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Cage python #21

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@wizardfan wizardfan commented Jun 12, 2020

this pull request contains all changes in the bug_fix PR (which can be ignored).

Apart from the changes included in the bug_fix PR, this pull request include further features:

  1. enable CAGE-seq validation
  2. automatic conversion from string to float for ratio and number columns
  3. check mandatory fields can not be empty
  4. new data structure which is more flexible, intuitive and informative which will make validation easier
  5. the commits in the base branch (new_python_validator) have been merged

wizardfan and others added 30 commits April 3, 2020 16:48
@wizardfan
update requirements.txt
fabe72c
@wizardfan
improve experiment xml converter
552dc3c
@wizardfan
annotate and add more mandatory fields in constant.py
d34d53e
@wizardfan
bug fix: extract date value for run_date, rename variables to improve…
98ce395 
… readability, improve comments
@wizardfan
distinguish whether study referenced in experiment is new or existing
0b15206
@wizardfan
improve comments
466b8ea
@wizardfan
fix multiple TODO items in previous commit
5b50f7a
@wizardfan
refactor: introduce new constants
faf92fd
@wizardfan
expect readme sheet in the template file
baa1958
@wizardfan
introduce id columns, refactor in validation section
3c36ecc
@wizardfan
deal with the run_date value is a string rather than a date
c0f00bb
@wizardfan
add template version control to the readme sheet
354e2dc
@wizardfan
make all keys are snake cased
293f797
@wizardfan
improve ruleset and template reading part
ba8d8e9
@wizardfan
cleaner code: split complex function get_ruleset_json into three func…
8c93dde 
…tions
@wizardfan
improve hard-code part on module ruleset
6dab35f
@Alexey-ebi @wizardfan
Fixing bugs
d3d4ca2
@Alexey-ebi @wizardfan
Adding submission, organization and person information and fixing bugs
59bc6e0
@Alexey-ebi @wizardfan
Removing underscores
d104870
@Alexey-ebi @wizardfan
Fixing bugs
6552bb7
@wizardfan
save up for merge from new_python_validator via bug_fix branch
d04ce34
@Alexey-ebi @wizardfan
Fixing bugs
2bde6ce
@Alexey-ebi @wizardfan
Adding submission, organization and person information and fixing bugs
fe214fa
@Alexey-ebi @wizardfan
Removing underscores
9f53797
@Alexey-ebi @wizardfan
Fixing bugs
6ba0ef0
@wizardfan
Merge from new_python_validator for bug fixing in ChIP-seq validation
c14c30c
@wizardfan
temp save before merge
2f4bbea
@wizardfan
Merge to new_python_validator bug fix for chipseq
7d2a7b4
@wizardfan
check uniqueness of id values
5061a3a
@wizardfan
add check on empty mandatory fields
9fb7021
wizardfan added 6 commits June 10, 2020 00:12
@wizardfan
add function to automatic convert string to float for field having na…
2bb28e5 
…me ending with ratio or number
@wizardfan
patch to make Elixir validator could deal with - and : in the field n…
8ae83bf 
…ame properly
@wizardfan
add hard-coded to sanitize part due to the discrepency between rulese…
9ba3126 
…t and template and strange section name in the current system
@wizardfan
rename to get_constant_value for a wider usage
ae515ab
@wizardfan
make the new data structure work fully: 1) convert new structure to o…
d61cf2a 
…ld structure to make current validation code work 2) add missing date value processing 3) remove empty fields in the data to make the validation result from error to warning
@wizardfan
remove redundant codes
1ce4ce8
@Aksh77 Aksh77 force-pushed the new_python_validator branch from 2f0d366 to d0bd545 Compare October 29, 2021 13:46
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3 participants

@wizardfan @Alexey-ebi