Remove developmental stage from harmonized metadata table #163
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…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
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jaclyn-taroni
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* 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>
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It does exactly what the title says. Closes #159.