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Beta #90

Merged
merged 334 commits into from
Sep 20, 2019
Merged

Beta #90

merged 334 commits into from
Sep 20, 2019
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jul 25, 2019

  1. Create Search Filter for the Persisted Mapping Entities

    @sprintell
    sprintell committed Jul 25, 2019
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  2. Write treatments to H2 DB

    @sprintell
    sprintell committed Jul 25, 2019
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  3. Create mapping rest endpoint with search filters 

    Added pagination services and pageable feature to H2 mapping services
    @sprintell
    sprintell committed Jul 25, 2019
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  4. Properly handle any case combination in mapping entity filter search

    @sprintell
    sprintell committed Jul 25, 2019
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  5. Save unmapped treatments into database during dataloading

    @sprintell
    sprintell committed Jul 25, 2019
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  6. Save unmapped treatments into database during dataloading

    @sprintell
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  7. Reconfigure travisci dependency from oraclejdk8 to openjdk8 - oracle … 

    …licensing has changed
    @sprintell
    sprintell committed Jul 25, 2019
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  8. Validate page and size request to avoid negative page request error

    @sprintell
    sprintell committed Jul 25, 2019
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  9. Added filter to query for missing mappings 

    Added filter to query for mapType
    @sprintell
    sprintell committed Jul 25, 2019
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Commits on Jul 26, 2019

  1. UPDOG separate metadata loading

    @CsabaHalmagyi
    CsabaHalmagyi committed Jul 26, 2019
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  2. Get MappingedEntities By type from DB and Load mapping suggestions fr… 

    …om Knowledge Base for unmapped terms
    @sprintell
    sprintell committed Jul 26, 2019
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  3. Get MappingedEntities By type from DB and Load mapping suggestions fr… 

    …om Knowledge Base for unmapped terms
    @sprintell
    sprintell committed Jul 26, 2019
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  4. Angular Front end retrieves unmapped treatments and diagnosis and dis… 

    …play on corresponding css badge
    @sprintell
    sprintell committed Jul 26, 2019
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  5. Add filter to mappings endpoint for retrieving all mapped terms

    @sprintell
    sprintell committed Jul 26, 2019
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Commits on Jul 29, 2019

  1. ANgular UI, cleanup

    @sprintell
    sprintell committed Jul 29, 2019
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  2. Compute mapping summary statistics on the server for the angular client

    @sprintell
    sprintell committed Jul 29, 2019
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  3. Refactor mapping summary page to use summary statistics data from the… 

    … server
    @sprintell
    sprintell committed Jul 29, 2019
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  4. Create entitytype filter (treatment, diagnosis, ...) for mapping summ… 

    …ary by data source
    @sprintell
    sprintell committed Jul 29, 2019
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Commits on Jul 30, 2019

  1. Update loader to use new template format

    @CsabaHalmagyi
    CsabaHalmagyi committed Jul 30, 2019
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  2. Implement dynamic datasource-summary angular component and template f… 

    …or treatment, diagnosis and ...
    @sprintell
    sprintell committed Jul 30, 2019
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Commits on Jul 31, 2019

  1. Show datasource specific table only if missing mapping entity exists

    @sprintell
    sprintell committed Jul 31, 2019
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  2. Dynamically retrieve center specific columns and row contents

    @sprintell
    sprintell committed Jul 31, 2019
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  3. Extend the Data Transfer Object Interface in angular to capture pagin… 

    …ation info
    @sprintell
    sprintell committed Jul 31, 2019
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  4. Add pagination feature in angular front end

    @sprintell
    sprintell committed Jul 31, 2019
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  5. Complete Pagination Navigation and make it respond to param changes o… 

    …n thesame route path
    @sprintell
    sprintell committed Jul 31, 2019
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  6. Fix misplaced text

    @sprintell
    sprintell committed Jul 31, 2019
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Commits on Aug 1, 2019

