 1, 2022

• assuming metadata fields with restrictions are already created before metadata entry creation

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• starting to create a new api endpoint to create metadata fields with restrictions

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Commits on Nov 2, 2022

• fixing create metadata fields api endpoint

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• removing commented out code

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Commits on Nov 3, 2022

• storing a separate session for each project

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• removing redirection on completion

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• adding quick and dirty way to strip leading & trailing whitespace from file data

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• fixing tests

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Commits on Nov 4, 2022

• starting to create new batch api endpoints

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• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-restrictions

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• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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Commits on Nov 7, 2022

• adding table empty

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• adding table title

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• using useMemo for table dataSouce

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Commits on Nov 9, 2022

• sending requests in chunks

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• fixing error handling

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Commits on Nov 10, 2022

• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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• Merge branch 'metadata-uploader-base' into metadata-uploader-restrictions

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  8e8f642

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• changing 'Map Headers' to 'Map Columns'

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• fixing formatting

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• working on showing existing and target restrictions

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• converting TargetMetadataRestriction.jsx to typescript

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Commits on Nov 15, 2022

• starting to add unique key on label for metadata_field table

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• replacing select with radio group buttons in TargetMetadataRestrictions.tsx

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Commits on Nov 16, 2022

• fixing test

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• renaming 'Upload File' to 'Select File'

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• changing ant design upload options so it does not do a post request

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• changing ant design upload options so it does not do a post request

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• making create project modal wider

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• updating project settings metadata fields to use radio group buttons

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• updating project settings metadata fields to use radio group buttons

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Commits on Nov 17, 2022

• removing unused params

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• renaming MetadataFieldModel.java to MetadataEntryModel.java

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• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-restrictions

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• replacing metadata restrictions select with radio group buttons for sample details modal

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• fixing tests

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Commits on Nov 18, 2022

• getting the locked samples for a project

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Commits on Nov 21, 2022

• adding locked sample column to review table

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• moving locked samples into an alert

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• fixing complete stats

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Commits on Nov 23, 2022

• Merge pull request #1383 from phac-nml/metadata-uploader-restrictions

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• disabling buttons and table during loading

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• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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Commits on Nov 25, 2022

• adding promise chaining back in

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Commits on Dec 1, 2022

• replacing step progress bar with table overlay progress bar

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Commits on Dec 2, 2022

• moving loading text into spinner

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Commits on Dec 5, 2022

• moving returning ResponseEntity into controller

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• fixing broken test

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• fixing create project sample from modal

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• moving returning ResponseEntity into controller

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• Merge pull request #1419 from phac-nml/metadata-uploader-progress-bar

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• adding more tests

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• adding comments

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• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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• fixing unmounted component error

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Commits on Dec 6, 2022

• starting to work on handling duplicate file header names

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• starting to work on handling duplicate file header names

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Commits on Dec 7, 2022

• starting to work on handling duplicate file header names

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• changing path names

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• returning a mult-status response from controller

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• adding functionality to calculate chunk size

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Commits on Dec 8, 2022

• creating CreateSampleResponse and UpdateSampleResponse objects

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• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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• fixing tests

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Commits on Dec 9, 2022

• playing with a second web driver to have seperate users logged in simultanelously to test deleting a project during a metadata import

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• cleaning up unused, old code

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• Merge branch 'metadata-uploader-base' into metadata-uploader-validate-file

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• replacing notification with alert

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Commits on Dec 12, 2022

• setting up delete samples during import test

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• setting up create new sample during import test

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• setting up remove access during import test

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Commits on Dec 16, 2022

• finishing tests

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• updating documentation

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• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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Commits on Dec 19, 2022

• trying to fix flaky tests

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• trying to fix flaky tests

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Commits on Dec 20, 2022

• trying to fix flaky tests

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Commits on Dec 21, 2022

• removing old restriction code

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• adding more comments

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• using metadataSaveDetails from state

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• removing log statements

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• adding partial success upload notification

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• removing returned metadataSaveDetails as it is redundant

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• creating a import-utilities.js file for refactoring

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• simplifying code and calling Promise.all

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• using forEach instead of map

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• returning more explicit filter

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Commits on Dec 22, 2022

• adding comments

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• more refactoring

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Commits on Dec 23, 2022

• more refactoring

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Commits on Jan 4, 2023

• fixing some tests

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Commits on Jan 5, 2023

• adding a test

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• Merge branch 'development' into metadata-uploader-base

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• Merge branch 'metadata-uploader-base' into metadata-uploader-validate-file

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Commits on Jan 6, 2023

• Merge branch 'metadata-uploader-base' into metadata-uploader-batch-endpoints

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• fixing chunkArray function

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• fixing chunkArray function

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• taking care of all the 'any' types

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• memorizing filter

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• applying eslint suggestions

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• making a clone of param because splice is destructive

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• resolving typescript warning

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• resolving typescript warning

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• renaming type

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Commits on Jan 7, 2023

• fixing tests

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Commits on Jan 9, 2023

• applying eslint suggestion

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• renaming SampleItemResponse

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Commits on Jan 10, 2023

• adding space between drag'n'drop and alert

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• updating text in message.properties

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• Merge pull request #1408 from phac-nml/metadata-uploader-batch-endpoints

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Commits on Jan 11, 2023

• reading file into a multidimensional array

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• Merge branch 'metadata-uploader-base' into metadata-uploader-validate-file

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• fixing tests

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