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Ce ubuntu18 upgrade #192

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Ce ubuntu18 upgrade #192

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Commits on Mar 10, 2021

  1. update schema and create test data for award and experiment

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  2. updated biofile

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  3. link biospecimen with experiment through biofile

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  4. embed biofile in biospecimen

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  5. enmed biofile in patient, add file path in biofile

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  6. move award from dataset to biofile

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  7. add award in biofile test data

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  8. embed biofile.award

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  9. update bioexperiment.js

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  10. update test data for genomics

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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  11. remove document in biospecimen

    @mingjiecn
    mingjiecn committed Mar 10, 2021
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Commits on Mar 11, 2021

  1. clean up

    @mingjiecn
    mingjiecn committed Mar 11, 2021
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  2. add more test data

    @mingjiecn
    mingjiecn committed Mar 11, 2021
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  3. fix test data

    @mingjiecn
    mingjiecn committed Mar 11, 2021
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  4. update UI for biospecimen

    @mingjiecn
    mingjiecn committed Mar 11, 2021
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Commits on Mar 12, 2021

  1. fix test data

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  2. update facet and column for bioexperiment

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  3. embed biofile.award for biospecimen

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  4. add facets

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  5. shown project list in experiment

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  6. update assay term enum and project enum

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  7. update genomicsTable

    @mingjiecn
    mingjiecn committed Mar 12, 2021
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  8. First pass at reorder of filters. Close #387.

    @vsmalladi
    vsmalladi committed Mar 12, 2021
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Commits on Mar 15, 2021

  1. Refort surgery to pathreport for better linkage.

    @vsmalladi
    vsmalladi committed Mar 15, 2021
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  2. Fix links.

    @vsmalladi
    vsmalladi committed Mar 15, 2021
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Commits on Mar 16, 2021

  1. Update mapping for biospecimen to surgery pathology report.

    @vsmalladi
    vsmalladi committed Mar 16, 2021
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  2. fix issue #392

    @mingjiecn
    mingjiecn committed Mar 16, 2021
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  3. add period

    @mingjiecn
    mingjiecn committed Mar 16, 2021
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  4. change patient limit to <= 10

    @mingjiecn
    mingjiecn committed Mar 16, 2021
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  5. Merge pull request #396 from utsw-bicf/392-minimum 

    Limit the number of patients to view. If less than 10 can't view.

Close #392
    @vsmalladi
    vsmalladi authored Mar 16, 2021
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Commits on Mar 18, 2021

  1. Change syntax.

    @vsmalladi
    vsmalladi committed Mar 18, 2021
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  2. Fix mapping.

    @vsmalladi
    vsmalladi committed Mar 18, 2021
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  3. Fix mapping to surgery procedure.

    @vsmalladi
    vsmalladi committed Mar 18, 2021
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  4. Fix calc field.

    @vsmalladi
    vsmalladi committed Mar 18, 2021
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Commits on Mar 22, 2021

  1. update calculated fields

    @mingjiecn
    mingjiecn committed Mar 22, 2021
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  2. Fix calculated fields.

    @vsmalladi
    vsmalladi committed Mar 22, 2021
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  3. Fix merge.

    @vsmalladi
    vsmalladi committed Mar 22, 2021
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  4. Fix merge.

    @vsmalladi
    vsmalladi committed Mar 22, 2021
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Commits on Mar 23, 2021

  1. update patientPathTable.js

    @mingjiecn
    mingjiecn committed Mar 23, 2021
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  2. update surgery.js

    @mingjiecn
    mingjiecn committed Mar 23, 2021
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  3. fix surgery search view

    @mingjiecn
    mingjiecn committed Mar 23, 2021
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Commits on Mar 24, 2021

  1. update path report ui in biospecimen.js

    @mingjiecn
    mingjiecn committed Mar 24, 2021
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  2. Remove status.

    @vsmalladi
    vsmalladi committed Mar 24, 2021
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  3. Updagte change log.

    @vsmalladi
    vsmalladi committed Mar 24, 2021
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  4. Merge branch 'kce' into 333-surgical_reformat

    @vsmalladi
    vsmalladi committed Mar 24, 2021
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  5. revert back summary.js.

    @vsmalladi
    vsmalladi committed Mar 24, 2021
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  6. Update the display to remove NOS for site.