  1. Fix mapping suggestions

    @sprintell
    sprintell committed Aug 1, 2019
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  2. Extend back end service to get MappingEntity By Id

    @sprintell
    sprintell committed Aug 1, 2019
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  3. Implement dynamic column for suggestion table

    @sprintell
    sprintell committed Aug 1, 2019
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Commits on Aug 2, 2019

  1. Create detailed notification view on curator selection of unmapped term

    @sprintell
    sprintell committed Aug 2, 2019
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  2. Load and manage Knowledge base from Finder on the curation interface

    @sprintell
    sprintell committed Aug 2, 2019
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  3. Allow part submission of curated terms

    @sprintell
    sprintell committed Aug 2, 2019
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  4. Validate batch submission and discard unmapped terms

    @sprintell
    sprintell committed Aug 2, 2019
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  5. Add data size to page navigation

    @sprintell
    sprintell committed Aug 2, 2019
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Commits on Aug 5, 2019

  1. Merge pull request #76 from PDXFinder/updog_refactoring 

    Updog refactoring
    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 5, 2019
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  2. Reposition the page size drop down selector to the far right

    @sprintell
    sprintell committed Aug 5, 2019
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  3. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Aug 5, 2019
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  4. Get suggestions only if mapped term is missing

    @sprintell
    sprintell committed Aug 5, 2019
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Commits on Aug 6, 2019

  1. Make component's type Drug by default

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 6, 2019
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  2. Remove treatment type standardization

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 6, 2019
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  3. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 6, 2019
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  4. Remove unused methods

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 6, 2019
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  5. Add ontology term to treatment list

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 6, 2019
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  6. Save Curated Mapped Diagnosis in Admin - PDXI-469

    @sprintell
    sprintell committed Aug 6, 2019
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  7. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Aug 6, 2019
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Commits on Aug 7, 2019

  1. Extend utilityService file writer to allow caller to specify destinat… 

    …ion and append mode
    @sprintell
    sprintell committed Aug 7, 2019
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  2. Write updated mapped terms to the file system and backup old file

    @sprintell
    sprintell committed Aug 7, 2019
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  3. Add transcriptomics attributes

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 7, 2019
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  4. Make UPDOG load transcriptomics

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 7, 2019
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  5. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 7, 2019
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  6. ADMIN INTERFACE 8 : Extend Service to retrieve mapping rules by status

    @sprintell
    sprintell committed Aug 7, 2019
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  7. Avoid submission of empty mapping list

    @sprintell
    sprintell committed Aug 7, 2019
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Commits on Aug 8, 2019

  1. ADMIN: Added behaviour to notify user of success or failure after sub… 

    …mitting curation
    @sprintell
    sprintell committed Aug 8, 2019
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  2. ADMIN: Added behaviour to request approval before submit curation

    @sprintell
    sprintell committed Aug 8, 2019
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  3. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Aug 8, 2019
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Commits on Aug 9, 2019

  1. Update urls for jax

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 9, 2019
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  2. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 9, 2019
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  3. ADMIN: Added components&interfaces to manage skipped terms, archive t… 

    …erms, and mappings created by curators but not yet approved by centers
    @sprintell
    sprintell committed Aug 9, 2019
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  4. Add Floating action Button Feature

    @sprintell
    sprintell committed Aug 9, 2019
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Commits on Aug 12, 2019

  1. Retrieve and present mappings created by curators but not yet approve… 

    …d by centers on maanage-curator page
    @sprintell
    sprintell committed Aug 12, 2019
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  2. Add pagination and feature to retrieve curated data status to manage-… 

    …curation
    @sprintell
    sprintell committed Aug 12, 2019
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  3. Add Search Filter and Filter Bar UI Components for manage-curations

    @sprintell
    sprintell committed Aug 12, 2019
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  4. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Aug 12, 2019
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  5. Fix double conversion error

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 12, 2019
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  6. Refactor harcoded list of curation filter to dynamically load from da… 

