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Improve/variant creation form#588

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loeswerkman wants to merge 99 commits intorelease/3.5LOVDnl/LOVD3:release/3.5from improve/variantCreationFormLOVDnl/LOVD3:improve/variantCreationFormCopy head branch name to clipboard

+777-178

Commits

Commits on Oct 6, 2021

• Add 'relative to' message to both DNA fields

  loeswerkman

  committed
  475c3ee

Commits on Oct 7, 2021

• Allow element data to be added into HTML via viewForm

  loeswerkman

  committed
  998fd1b

• Add genome build as element data into viewForm

  loeswerkman

  committed
  eb3b9ea

• Redo code to add source to variants using element data

  loeswerkman

  committed
  1d121fd

• Add map button to all DNA fields in variant data entry form

  loeswerkman

  committed
  2fc7097

Commits on Oct 8, 2021

• Remove disabled method.

  ifokkema

  committed
  1d3dad7

• When adding to the DNA field description, don't overwrite anything.

  ifokkema

  committed
  e607423

• Improved efficiency of variables a bit, shortening the code.

  ifokkema

  committed
  77a3e86

• Clean up the code a bit, and simply selecting VOG/DNA fields in JS.

  ifokkema

  committed
  68f4ff4

Commits on Oct 15, 2021

• Add IsHGVS function and Unit test

  loeswerkman

  committed
  a9dbc6d

Commits on Jan 21, 2022

• Open checkHGVS dialogue in variant creation form

  Show description for 4e83069
  loeswerkman

  committed
  4e83069

Commits on Jan 27, 2022

• Create and implement the isHGVS wrapper function

  Show description for 8949e05
  loeswerkman

  committed
  8949e05

Commits on Feb 10, 2022

• Merge branch 'release/3.5' into improve/variantCreationForm

  loeswerkman

  committed
  5ef4aeb

• Add an '@' before the ob_end_flush()

  loeswerkman

  committed
  d94faee

• Add 'supported_by_VV' to GBs in

  loeswerkman

  committed
  2d9c9c7

• Fix spelling

  loeswerkman

  committed
  b1ccf66

• WIP: Redoing the mapping and validation through VV

  Show description for e0b4d90
  loeswerkman

  committed
  e0b4d90

Commits on Feb 21, 2022

• Simplify and clean up code; shorten the output

  Show description for 63e05e5
  loeswerkman

  committed
  63e05e5

• Document the fact that flush() does not work here

  Show description for fce7fb8
  loeswerkman

  committed
  fce7fb8

Commits on Feb 23, 2022

• Replaced flush() calls with recursive calls

  Show description for d7d5282
  loeswerkman

  committed
  d7d5282

Commits on Feb 24, 2022

• Allow variants which VV cannot validate into the DB

  Show description for 4f3e8e5
  loeswerkman

  committed
  4f3e8e5

• Clean up the output and accredit VariantValidator

  Show description for 5227038
  loeswerkman

  committed
  5227038

• Remove redundant VV call for multiple transcripts

  loeswerkman

  committed
  723cd57

• Change line separators from CRLF to LF

  loeswerkman

  committed
  32cbf30

• Reset the output if the variant is an empty string

  loeswerkman

  committed
  9915eda

• Handle exit as a statement instead of a function

  loeswerkman

  committed
  6e4e443

Commits on Feb 25, 2022

• Clean up bits of the code

  loeswerkman

  committed
  ea1e4bd

Commits on Feb 26, 2022

• WIP: Save md5 translation of validated variants

  Show description for 4f57803
  loeswerkman

  committed
  4f57803

Commits on Feb 28, 2022

• WIP: Save md5 translation of validated variants

  Show description for 4562560
  loeswerkman

  committed
  4562560

Commits on Mar 1, 2022

• Fix bug when no transcripts are given

  loeswerkman

  committed
  0ba1f0c

• Fix issue causing blocked fields to not reach POST

  Show description for b0ffbbe
  loeswerkman

  committed
  b0ffbbe

• Fix issue when setting the md5 key after validation

  Show description for a8afce5
  loeswerkman

  committed
  a8afce5

• Merge branch 'improve/variantCreationForm' of github.com:LOVDnl/LOVD3 into improve/variantCreationForm