    @vsmalladi
    vsmalladi committed Mar 24, 2021
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  7. Update filters

    @vsmalladi
    vsmalladi committed Mar 24, 2021
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Commits on Mar 25, 2021

  1. add status back to columns in surgery

    @mingjiecn
    mingjiecn committed Mar 25, 2021
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  2. Merge pull request #394 from utsw-bicf/333-surgical_reformat 

    surgical and pathology reformat
Close #333
    @vsmalladi
    vsmalladi authored Mar 25, 2021
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  3. Merge KCE.

    @vsmalladi
    vsmalladi committed Mar 25, 2021
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Commits on Mar 26, 2021

  1. Fix summary display.

    @vsmalladi
    vsmalladi committed Mar 26, 2021
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  2. Merge pull request #400 from utsw-bicf/399-specimen_site 

    Update the display to remove NOS for site. Close #399
    @vsmalladi
    vsmalladi authored Mar 26, 2021
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Commits on Apr 1, 2021

  1. add new consent schema and test data for loading real data

    @SenseCode
    SenseCode committed Apr 1, 2021
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  2. add scanned copy as required field

    @SenseCode
    SenseCode committed Apr 1, 2021
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  3. add sugery info in biospecimen table

    @mingjiecn
    mingjiecn committed Apr 1, 2021
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  4. change status, add facets and columns, edit description

    @SenseCode
    SenseCode committed Apr 1, 2021
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Commits on Apr 9, 2021

  1. update consent schemas according to real data

    @SenseCode
    SenseCode committed Apr 9, 2021
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Commits on Apr 12, 2021

  1. edit status.js and test patient status

    @SenseCode
    SenseCode committed Apr 12, 2021
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Commits on Apr 19, 2021

  1. testing branch

    @SenseCode
    SenseCode committed Apr 19, 2021
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  2. test to add a calculated field

    @SenseCode
    SenseCode committed Apr 19, 2021
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Commits on May 3, 2021

  1. recovered genomic_released

    @SenseCode
    SenseCode committed May 3, 2021
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Commits on May 4, 2021

  1. embed patient failed through embed from path. Need help the embed way

    @SenseCode
    SenseCode committed May 4, 2021
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  2. switch branch

    @SenseCode
    SenseCode committed May 4, 2021
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Commits on May 5, 2021

  1. Test consent.

    @vsmalladi
    vsmalladi committed May 5, 2021
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Commits on May 6, 2021

  1. hide the genomic table in biospecimen page

    @SenseCode
    SenseCode committed May 6, 2021
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Commits on May 11, 2021

  1. edit patient genomic_release

    @SenseCode
    SenseCode committed May 11, 2021
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  2. remove patient genomice_release

    @SenseCode
    SenseCode committed May 11, 2021
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  3. test and consent_list are none, need to try embed from other ways

    @SenseCode
    SenseCode committed May 11, 2021
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Commits on May 12, 2021

  1. add filegallary in bioexperiment

    @SenseCode
    SenseCode committed May 12, 2021
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  2. clean codes

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    SenseCode committed May 12, 2021
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  3. Merge pull request #403 from utsw-bicf/381-specimen_table 

    add sugery info in biospecimen table
Close #381
    @vsmalladi
    vsmalladi authored May 12, 2021
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  4. add bioexperiment genomic_release field

    @SenseCode
    SenseCode committed May 12, 2021
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  5. add genomic_release status in facet.

    @SenseCode
    SenseCode committed May 12, 2021
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  6. hide filegallary accordding to genomic_release status

    @SenseCode
    SenseCode committed May 12, 2021
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  7. add tooltips and dictionary for tumor stage

    @SenseCode
    SenseCode committed May 12, 2021
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  8. edit tooltips and dictionary with at presentation

    @SenseCode
    SenseCode committed May 12, 2021
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  9. add pN2

    @SenseCode
    SenseCode committed May 12, 2021
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Commits on May 13, 2021

  1. remove pT0, pM0

    @SenseCode
    SenseCode committed May 13, 2021
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  2. Merge branch 'kce' into 371-tumorstage_tooltips

    @vsmalladi
    vsmalladi committed May 13, 2021
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  3. Merge pull request #402 from utsw-bicf/391-consent 

    Adds in updates for consent schema.
    @vsmalladi
    vsmalladi authored May 13, 2021
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  4. Update some of the verbage.