    …tabase
    @sprintell
    sprintell committed Aug 12, 2019
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Commits on Aug 13, 2019

  1. Remove getDrugName

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 13, 2019
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  2. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 13, 2019
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  3. Add Jacoco code coverage reporting

    @rmwthorne
    rmwthorne committed Aug 13, 2019
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  4. Merge remote-tracking branch 'origin/dev' into dev

    @rmwthorne
    rmwthorne committed Aug 13, 2019
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  5. Added feature for multiple filter query using Checkboxes in manage-cu… 

    …ration component/template
    @sprintell
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  6. Add custom col-lg-2.5 to bootstrap grid system

    @sprintell
    sprintell committed Aug 13, 2019
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  7. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Aug 13, 2019
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  8. Refactor mappingService and repository to allow multiple parameters o… 

    …n search filter
    @sprintell
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Commits on Aug 14, 2019

  1. Extend BaseLoader to set access modality groups for models

    @rmwthorne
    rmwthorne committed Aug 14, 2019
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Commits on Aug 15, 2019

  1. Retrieve missing mapping data by status column, Allow submission of s… 

    …kipped curation terms
    @sprintell
    sprintell committed Aug 15, 2019
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  2. Add feature to skip desired term during curation

    @sprintell
    sprintell committed Aug 15, 2019
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  3. Add components for archive and skipped terms interface

    @sprintell
    sprintell committed Aug 15, 2019
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  4. Refactor angular services and add badge notification for orphaned terms

    @sprintell
    sprintell committed Aug 15, 2019
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  5. Merge pull request #77 from PDXFinder/baseloader_access_modalities 

    Extend BaseLoader to set access modality groups for models
    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 15, 2019
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  6. Add Treatment similarity index rule

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 15, 2019
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  7. Add UI to manage orphaned terms skipped from unmapped terms

    @sprintell
    sprintell committed Aug 15, 2019
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  8. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
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  9. Extend IRCC loader to set access modalities on all models

    @rmwthorne
    rmwthorne committed Aug 15, 2019
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  10. wip tests

    @rmwthorne
    rmwthorne committed Aug 15, 2019
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  11. Add files via upload 

    Unit tests for TreatmentProtocol DAO and DataImportService
    @Afollet
    Afollet committed Aug 15, 2019
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  12. Rename TreatmentProtocolTest.java to data-services/src/test/java/org/… 

    …pdxfinder/services/DataImportServicesTests.java
    @Afollet
    Afollet committed Aug 15, 2019
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  13. Delete DataImportServiceTests.java

    @Afollet
    Afollet committed Aug 15, 2019
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  14. Delete DataImportServicesTests.java

    @Afollet
    Afollet committed Aug 15, 2019
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Commits on Aug 16, 2019

  1. Unit Tests for TreatmentProtocol DAO and DataImportService

    @Afollet
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  2. Refactored Unit Tests for DataImportServices

    @Afollet
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Commits on Aug 19, 2019

  1. Add Email Notification Service - PDXI-368

    @sprintell
    sprintell committed Aug 19, 2019
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  2. Add thymeleaf Email template for sending dynamically generated HTML E… 

    …-mail
    @sprintell
    sprintell committed Aug 19, 2019
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  3. Add templateResolver configuration to dataService TestConfig for Mult… 

    …ipart HTML E-mail service
    @sprintell
    sprintell committed Aug 19, 2019
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  4. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into imp… 

    …cc_access_modalities
    @rmwthorne
    rmwthorne committed Aug 19, 2019
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  5. Start fixing indexer mocks

    @rmwthorne
    rmwthorne committed Aug 19, 2019
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  6. Extend Admin back end service to allow download of csv file of curati… 

    …ons for data providers
    @sprintell
    sprintell committed Aug 19, 2019
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  7. Add front end feature to export csv file of curations for data providers

    @sprintell
    sprintell committed Aug 19, 2019
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Commits on Aug 20, 2019

  1. Sort missing mapped terms by 'unmapped column'

    @sprintell
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  2. Add front End Components for managing validated curations based on pr… 

    …oviders approval
    @sprintell
    sprintell committed Aug 20, 2019
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  3. Refactored and cleaned code. Rearranged variables.

