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

Merge 2.0 to master #157

Merged
merged 87 commits into from
Jun 20, 2024
Merged

Merge 2.0 to master #157

merged 87 commits into from
Jun 20, 2024

Conversation

celinepelletier
Copy link
Member

No description provided.

devbyaccident and others added 30 commits November 21, 2022 15:26
@devbyaccident
Create next.deploy
e55b8be
@devbyaccident
Merge pull request #59 from kids-first/devbyaccident-patch-2
3db074f 
Create next.deploy
@devbyaccident
fixing name to match current resources
87fb2a6
@evans-g-crsj
🐛 Avoid logging an empty object (#60)
3780bb0
@evans-g-crsj
:bugs: Fix arranger-project (genes.cosmic.tumour_types_germline) (#63)
8f42981
@evans-g-crsj
🔧 Add main_branch entry to next.deploy (#64)
ca09ea1
@evans-g-crsj
🔧 Add members to arranger-project (#65)
4d4aa63
@evans-g-crsj
🔧 Add helper script to add aliases (#66)
c9f2978
@evans-g-crsj
✨ Add variants to sets (#67)
3615b9b
@evans-g-crsj
🔧 Implement searchAfter for participants (phenotypes) (#68)
40ee2e0 
* 🔧 Implement searchAfter for participants (phenotypes)

* ♻️ Incorporate code review comments

* 🔧 Fix imports
@evans-g-crsj
🔧 Update conf for specimens (#69)
5abf703
@celinepelletier
Small fixes for UCSF (using public key and pass esUser and esPass to …
4e175a6 
…EsClient)
@celinepelletier
Review comments
697858a
@celinepelletier
fix: UCSF-000 fix try to match regex on something that is not a string
ff0408d
@evans-g-crsj
🔧 Create include-next-deploy
f79e5e7
@evans-g-crsj
📝 Rename include-next-deploy to include.next.deploy
c8a23cf
@evans-g-crsj
📝 Update include.next.deploy
5169e1a
@evans-g-crsj
🔧 Prepare admin conf for INCLUDE
61e558a
@evans-g-crsj
🔧 Change arranger project name
0abb6b7
@adipaul1981
Merge pull request #86 from kids-first/feat-conf-include-qa
7e5f4aa 
🔧 Prepare admin conf for INCLUDE
@devbyaccident
Add prd cidr to next.deploy
93cd8c4
@devbyaccident
Merge pull request #87 from kids-first/devbyaccident-patch-2
59bab06 
Add prd cidr to next.deploy
@devbyaccident
Update include.next.deploy
9369ca8
@devbyaccident
Update include.next.deploy
9905931
@devbyaccident
Merge pull request #92 from kids-first/feature/cbl/add-security-headers
f14385d 
Update include.next.deploy
@evans-g-crsj
🐛 Incorporate bug fix for resolveSet (#93)
a9e34e5
@evans-g-crsj
🔧 Add extended mapping to arranger project (source_text_tumor_locatio…
9cdbd7f 
…n) (#94)
@devbyaccident
🔒️ Add container vulnerability scan
5e988cc
@devbyaccident
Merge pull request #95 from kids-first/feature/cbl/container-scan
6b000df 
Add container scan
@evans-g-crsj
🐛 Make sure that numbers checks are supported when testing regex in r…
983645d 
…eplaceSetByIds (#97)
evans-g-crsj and others added 25 commits April 5, 2024 10:53
@evans-g-crsj
🔧 Update study mocks (#132)
cc8a17c
@aperron-ferlab
feat: SJIP-768 add studies participant count, variants count, genomes…
ec983fe 
… and transcriptomes (#133)

* feat: SJIP-768 add studies participant count

* feat: SJIP-768 add genomes/variants/transcriptomes
@aperron-ferlab
fix: SJIP-768 remove unused env variable (#134)
5c69ff5 
* fix: SJIP-768 remove unused env variable
@evans-g-crsj
📝 Update studies mock (#135)
2542ab8
@aperron-ferlab
fix: SJIP-768 adjust genomes and transcriptomes values (#136)
e826c56 
* fix: SJIP-768 adjust genomes and transcriptomes values
@aperron-ferlab
fix: SJIP-768 increase size for studies population count (#137)
acf6c67 
* fix: SJIP-768 increase size for studies population count
@aperron-ferlab
fix: SJIP-768 adjust stats queries to take participant count (#138)
6ea71be 
* fix: SJIP-768 adjust stats queries to take participant count
@evans-g-crsj
📝 Update domains and study_designs fields (#139)
27dc0bd
@aperron-ferlab
feat: SJIP-812 add demographics to public routes (#140)
abccd1d
@aperron-ferlab
feat: SJIP-768 add top mondo diagnosis to public route (#141)
76703e7
@aperron-ferlab
fix: SJIP-812 replace ethnicity with race in statistic route (#142)
8bfb201
@evans-g-crsj
🥅 Add extra condition before deleting indices from a given release (#143
2f2575d 
)
@evans-g-crsj
🔊 Show if duplicates exist in checkReleaseStats (#144)
074c668
@aperron-ferlab
feat: SKFP-1077 add members count stats (#145)
0d31f3e
@aperron-ferlab
fix: SKFP-1077 remove usage of env vars for members count (#146)
19a3eeb
@aperron-ferlab
fix: SKFP-1077 check if indices exist for members (#147)
4df26d2
@aperron-ferlab
fix: SJIP-768 adjust top mondo hits to use display_term (#148)
4688d7a
@evans-g-crsj
🔧 Update projects conf (#149)
5add1af
@aperron-ferlab
fix: SKFP-1097 adjust auth studies allowed files count (#151)
ee29634 
* fix: SKFP-1097 adjust auth studies allowed files count
@aperron-ferlab
fix: SKFP-1097 remove controlled condition to match condition query (#…
1f32b1e 
…152)
@evans-g-crsj
🔧 Remove fields from mock studies (#153)
2f4ae8e
@evans-g-crsj
🔧 Add new script and improve others (admin) (#154)
b9eb67b
@evans-g-crsj
🔧 Remove data_types from studies mock and add new script to inspect E…
c8f5ba9 
…S mappings (#155)
@evans-g-crsj
❇️ Add script to help build stepfn etl payload (#156)
c802656 
* ❇️ Add script to help build stepfn etl payload

* 📝 Make sure a valid JSON is printed
@celinepelletier
fix: SKFP-1033 merge 2.0 to master
eb03194
@celinepelletier celinepelletier merged commit aca210e into master Jun 20, 2024
3 of 4 checks passed
@celinepelletier celinepelletier deleted the fix/SKFP-1033-merge-2-0 branch June 20, 2024 18:20
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@evans-g-crsj evans-g-crsj evans-g-crsj approved these changes

@aperron-ferlab aperron-ferlab Awaiting requested review from aperron-ferlab

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

Successfully merging this pull request may close these issues.
5 participants
@celinepelletier @evans-g-crsj @devbyaccident @adipaul1981 @aperron-ferlab