    @vsmalladi
    vsmalladi committed May 13, 2021
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  5. Merge branch 'kce' into 371-tumorstage_tooltips

    @vsmalladi
    vsmalladi committed May 13, 2021
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  6. Merge pull request #405 from utsw-bicf/371-tumorstage_tooltips 

     Add tumorstage tooltips close #371
    @vsmalladi
    vsmalladi authored May 13, 2021
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  7. Resolve conflicts.

    @vsmalladi
    vsmalladi committed May 13, 2021
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  8. Remove venv.

    @vsmalladi
    vsmalladi committed May 13, 2021
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Commits on May 14, 2021

  1. Fix embedding logic.

    @vsmalladi
    vsmalladi committed May 14, 2021
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  2. add restriction in status, test work, update biofile status with geno… 

    …mic_release correlation to biospecimen
    @SenseCode
    SenseCode committed May 14, 2021
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  3. edit biofile insert for test revoked biospecimen

    @SenseCode
    SenseCode committed May 14, 2021
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  4. cleaning codes

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    SenseCode committed May 14, 2021
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  5. fix bioexperiment page cannot show

    @SenseCode
    SenseCode committed May 14, 2021
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Commits on May 18, 2021

  1. remove genomic_release in biofile, edit biofile inserts with restricted

    @SenseCode
    SenseCode committed May 18, 2021
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  2. remove genomice_release

    @SenseCode
    SenseCode committed May 18, 2021
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  3. remove biofile genome_release, edit biofile inserts

    @SenseCode
    SenseCode committed May 18, 2021
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  4. fix merge

    @SenseCode
    SenseCode committed May 18, 2021
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  5. edit insert data

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    SenseCode committed May 18, 2021
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Commits on May 19, 2021

  1. fix biodataset

    @SenseCode
    SenseCode committed May 19, 2021
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  2. Merge pull request #404 from utsw-bicf/consent_genomic 

    Add consent to govern view of genomics. 

Close #390
Close #395
Close #391
Close #397,
    @vsmalladi
    vsmalladi authored May 19, 2021
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  3. Merge.

    @vsmalladi
    vsmalladi committed May 19, 2021
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  4. Update the logig of consent.

    @vsmalladi
    vsmalladi committed May 19, 2021
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  5. Fix issues raised in review.

    @vsmalladi
    vsmalladi committed May 19, 2021
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Commits on May 20, 2021

  1. Fix supportive meds.

    @vsmalladi
    vsmalladi committed May 20, 2021
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  2. Merge pull request #393 from utsw-bicf/387-patient_filters 

    Reorder of patient filters. Close #387.
    @vsmalladi
    vsmalladi authored May 20, 2021
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  3. modify dominant tumor

    @mingjiecn
    mingjiecn committed May 20, 2021
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  4. fix bug

    @mingjiecn
    mingjiecn committed May 20, 2021
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  5. Fix typo.

    @vsmalladi
    vsmalladi committed May 20, 2021
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  6. Update page order and add in medication.

    @vsmalladi
    vsmalladi committed May 20, 2021
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Commits on May 21, 2021

  1. fix audit UnboundLocalError

    @mingjiecn
    mingjiecn committed May 21, 2021
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  2. Update surgical mangement.

    @vsmalladi
    vsmalladi committed May 21, 2021
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  3. Merge pull request #409 from utsw-bicf/383-audit_error 

    fix audit UnboundLocalError
Close #383
    @vsmalladi
    vsmalladi authored May 21, 2021
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  4. Merge pull request #408 from utsw-bicf/374-report_bug 

    Fix report bug and some extra dominant tumor.
Close #374
    @vsmalladi
    vsmalladi authored May 21, 2021
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  5. fix bioreplicate and biolibrary, biofile in bioexperiment link, still… 

    … no filegallary
    @SenseCode
    SenseCode committed May 21, 2021
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  6. fix filegallary

    @SenseCode
    SenseCode committed May 21, 2021
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Commits on May 22, 2021

  1. Fix title.

    @vsmalladi
    vsmalladi committed May 22, 2021
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  2. Update surgical pathology serach with suggestions.

    @vsmalladi
    vsmalladi committed May 22, 2021
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Commits on May 24, 2021

  1. Add unknown.

    @vsmalladi
    vsmalladi committed May 24, 2021
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  2. Add in FNA in mets biopsy.

    @vsmalladi
    vsmalladi committed May 24, 2021
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  3. Update logic.

    @vsmalladi
    vsmalladi committed May 24, 2021
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Commits on May 25, 2021

  1. Add a diagnosis procedure that duplicates nephrectomy.

    @vsmalladi
    vsmalladi committed May 25, 2021
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  2. Fix variable name.