    @Afollet
    Afollet committed Aug 20, 2019
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  4. Added file upload page and angular service to transfer uploaded files

    @sprintell
    sprintell committed Aug 20, 2019
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  5. Add uploaded MultipartFile serializer to UtilityService

    @sprintell
    sprintell committed Aug 20, 2019
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Commits on Aug 21, 2019

  1. Shift treatment columns

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 21, 2019
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  2. Add Camel Case converters to utilties

    @sprintell
    sprintell committed Aug 21, 2019
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  3. Generate csv files with human readable header

    @sprintell
    sprintell committed Aug 21, 2019
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  4. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
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  5. Save harmonization report in csv

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 21, 2019
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Commits on Aug 22, 2019

  1. Add Validation rules for upload CSV headers and contents ensuring the… 

    …y originated from the database previously
    @sprintell
    sprintell committed Aug 22, 2019
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  2. Ensure treatment-mapping csv upload passes validation test

    @sprintell
    sprintell committed Aug 22, 2019
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  3. Fix unit test

    @jmason-ebi
    jmason-ebi committed Aug 22, 2019
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  4. Merge pull request #78 from PDXFinder/fix_indexer_mocks 

    Fix indexer mocks
    @rmwthorne
    rmwthorne committed Aug 22, 2019
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  5. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into imp… 

    …cc_access_modalities
    @rmwthorne
    rmwthorne committed Aug 22, 2019
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  6. Omic loader to load from various file formats

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 22, 2019
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  7. Check write permission for log dir

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 22, 2019
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  8. Move test resources in line with correct directory sturcture

    @rmwthorne
    rmwthorne committed Aug 22, 2019
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  9. Merge pull request #79 from PDXFinder/fix_indexer_mocks 

    Move test resources in line with correct directory sturcture
    @rmwthorne
    rmwthorne committed Aug 22, 2019
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  10. Added feature to upload, validate and update validate terms in H2 DB

    @sprintell
    sprintell committed Aug 22, 2019
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  11. Extend front end for validation file upload

    @sprintell
    sprintell committed Aug 22, 2019
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  12. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
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Commits on Aug 23, 2019

  1. Add missing log msg

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 23, 2019
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  2. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 23, 2019
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  3. Extend front end to allow curator review uploaded csv content in brow… 

    …ser before push to server
    @sprintell
    sprintell committed Aug 23, 2019
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  4. Create load test on DataProjection 

    Test Ignored by default. Created new tests configurations
and base test for separation configurations for persistence.
    @Afollet
    Afollet committed Aug 23, 2019
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  5. Link regimens to treatments using slash separator

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 23, 2019
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  6. wip Add unit tests for load specimens

    @rmwthorne
    rmwthorne committed Aug 23, 2019
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Commits on Aug 27, 2019

  1. Add newline at end of files

    @rmwthorne
    rmwthorne committed Aug 27, 2019
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  2. Deal with trailing slashes in data dir option

    @rmwthorne
    rmwthorne committed Aug 27, 2019
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  3. Add unit test for loading specimens

    @rmwthorne
    rmwthorne committed Aug 27, 2019
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  4. Fix code smell (test arguments wrong way round)

    @rmwthorne
    rmwthorne committed Aug 27, 2019
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  5. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into imp… 

    …cc_access_modalities

Fix Conflicts:
 indexer/src/main/java/org/pdxfinder/commands/dataloaders/LoadIRCC.java
    @rmwthorne
    rmwthorne committed Aug 27, 2019
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  6. Properly handle error report on csv file upload

    @sprintell
    sprintell committed Aug 27, 2019
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Commits on Aug 28, 2019