  loeswerkman

  committed
  aa272d0

• Update documentation to better fit the code

  loeswerkman

  committed
  07b52e6

• Fix indentation

  loeswerkman

  committed
  7e75c35

• Merge branch 'release/3.5' into gb/mapNewVariants

  loeswerkman

  committed
  cc0dcda

• Merge branch 'gb/mapNewVariants' into improve/variantCreationForm

  loeswerkman

  committed
  82abf86

Commits on Mar 2, 2022

• Fetch GB IDs using the data element and not SQL

  Show description for fc90491
  loeswerkman

  committed
  fc90491

• Clean up code that checks refSeqs in description

  Show description for afda306
  loeswerkman

  committed
  afda306

• Stop blocking the 'Ignore this transcript' button

  Show description for 20ea1e3
  loeswerkman

  committed
  20ea1e3

• Fix bug and add comment to code which resets values

  Show description for d9bf913
  loeswerkman

  committed
  d9bf913

Commits on Mar 3, 2022

• Reset all values when the dialogue is called

  Show description for 0a82e7f
  loeswerkman

  committed
  0a82e7f

• Add the source of the variant when it is mapped

  loeswerkman

  committed
  a9f8773

• Trigger HGVS check when the chromosome is updated

  loeswerkman

  committed
  daee268

• Stop expiring the cache for inc-js-variants.php

  loeswerkman

  committed
  ee315bb

• Add css classes to the input fields to show status

  Show description for 3e3b691
  loeswerkman

  committed
  3e3b691

• Fix bug when resetting the script

  Show description for fb3ce67
  loeswerkman

  committed
  fb3ce67

• Simplify code and add class to RNA&Protein fields

  loeswerkman

  committed
  534d05f

• Disable the Enter for all DNA fields

  Show description for bc8b39c
  loeswerkman

  committed
  bc8b39c

• Fix all code that has to do with URL encoding

  loeswerkman

  committed
  83b07f0

• Reset all values based on whether mapping status

  Show description for 4fa5279
  loeswerkman

  committed
  4fa5279

• Make sure the dialog is closed if an error occurs

  loeswerkman

  committed
  bb648a1

• Remove md5 key; Use checkFields to check input

  Show description for 3ea60b2
  loeswerkman

  committed
  3ea60b2

• Add documentation to the checkFields addition

  loeswerkman

  committed
  186176b

• Get rid of the $_GET['chromosome'] usage

  Show description for c9cbda4
  loeswerkman

  committed
  c9cbda4

Commits on Mar 4, 2022

• Remove MD5 key function that is no longer used

  loeswerkman

  committed
  b4abbe2

• Remove hidden codedVariants field (md5 key)

  Show description for 6f154b2
  loeswerkman

  committed
  6f154b2

• Removing flush()

  loeswerkman

  committed
  be5f3e6

• Take string, not int in update_images_per_step()

  loeswerkman

  committed
  ca7a8e4

• Clean up code around update_dialogue() calls

  loeswerkman

  committed
  34b397e

• Add documentation to the possible reset

  loeswerkman

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  e691e0e

• Fix old typing in documentation

  loeswerkman

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  4f976d6

• Add and update documentation

  loeswerkman

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  58e2165

• Add addslashes() for safe keeping

  loeswerkman

  committed
  0e983f3

• Remove old code related to the md5 key

  loeswerkman

  committed
  88e9ba7

• Fix strange line separation

  loeswerkman

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  3f9d7e3

• Restore cache header

  loeswerkman

  committed
  7a63d5e

• Add documentation to lovd_checkHGVS()

  loeswerkman

  committed
  08cbb5f

Commits on Mar 25, 2022

• Update header

  loeswerkman

  committed
  4362e90

• Clear up class name 'acc' to 'accept

  loeswerkman

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  e9eea63

• Stop resetting values if an empty string is passed

  loeswerkman

  committed
  b11ff02

• Remove use of variables for buttons and images

  loeswerkman

  committed
  f436950

• Remove display:none and .show() for all imgs

  loeswerkman

  committed
  aa1c715

• Fix issue regarding oChromosome variable

  loeswerkman

  committed
  9e450dc

• Clean up the selection of an object by its data

  loeswerkman

  committed
  e783dc0

• Fill in fields that remained empty after mapping

  loeswerkman

  committed
  ff584cf

• Use strpos instead of regex to find DNA fields

  loeswerkman

  committed
  752fd19

• Fix and clean code that checks the variant format

  loeswerkman

  committed
  f626d4e

• Use 'https' instead of 'http' for the HGVS link

  loeswerkman

  committed
  ac3de94

• Fill and deactivate empty fields after mapping

  Show description for 9436ec7
  loeswerkman

  committed
  9436ec7

• Clarify message when VV threw a syntax/build

  loeswerkman

  committed
  2d443ac

• Remove RefSeq from description in OKCouldBeValid

  loeswerkman

  committed
  121a300

Commits on Mar 31, 2022

• Fix concatenations of strings and strings

  loeswerkman

  committed
  6f9bef4

• Get rid of negative selection to fill empty fields

  loeswerkman

  committed
  66f7a76

• Fix code around strpos that finds 'DNA'

  loeswerkman

  committed
  5c3cc75

• Fix dates

  loeswerkman

  committed
  a96825a

Commits on Apr 8, 2022

• Only reset values if the DB holds human GBs

  Show description for a906b9c
  loeswerkman

  committed
  a906b9c

• Fix dates

  loeswerkman

  committed
  e156a4e

Commits on Apr 11, 2022

• WIP: Only mapping GBs recognised by LOVD and VV

  loeswerkman

  committed
  a00ddfc

Commits on Apr 12, 2022

• Remove floating var_dump

  loeswerkman

  committed
  03c995a

• Remove refseq from not-accepted variants

  loeswerkman

  committed
  03f5a4b

• Update dates

  loeswerkman

  committed
  3639e62

• Use htmlspecialchars around all REQUEST variables

  loeswerkman

  committed
  b5d5c49

• Add documentation regarding REQUEST/POST/GET

  loeswerkman

  committed
  c89a307

Commits on Apr 13, 2022

• Make sure all variables in output are safe

  Show description for eda072b
  loeswerkman

  committed
  eda072b

• Fix minor issue in refSeq ternary if

  loeswerkman

  committed
  8d6dfa0

• Update dates

  loeswerkman

  committed
  cd542ba

• Clarify error message that is thrown when VV fails

  Show description for 6c9c5c2
  loeswerkman

  committed
  6c9c5c2

Commits on Jun 9, 2022

• Fix issues concerning URL en- & decoding

  loeswerkman

  committed
  6a38123