    @vsmalladi
    vsmalladi committed May 25, 2021
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  3. Add not available

    @vsmalladi
    vsmalladi authored May 25, 2021
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  4. Add back procedure in columns.

    @vsmalladi
    vsmalladi committed May 25, 2021
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Commits on May 27, 2021

  1. update diagnosis date

    @mingjiecn
    mingjiecn committed May 27, 2021
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  2. fix y-axis

    @SenseCode
    SenseCode committed May 27, 2021
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Commits on May 28, 2021

  1. Merge pull request #410 from utsw-bicf/406-filegallary_fix 

    Fix the file gallery Close #406
    @vsmalladi
    vsmalladi authored May 28, 2021
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  2. Remove duplicate medication.

    @vsmalladi
    vsmalladi committed May 28, 2021
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  3. Update some patient display.

    @vsmalladi
    vsmalladi committed May 28, 2021
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  4. Merge branch 'kce' into 388-surgery-filters

    @vsmalladi
    vsmalladi committed May 28, 2021
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  5. Update view on surgery page.

    @vsmalladi
    vsmalladi committed May 28, 2021
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  6. Merge pull request #411 from utsw-bicf/388-surgery-filters 

    Update surgery filters and logic Close #388
    @vsmalladi
    vsmalladi authored May 28, 2021
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  7. Add authentication to utsouthwestern microsoft.

    @vsmalladi
    vsmalladi committed May 28, 2021
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Commits on Jun 1, 2021

  1. remove >, fix cannot log in

    @SenseCode
    SenseCode committed Jun 1, 2021
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Commits on Jun 8, 2021

  1. Update labs.

    @vsmalladi
    vsmalladi committed Jun 8, 2021
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  2. Fix email.

    @vsmalladi
    vsmalladi committed Jun 8, 2021
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Commits on Jun 9, 2021

  1. Fix the redirect issue.

    @vsmalladi
    vsmalladi committed Jun 9, 2021
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  2. Merge pull request #412 from utsw-bicf/19-utsw_login 

    Add authentication to utsouthwestern microsoft. Close #19
    @vsmalladi
    vsmalladi authored Jun 9, 2021
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  3. Add in logic for medication.

    @vsmalladi
    vsmalladi committed Jun 9, 2021
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  4. Add test data.

    @vsmalladi
    vsmalladi committed Jun 9, 2021
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  5. update status for data protection

    @mingjiecn
    mingjiecn committed Jun 9, 2021
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Commits on Jun 10, 2021

  1. fix publication

    @mingjiecn
    mingjiecn committed Jun 10, 2021
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  2. Fix logic.

    @vsmalladi
    vsmalladi committed Jun 10, 2021
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  3. fix summary

    @mingjiecn
    mingjiecn committed Jun 10, 2021
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  4. update barchart

    @mingjiecn
    mingjiecn committed Jun 10, 2021
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  5. Merge branch '413-genomics_count' of https://github.com/utsw-bicf/pan… 

    …diseased into 413-genomics_count
    @mingjiecn
    mingjiecn committed Jun 10, 2021
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  6. update barchart label and text

    @mingjiecn
    mingjiecn committed Jun 10, 2021
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Commits on Jun 11, 2021

  1. Provde greater security and control. Also add in language to protect … 

    …downloads and identification of patients. Close #389.
    @vsmalladi
    vsmalladi committed Jun 11, 2021
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  2. Try to protect all item pages.

    @vsmalladi
    vsmalladi committed Jun 11, 2021
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Commits on Jun 21, 2021

  1. add tickangle for yaxis

    @mingjiecn
    mingjiecn committed Jun 21, 2021
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Commits on Jun 22, 2021

  1. adjust chart setting

    @mingjiecn
    mingjiecn committed Jun 22, 2021
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  2. Merge pull request #414 from utsw-bicf/361-experimental_meds 

    Updated experimental mediations and likelwise updated the visualization of the to be formateed better.

Close #361
    @vsmalladi
    vsmalladi authored Jun 22, 2021
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  3. resolve merge conlfict on patients.