  1. Final refactoring 

    Uppercased static finals. Clarified variables.
Cleaned up code.
    @Afollet
    Afollet committed Aug 28, 2019
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  2. Provide an option for curator to increase and reduce text size to des… 

    …ired size and reset to default size
    @sprintell
    sprintell committed Aug 28, 2019
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  3. Abstracted Byte to String Conversion

    @Afollet
    Afollet committed Aug 28, 2019
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  4. Address QA and fix name spacing 

    QA raised an issue with name spacing: `indexer/src/test/java/org.pdxfinder/commands/` existed.
This was changed to `indexer/src/test/java/org/pdxfinder` directory was renamed and the contents of `commands` was moved into the parent directory.
    @rmwthorne
    rmwthorne committed Aug 28, 2019
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  5. Removed method getPatient() And changed naming conventions 

    Refactored dependent methods. Put NullPointExceptions on
GetPatientSnapshot and CreatePatient so they will
quietly throw exceptions for creating a patient with
a NULL id. Refactored TreatmentProtocols for readability
changing their method names to clarify testing behaviors.
    @Afollet
    Afollet committed Aug 28, 2019
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  6. Implement separate table area color for Missing Mapping table to clea… 

    …rly differentiate it from the table area that shows suggestions
    @sprintell
    sprintell committed Aug 28, 2019
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  7. Add feature to click on suggested terms and see a detailed view as it… 

    … is with Missing mapping table
    @sprintell
    sprintell committed Aug 28, 2019
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Commits on Aug 29, 2019

  1. Add dash parsing and vocab filtering

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 29, 2019
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  2. FRONT END UI ADJUSTMENT - PDXI-627

    @sprintell
    sprintell committed Aug 29, 2019
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  3. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Aug 29, 2019
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  4. Merge pull request #80 from PDXFinder/impcc_access_modalities 

    Impcc access modalities
    @rmwthorne
    rmwthorne committed Aug 29, 2019
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  5. Save relationships for regimens

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 29, 2019
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Commits on Aug 30, 2019

  1. Made Given When Then naming convention consistent 

    Added Null tests to getPatientSnapshot. Made added
blank string checks to creatPatient and getPatientSnapshot
in dataImportServices.
    @Afollet
    Afollet committed Aug 30, 2019
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  2. Made Given When Then naming convention consistent 

    Added Null tests to getPatientSnapshot. Made added
blank string checks to creatPatient and getPatientSnapshot
in dataImportServices.
    @Afollet
    Afollet committed Aug 30, 2019
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  3. The birth of Ontolia

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  4. Fixed byte to string conversion

    @Afollet
    Afollet committed Aug 30, 2019
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  5. Fixed byte to string conversion

    @Afollet
    Afollet committed Aug 30, 2019
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  6. Merge branch 'treatmentcombo' into dev 

    # Conflicts:
#	indexer/src/main/java/org/pdxfinder/envload/LoadNCITDrugs.java
    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  7. Refactor opening excel files

    @rmwthorne
    rmwthorne committed Aug 30, 2019
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  8. Fix ircc omic loading directory error

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  9. Enable Ontolia

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  10. Merge pull request #84 from PDXFinder/UpdogRefactorGetWorkbook 

    Refactor opening excel files
    @rmwthorne
    rmwthorne committed Aug 30, 2019
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  11. Cleanup

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  12. Add OntoliaMatrix

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  13. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Aug 30, 2019
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  14. Added Angular Material Components

    @sprintell
    sprintell committed Aug 30, 2019
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Commits on Sep 2, 2019

  1. Don't allow loading duplicates for terms

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 2, 2019
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  2. Ontolia: 

    - add scoring
- implement bestCompleteMatch and bestMatch
    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 2, 2019
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  3. Load industrial aid branch as well

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 2, 2019
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Commits on Sep 3, 2019

  1. Reduce log noise

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  2. Fix passage parsing error

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  3. Get hoststrain by symbol

