Feat/bhcdatastaging april release

[mfshao]

• Deploy April release services to BRAIN data prep
• Added publication page
• Added export to workspace buttons
• Change root dir of jupyter nb to /pd
• Added R studio
• Added configs for sower and pelican

[PlanXCyborg]

dataprep.braincommons.org/manifest.json

Deployment changes

• fence
  • In fence-config, the region field of S3_BUCKETS is now required: if not specified, Fence will print a warning and try to call GetBucketLocation. Fence will error at startup if that doesn't work. (Fix/make region required for s3 bucket config fence#749)
• guppy
  • Increased node.js max header size to prevent issue with large NIH login session cookies hitting request header limit. ((PXP-5570) Bump header size limit to 16kb guppy#79)
• hatchery
  • New pull_policy option is available for hatchery.containers entries, eg: (feat(pods): add pull policy to containers config hatchery#1)
  • { (feat(pods): add pull policy to containers config hatchery#1)
  • "target-port": 8787, (feat(pods): add pull policy to containers config hatchery#1)
  • "cpu-limit": "1.0", (feat(pods): add pull policy to containers config hatchery#1)
  • "memory-limit": "512Mi", (feat(pods): add pull policy to containers config hatchery#1)
  • "pull_policy": "Always", (feat(pods): add pull policy to containers config hatchery#1)
  • "name": "R Studio", (feat(pods): add pull policy to containers config hatchery#1)
  • "image": "heliumdatastage/rstudio-server:1", (feat(pods): add pull policy to containers config hatchery#1)
  • "env": { (feat(pods): add pull policy to containers config hatchery#1)
  • "DISABLE_AUTH": "true" (feat(pods): add pull policy to containers config hatchery#1)
  • }, (feat(pods): add pull policy to containers config hatchery#1)
  • "args": [], (feat(pods): add pull policy to containers config hatchery#1)
  • "path-rewrite": "/", (feat(pods): add pull policy to containers config hatchery#1)
  • "use-tls": "false", (feat(pods): add pull policy to containers config hatchery#1)
  • "ready-probe": "/" (feat(pods): add pull policy to containers config hatchery#1)
  • } (feat(pods): add pull policy to containers config hatchery#1)

• pidgin
  • added required configuration variable "API_HEALTH_URL" for status endpoint (Fix/_status pidgin#31)
  • use the latest version of the python 3 base image (Chore/bump image pidgin#29)
• portal
  • The Terra template attribute in gitops.json now expects a list of strings, not just a single string. (uc-cdis/portal#663)
  • Added footer link configuration to portal config: components.footer.links is an array of { text: <string, optional>, href: <string> }. (uc-cdis/portal#661)
  • Added a new property to gitops.json: components.login.contact_link: { text: string, href: string }. If login.contact_link is present, it will be displayed instead of login.email. Email links can be represented in contact_link using "mailto:email@address" as the "href". (uc-cdis/portal#660)
  • Updated tiered access logic requires Guppy server >= 0.4.0 (uc-cdis/portal#650)
  • New optional title parameter in Terra Export Warning configuration: terraExportWarning: { subjectThreshold: int, title: string(optional), message: string(optional) } (uc-cdis/portal#656)
  • Added terraExportWarning: { subjectThreshold: <number>, message: <string, optional> } to portal config. (uc-cdis/portal#642)
  • New optional portal config flag: dataExplorerConfig.terraTemplate. The value of this parameter is placed in the Terra export URL as the value of the query parameter 'template'. (uc-cdis/portal#645)
• sheepdog
  • The environment's user.yaml needs to be updated to add the new Sheepdog admin policy/resources/roles; for each user that has admin: true, grant them the new policy. See https://github.com/uc-cdis/commons-users/pull/810 for an example. (PXP-4102 Feat/arb admin sheepdog#319)
  • Fix Travis coverage reports (combine the results of all 3 tests into one coverage report). (PXP-3408 Update Sheepdog to Python3 sheepdog#314)
• wts
  • use the latest version of the python 3 base image (uc-cdis/wts#14)

[haraprasadj]

+1

[PlanXCyborg]

dataprep.braincommons.org/manifest.json

Deployment changes

• fence
  • In fence-config, the region field of S3_BUCKETS is now required: if not specified, Fence will print a warning and try to call GetBucketLocation. Fence will error at startup if that doesn't work. (Fix/make region required for s3 bucket config fence#749)
• guppy
  • Increased node.js max header size to prevent issue with large NIH login session cookies hitting request header limit. ((PXP-5570) Bump header size limit to 16kb guppy#79)
• hatchery
  • New pull_policy option is available for hatchery.containers entries, eg: (feat(pods): add pull policy to containers config hatchery#1)
  • { (feat(pods): add pull policy to containers config hatchery#1)
  • "target-port": 8787, (feat(pods): add pull policy to containers config hatchery#1)
  • "cpu-limit": "1.0", (feat(pods): add pull policy to containers config hatchery#1)
  • "memory-limit": "512Mi", (feat(pods): add pull policy to containers config hatchery#1)
  • "pull_policy": "Always", (feat(pods): add pull policy to containers config hatchery#1)
  • "name": "R Studio", (feat(pods): add pull policy to containers config hatchery#1)
  • "image": "heliumdatastage/rstudio-server:1", (feat(pods): add pull policy to containers config hatchery#1)
  • "env": { (feat(pods): add pull policy to containers config hatchery#1)
  • "DISABLE_AUTH": "true" (feat(pods): add pull policy to containers config hatchery#1)
  • }, (feat(pods): add pull policy to containers config hatchery#1)
  • "args": [], (feat(pods): add pull policy to containers config hatchery#1)
  • "path-rewrite": "/", (feat(pods): add pull policy to containers config hatchery#1)
  • "use-tls": "false", (feat(pods): add pull policy to containers config hatchery#1)
  • "ready-probe": "/" (feat(pods): add pull policy to containers config hatchery#1)
  • } (feat(pods): add pull policy to containers config hatchery#1)

• pidgin
  • added required configuration variable "API_HEALTH_URL" for status endpoint (Fix/_status pidgin#31)
  • use the latest version of the python 3 base image (Chore/bump image pidgin#29)
• portal
  • The Terra template attribute in gitops.json now expects a list of strings, not just a single string. (uc-cdis/portal#663)
  • Added footer link configuration to portal config: components.footer.links is an array of { text: <string, optional>, href: <string> }. (uc-cdis/portal#661)
  • Added a new property to gitops.json: components.login.contact_link: { text: string, href: string }. If login.contact_link is present, it will be displayed instead of login.email. Email links can be represented in contact_link using "mailto:email@address" as the "href". (uc-cdis/portal#660)
  • Updated tiered access logic requires Guppy server >= 0.4.0 (uc-cdis/portal#650)
  • New optional title parameter in Terra Export Warning configuration: terraExportWarning: { subjectThreshold: int, title: string(optional), message: string(optional) } (uc-cdis/portal#656)
  • Added terraExportWarning: { subjectThreshold: <number>, message: <string, optional> } to portal config. (uc-cdis/portal#642)
  • New optional portal config flag: dataExplorerConfig.terraTemplate. The value of this parameter is placed in the Terra export URL as the value of the query parameter 'template'. (uc-cdis/portal#645)
• sheepdog
  • Fix Travis coverage reports (combine the results of all 3 tests into one coverage report). (PXP-3408 Update Sheepdog to Python3 sheepdog#314)
• wts
  • use the latest version of the python 3 base image (uc-cdis/wts#14)