Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add sample redcap files #67

Merged
merged 5 commits into from
Jul 5, 2024
Merged

add sample redcap files #67

merged 5 commits into from
Jul 5, 2024

Conversation

kcranston
Copy link
Member

Adding sample files for RedCap exports

@kcranston kcranston requested a review from mshadbolt July 5, 2024 18:37
mshadbolt
mshadbolt reviewed Jul 5, 2024
View reviewed changes
README.md Outdated Show resolved Hide resolved
mshadbolt
mshadbolt reviewed Jul 5, 2024
View reviewed changes
Copy link
Contributor

@mshadbolt mshadbolt left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thought it might be neater to keep all the example files inside the one sample_inputs directory . Made some adjustments to the README because of the folder structure change

@kcranston
Copy link
Member Author

Thanks for making it better! Feel free to approve & merge.

@mshadbolt mshadbolt merged commit 75046bf into develop Jul 5, 2024
2 checks passed
@mshadbolt mshadbolt deleted the add-redcap-files branch July 5, 2024 21:04
yavyx pushed a commit that referenced this pull request Aug 9, 2024
@kcranston @mshadbolt @yavyx
add sample redcap files (#67)
66b5ddc 
* add sample redcap files

* restructure suggestion

* mv sample files

* update sample inputs links and info

* Update README.md

---------

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
mshadbolt added a commit that referenced this pull request Aug 20, 2024
@mshadbolt @yavyx @kcranston
Stable candidate v3.0.0 (#74)
4d06105 
* adding date format to date intervals

* addded date format

* updated docs

* updated test date formats

* make exceptions more readable

* make exception specific

* cleanup

* cleanup

* Update src/clinical_etl/CSVConvert.py

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>

* exception when parser fails

* update reference date docs

* improved error catching in manifest

* better error msg

* fix month intervals

* remove import

* minor fixes

* add sample redcap files (#67)

* add sample redcap files

* restructure suggestion

* mv sample files

* update sample inputs links and info

* Update README.md

---------

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>

* create mohschemav3 class

* validate v3 donors

* validate primary diagnoses

* validate specimens

* validation logic fix

* validate treatments

* treatment validation fix

* validate systemic & radiation therapies

* validate followups

* replace match with if, less indentation

* validate exposures & comorbidities

* rename v3 to lowercase

* sample registration validation (required)

* validate surgeries

* added missing argument

* fix nested schemas

* update references to v3

* fix test

* fix test, using v2 by default

* update default templates

* update test data files

* manual mapping function changes to csv templates

* update test yamls

* update tests

* add biomarker validation, edit resolution to work

* update templates

* fix typo

* fix missing comma

* remove extra staging validation

* rename v2 template

* added multisheet line for testing

* stage group validation fix

* validate systemic therapy dates

* test systemic therapy date validation

* add sample redcap files (#67)

* add sample redcap files

* restructure suggestion

* mv sample files

* update sample inputs links and info

* Update README.md

---------

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>

* Fix up some of the validations (#69)

* fix for loop

* fix keyerror

* fix if elses

* another fix

* update tests

* revert elif

* update to version 3 (#70)

---------

Co-authored-by: Javier Castillo-Arnemann <javiercastilloar@gmail.com>
Co-authored-by: Javi <30913679+yavyx@users.noreply.github.com>
Co-authored-by: Karen Cranston <karen.cranston@gmail.com>
mshadbolt added a commit that referenced this pull request Sep 30, 2024
@mshadbolt @yavyx
@kcranston @daisieh
Stable candidate v3.1.0 (#84)
0458bf8 
* adding date format to date intervals

* addded date format

* updated docs

* updated test date formats

* make exceptions more readable

* make exception specific

* cleanup

* cleanup

* Update src/clinical_etl/CSVConvert.py

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>

* exception when parser fails

* update reference date docs

* improved error catching in manifest

* better error msg

* fix month intervals

* remove import

* minor fixes

* add sample redcap files (#67)

* add sample redcap files

* restructure suggestion

* mv sample files

* update sample inputs links and info

* Update README.md

---------

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>

* create mohschemav3 class

* validate v3 donors

* validate primary diagnoses

* validate specimens

* validation logic fix

* validate treatments

* treatment validation fix

* validate systemic & radiation therapies

* validate followups

* replace match with if, less indentation

* validate exposures & comorbidities

* rename v3 to lowercase

* sample registration validation (required)

* validate surgeries

* added missing argument

* fix nested schemas

* update references to v3

* fix test

* fix test, using v2 by default

* update default templates

* update test data files

* manual mapping function changes to csv templates

* update test yamls

* update tests

* add biomarker validation, edit resolution to work

* update templates

* fix typo

* fix missing comma

* remove extra staging validation

* rename v2 template

* added multisheet line for testing

* stage group validation fix

* validate systemic therapy dates

* test systemic therapy date validation

* add sample redcap files (#67)

* add sample redcap files

* restructure suggestion

* mv sample files

* update sample inputs links and info

* Update README.md

---------

Co-authored-by: Marion <mshadbolt@users.noreply.github.com>

* Fix up some of the validations (#69)

* fix for loop

* fix keyerror

* fix if elses

* another fix

* update tests

* revert elif

* update to version 3 (#70)

* Add RedCap export splitting script (#78)

* add splitting script

* minor refactoring

* Update validation and test data for model 3.1 (#80)

* fix deceased validation

* change bools to single_vals

* fix more cause_of_death validations

* update test data, fix validations, update template/manifest

* update schema urls

* more schema changes in v3 templates

* DIG-1772 & DIG-1782: Handle -99 and 'Not available' as missing (#83)

* numeric not availabe and schema template update

* update default url

* improve template generation, add not_available to missingness

* update v3 template

* methods for -99 mappng

* update test template and test data

* update script and moh_diffs

* fix typo in validation

* updated mapping functions doc

* updates for latest version

---------

Co-authored-by: Javier Castillo-Arnemann <javiercastilloar@gmail.com>
Co-authored-by: Javi <30913679+yavyx@users.noreply.github.com>
Co-authored-by: Karen Cranston <karen.cranston@gmail.com>
Co-authored-by: Daisie Huang <daisieh@gmail.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mshadbolt mshadbolt mshadbolt approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@kcranston @mshadbolt