    @vsmalladi
    vsmalladi committed Jun 22, 2021
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Commits on Jul 8, 2021

  1. Merge pull request #415 from utsw-bicf/413-genomics_count 

    Close #413
Close #389
Without login, you can see main page, publication page, help page and material & methods page, but not any page that has data.
    @vsmalladi
    vsmalladi authored Jul 8, 2021
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Commits on Sep 7, 2021

  1. add ivp_a1v3 version, edit patient files

    @SenseCode
    SenseCode committed Sep 7, 2021
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  2. remove related kce class

    @SenseCode
    SenseCode committed Sep 7, 2021
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  3. can load data, clean codes

    @SenseCode
    SenseCode committed Sep 7, 2021
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  4. clean codes

    @SenseCode
    SenseCode committed Sep 7, 2021
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  5. add formstable

    @SenseCode
    SenseCode committed Sep 7, 2021
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  6. add fvp_a1v3

    @SenseCode
    SenseCode committed Sep 7, 2021
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  7. fix pie-chart, add pattern for patient no.

    @SenseCode
    SenseCode committed Sep 7, 2021
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  8. edit search.js

    @SenseCode
    SenseCode committed Sep 7, 2021
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Commits on Sep 9, 2021

  1. fix search page showing issue

    @SenseCode
    SenseCode committed Sep 9, 2021
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Commits on Sep 10, 2021

  1. add fvp schemas

    @SenseCode
    SenseCode committed Sep 10, 2021
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  2. add ivp schemas

    @SenseCode
    SenseCode committed Sep 10, 2021
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  3. add tvp schemas and concussion_history

    @SenseCode
    SenseCode committed Sep 10, 2021
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  4. add inserts fvp data

    @SenseCode
    SenseCode committed Sep 10, 2021
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  5. add test data of ivp

    @SenseCode
    SenseCode committed Sep 10, 2021
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  6. add test data of tvp and concussion_history

    @SenseCode
    SenseCode committed Sep 10, 2021
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  7. add ivp, fvp and tvp, concussion_history changelogs

    @SenseCode
    SenseCode committed Sep 10, 2021
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  8. add ivp, fvp, tvp and concussion_history py files, and m1 related files

    @SenseCode
    SenseCode committed Sep 10, 2021
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  9. edit formver, all loaded

    @SenseCode
    SenseCode committed Sep 10, 2021
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Commits on Sep 11, 2021

  1. recommit add all py files

    @SenseCode
    SenseCode committed Sep 11, 2021
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  2. update patient.js

    @SenseCode
    SenseCode committed Sep 11, 2021
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  3. embed all the schemas into patient

    @SenseCode
    SenseCode committed Sep 11, 2021
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Commits on Sep 14, 2021

  1. rewrite patient.py with new load order

    @SenseCode
    SenseCode committed Sep 14, 2021
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  2. add seperate line

    @SenseCode
    SenseCode committed Sep 14, 2021
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  3. successfully load all parts after commit version 1 and version 2

    @SenseCode
    SenseCode committed Sep 14, 2021
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Commits on Sep 15, 2021

  1. merge concussion_history_follow_up

    @SenseCode
    SenseCode committed Sep 15, 2021
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  2. add updrs schema

    @SenseCode
    SenseCode committed Sep 15, 2021
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  3. add visit_contact schema, connect with patient , put in showpage

    @SenseCode
    SenseCode committed Sep 15, 2021
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  4. add physical_exam schema, connect with patient, put on showpage

    @SenseCode
    SenseCode committed Sep 15, 2021
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  5. add moca schema

    @SenseCode
    SenseCode committed Sep 15, 2021
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  6. edit local tests and load all the local forms

    @SenseCode
    SenseCode committed Sep 15, 2021
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Commits on Sep 16, 2021

  1. edit concussion_history_follow_up

    @SenseCode
    SenseCode committed Sep 16, 2021
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Commits on Sep 22, 2021

  1. fix facets mapping issue in ivp_a5v3, m1

    @SenseCode
    SenseCode committed Sep 22, 2021
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  2. remove genetice_modification update json file, which bring mapping error

    @SenseCode
    SenseCode committed Sep 22, 2021
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Commits on Sep 24, 2021

  1. update schemas

    @SenseCode
    SenseCode committed Sep 24, 2021
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  2. edit test data, load all forms now

    @SenseCode
    SenseCode committed Sep 24, 2021
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  3. update loadxl.py file

    @SenseCode
    SenseCode committed Sep 24, 2021
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Commits on Oct 5, 2021

  1. rewrite formtable with separate version order

    @SenseCode
    SenseCode committed Oct 5, 2021
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  2. edit format, test load

    @SenseCode
    SenseCode committed Oct 5, 2021
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