-
Notifications
You must be signed in to change notification settings - Fork 4
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.
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
Remove developmental stage from harmonized metadata table #163
Merged
jaclyn-taroni
merged 1 commit into
master
from
jaclyn-taroni/159-no-harmonized-dev-stage
Jun 22, 2023
Merged
Remove developmental stage from harmonized metadata table #163
jaclyn-taroni
merged 1 commit into
master
from
jaclyn-taroni/159-no-harmonized-dev-stage
Jun 22, 2023
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
davidsmejia
approved these changes
Jun 22, 2023
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
LGTM
jaclyn-taroni
added a commit
that referenced
this pull request
Jul 17, 2023
…elopment workflow (#171) * Remove developmental stage from harmonized metadata table (#163) * Update README to reflect how to build locally * Add a little info about development, where to view docs * Update documentation to reflect recent harmonization-related changes (#172) * Remove sample strain from cell line source key * Also remove development stage from paragraph * Clarifying example of type casting (#164) * Explain multimapped source keys behavior (#160) Age is a special case * Add strain background to genetic info * Add note about when harmonization docs are effective Notes in Sphinx only seem to work in RST * Apply suggestions from code review * Apply suggestions from code review Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> * Apply suggestions from code review Co-authored-by: David <davidsmejia@gmail.com> * Wordsmithing * Add time source key to time harmonized key * Update docs and table to reflect how we generate variants Also move where we talk about the treatment of values * Multimapped values in alphanumeric ascending order * Update docs/main_text.md * Add sex to harmonized key table, remove reference to special case * Revert "Add sex to harmonized key table, remove reference to special case" This reverts commit 0a32c45. * Add sex back into harmonized keys table --------- Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> Co-authored-by: David <davidsmejia@gmail.com> --------- Co-authored-by: David <davidsmejia@gmail.com> Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org>
jaclyn-taroni
added a commit
that referenced
this pull request
Sep 8, 2023
jaclyn-taroni
added a commit
that referenced
this pull request
Sep 11, 2023
jaclyn-taroni
added a commit
that referenced
this pull request
Sep 12, 2023
* Improve README information on building locally and add info about development workflow (#171) * Remove developmental stage from harmonized metadata table (#163) * Update README to reflect how to build locally * Add a little info about development, where to view docs * Update documentation to reflect recent harmonization-related changes (#172) * Remove sample strain from cell line source key * Also remove development stage from paragraph * Clarifying example of type casting (#164) * Explain multimapped source keys behavior (#160) Age is a special case * Add strain background to genetic info * Add note about when harmonization docs are effective Notes in Sphinx only seem to work in RST * Apply suggestions from code review * Apply suggestions from code review Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> * Apply suggestions from code review Co-authored-by: David <davidsmejia@gmail.com> * Wordsmithing * Add time source key to time harmonized key * Update docs and table to reflect how we generate variants Also move where we talk about the treatment of values * Multimapped values in alphanumeric ascending order * Update docs/main_text.md * Add sex to harmonized key table, remove reference to special case * Revert "Add sex to harmonized key table, remove reference to special case" This reverts commit 0a32c45. * Add sex back into harmonized keys table --------- Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> Co-authored-by: David <davidsmejia@gmail.com> --------- Co-authored-by: David <davidsmejia@gmail.com> Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> * Add spell check (#173) * Port over initial spell check configuration from r.bio admin set up Leave the custom dictionary blank for now; on PR to dev, not main * Specify docs directory in config, remove sources from workflow * Fix spelling error * Populate custom dictionary Not sure how pyspelling handles plural words yet * Fix spelling error * Add plural words and possessives to the custom dictionary * Try ignoring code in markdown in config * Revert "Try ignoring code in markdown in config" This reverts commit 8859f2b. * A few more additions to the custom dictionary * Try setting ignore case to false * Test with lowercase ENA "ena" * Revert "Test with lowercase ENA "ena"" This reverts commit a04883a. * Bump spell check action version * Add spell check explainer to README * Add header and intro paragraph for Childhood Cancer Collections (#183) * Add header and intro paragraph for CCC Also stub in subsection * Add CCC to custom dictionary * Apply suggestions from code review Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> * Apply suggestions from code review * Apply suggestions from code review --------- Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> * Add header and intro paragraph for Tagged Terms (#184) * Add header and intro paragraph for CCC Also stub in subsection * Add CCC to custom dictionary * Add intro paragraph on tagged term Also stub in expected subsection headers * Apply suggestions from code review Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> * Update custom dictionary --------- Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> * Split main_text.md * Fix main_text.md * Add back harmonization-related changes from #163 and #172 (#188) * Add back changes from #163 and #172 * organism_name -> organism__name for txome filter (#189) --------- Co-authored-by: David <davidsmejia@gmail.com> Co-authored-by: Deepa Prasad <d.prasad@alexslemonade.org> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: Arkadii Yakovets <ark@ccdatalab.org>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
It does exactly what the title says. Closes #159.