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  4. Create specimen in cytogen loading if hoststrain is already present

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  5. Load custom list with Ontolia

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  6. Updated Angular dependencies for autocomplete

    @sprintell
    sprintell committed Sep 3, 2019
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  7. Added autocomplete libraries and styles

    @sprintell
    sprintell committed Sep 3, 2019
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  8. Added front end feature to allow curator manually type terms with sug… 

    …gestions from OLS
    @sprintell
    sprintell committed Sep 3, 2019
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  9. Enforce skip if file is not present

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  10. Disable sad node validation

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  11. Fix not loaded treatments bug

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 3, 2019
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  12. Added back end feature to allow curator get suggestions from OLS and … 

    …plug to UI
    @sprintell
    sprintell committed Sep 3, 2019
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  13. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Sep 3, 2019
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Commits on Sep 4, 2019

  1. Cleanup

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  2. Update data-services/src/test/java/org/pdxfinder/DataImportServiceTes… 

    …ts.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  3. Update data-services/src/main/java/org/pdxfinder/services/DataImportS… 

    …ervice.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  4. Update data-services/src/test/java/org/pdxfinder/DataImportServiceTes… 

    …ts.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  5. Update data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProt… 

    …ocol.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  6. Update data-model/src/test/java/org/pdxfinder/TestConfigWithPersisten… 

    …ce.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  7. Update data-model/src/test/java/org/pdxfinder/graph/dao/TreatmentProt… 

    …ocolTest.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  8. Update data-model/src/test/java/org/pdxfinder/graph/dao/TreatmentProt… 

    …ocolTest.java

Co-Authored-By: Ross Thorne <rmwthorne@googlemail.com>
    @Afollet @rmwthorne
    Afollet and rmwthorne committed Sep 4, 2019
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  9. Update DataImportServiceTests.java 

    Changed type in line 69
    @Afollet
    Afollet committed Sep 4, 2019
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  10. Update TreatmentComponent.java

    @Afollet
    Afollet committed Sep 4, 2019
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  11. Update BaseTestWithPersistence.java

    @Afollet
    Afollet committed Sep 4, 2019
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  12. Include regimen combinations to projection

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  13. Update TreatmentProtocolTest.java 

    updated method name upper casing to match other tests
    @Afollet
    Afollet committed Sep 4, 2019
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  14. Changed Imports in DataImportService 

    Instead of a static import wild card, only the necessary imports
are imported
    @Afollet
    Afollet committed Sep 4, 2019
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  15. Update h2-db directory for data loader

    @sprintell
    sprintell committed Sep 4, 2019
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  16. Update Ontobee URL to OLS url in admin Interface

    @sprintell
    sprintell committed Sep 4, 2019
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  17. Save frequently mutated genes in DP 

    Service to use DP
    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  18. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  19. Enable disabled methods

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  20. Change h2 dir

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  21. Use no arg constructor for queryresult

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  22. H2 location change

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  23. Get all ontology terms

    @sprintell
    sprintell committed Sep 4, 2019
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  24. Merge branches 'dev' and 'UnitTests' of https://github.com/PDXFinder/… 

    …pdxfinder into UnitTests

� Conflicts:
�	data-services/src/main/java/org/pdxfinder/services/DataImportService.java
    @Afollet
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  25. Merge pull request #83 from PDXFinder/UnitTests 

    Unit tests
    @Afollet
    Afollet committed Sep 4, 2019
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  26. Use lowercase entity types

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  27. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 4, 2019
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  28. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Sep 4, 2019
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  29. Ensure mapping entity type is lowercase before save

    @sprintell
    sprintell committed Sep 4, 2019
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Commits on Sep 5, 2019

  1. Log operation when unmapped terms is saved

    @sprintell
    sprintell committed Sep 5, 2019
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  2. Change h2 directory in Loader

    @sprintell
    sprintell committed Sep 5, 2019
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  3. Change h2 directory for data laoder

    @sprintell
    sprintell committed Sep 5, 2019
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Commits on Sep 6, 2019

  1. Add Null check on ProjectName And Log.Info on patient creation

    @Afollet
    Afollet committed Sep 6, 2019
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  2. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @Afollet
    Afollet committed Sep 6, 2019
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Commits on Sep 11, 2019

  1. Add patient treatment to DP

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 11, 2019
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  2. UX refining for the Admin Interface

    @sprintell
    sprintell committed Sep 11, 2019
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Commits on Sep 12, 2019

  1. Enable H2 Web access

    @sprintell
    sprintell committed Sep 12, 2019
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  2. Add ontology suggestion for treatment curation

    @sprintell
    sprintell committed Sep 12, 2019
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  3. Add caching to speed up ontology suggestions

    @sprintell
    sprintell committed Sep 12, 2019
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  4. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @sprintell
    sprintell committed Sep 12, 2019
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Commits on Sep 13, 2019

  1. ADMIN INTERFACE: Create a feature to allow editing of old mappings

    @sprintell
    sprintell committed Sep 13, 2019
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  2. Extend back end to allow edit of old mappings

    @sprintell
    sprintell committed Sep 13, 2019
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  3. Add orphaned mapping to summary table

    @sprintell
    sprintell committed Sep 13, 2019
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Commits on Sep 16, 2019

  1. Load additional treatment branches from NCIT

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 16, 2019
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  2. Fix patient treatment dp bug

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 16, 2019
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  3. Add patient treatment filter

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 16, 2019
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  4. Order treatment string components alphabetically

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 16, 2019
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Commits on Sep 17, 2019

  1. Add patient treatment filter

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 17, 2019
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  2. Load therapeutic procedures instead of radiotherapies

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 17, 2019
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  3. Fix url

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 17, 2019
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Commits on Sep 18, 2019

  1. Load clinical studies branch

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 18, 2019
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  2. Use datasource name for ds filter

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 18, 2019
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  3. Add attribute check to datasourceName

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 18, 2019
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  4. Add nullcheck

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 18, 2019
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  5. Add nullcheck to ds name

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 18, 2019
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Commits on Sep 19, 2019

  1. Disable IRCC-GC mutation visibility

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  2. Add log info

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  3. Add fold change to datamodel

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  4. Create a link to patient tab from search

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  5. Fix treatment number query bug

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  6. MappingService to be able to export treatment rules

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  7. Fixes Civic blank "Amino Acid Change" bug 

    Removes alert("JESUS IS LORD")
    @Afollet
    Afollet committed Sep 19, 2019
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  8. Format export mappings for EuroPDX

    @rmwthorne
    rmwthorne committed Sep 19, 2019
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  9. Merge pull request #85 from PDXFinder/MappingExport 

    Format export mappings for EuroPDX
    @rmwthorne
    rmwthorne committed Sep 19, 2019
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  10. Patient treatment can lead to multiple models

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  11. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 19, 2019
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  12. Fetch the harmonised treatment name for patient page

    @rmwthorne
    rmwthorne committed Sep 19, 2019
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Commits on Sep 20, 2019

  1. Merge pull request #86 from PDXFinder/HarmonisedTreatmentForPatient 

    Fetch the harmonised treatment name for patient page
    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  2. Fix cypher

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  3. Fix cypher as intended this time

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  4. Add msg

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  5. Merge pull request #87 from PDXFinder/dev 

    Dev
    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  6. Fix format call

    @rmwthorne
    rmwthorne committed Sep 20, 2019
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  7. Merge pull request #88 from PDXFinder/Hotfix 

    Fix format call
    @rmwthorne
    rmwthorne committed Sep 20, 2019
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  8. QA to be empty if missing

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  9. Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev

    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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  10. Merge pull request #89 from PDXFinder/dev 

    Dev
    @CsabaHalmagyi
    CsabaHalmagyi committed Sep 20, 2019
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