2025.09.18

State as demoed in Aberdeen week of 2025.09.08.

What's Changed

• 118 change our subnet configuration by @thecaffiend in #201
• fix: test excluding etl files from pyright by @mehalter in #205
• 200 document current process for using cape UI as is by @thecaffiend in #204
• Add Basic User Management by @mehalter in #203
• 207 extend users and groups with file based config by @thecaffiend in #209
• feat(tljh): add initial SSO implementation into jupyterhub by @mehalter in #208
• Update public pulumi stack configuration by @github-actions[bot] in #202
• 210 add additional local admin user and wire up to new identity pool and new default cape user role by @thecaffiend in #211
• Update public pulumi stack configuration by @github-actions[bot] in #212
• feat(tljh): add support for the logout button in JupyterHub by @mehalter in #213
• Migrate to a full JupyterHub installation by @mehalter in #216
• 215 add api gateway test lambda authorizer by @thecaffiend in #219
• Update public pulumi stack configuration by @github-actions[bot] in #214
• 221 consider move to opa policy engine by @thecaffiend in #222
• Connect JupyterHub to Cognito identity pool by @mehalter in #224
• 225 add user attributes store by @thecaffiend in #229
• 230 add new overall cape api by @thecaffiend in #234
• 236 add pre signed post get endpoint for s3 upload by @thecaffiend in #237
• 235 indeterminate order of target group resources by @thecaffiend in #238
• removed raw file post endpoint as it is OBE by @thecaffiend in #243
• 239 user attribute api gets by @thecaffiend in #246
• 241 s3 api gets by @thecaffiend in #247
• ETL and Crawler API Endpoints by @mehalter in #248
• DAP API Migration by @mehalter in #249
• Update public pulumi stack configuration by @github-actions[bot] in #223
• feat(private): allow group and user extra files to be missing by @mehalter in #252
• 254 pipeline profile additions by @thecaffiend in #255
• 257 fix pulumi diffs due to lambda layer zip file by @thecaffiend in #267
• Nextflow AWS Batch Squared by @mehalter in #264
• added stub for nsis tributary by @thecaffiend in #269
• Nextflow AWS Batch Squared Part 2 by @mehalter in #271
• Update public pulumi stack configuration by @github-actions[bot] in #253
• docs: add documentation on creating more VPN client endpoints and revoking their access by @mehalter in #256
• 258 allow metadata to be attached to a collection of uploaded files by @thecaffiend in #273
• Update /dap/submit endpoint to utilize the new AWS Batch pipeline submission by @mehalter in #277
• 259 support multi part file uploads by @thecaffiend in #281
• feat(api): add /dap/status and /dap/logs API endpoints by @mehalter in #280
• fix: update pypdf to v6 to get security fix by @mehalter in #283
• 263 produce report by @thecaffiend in #284
• Improving Bactopia ETLs by @mehalter in #285
• feat(cape-frontend): intial implementation of cape-frontend web application by @mehalter in #233
• 286 coors bypass for api gateway direct integration with aws resources by @thecaffiend in #287
• feat(dap): add Bactopia v3.2.0 to the DAP registry by @mehalter in #288
• feat(etl): allow bactopia results to run on just a tar file along with a gzip by @mehalter in #290
• 262 build athena query for reporting by @thecaffiend in #289
• Update template.html.j2 by @truemerrill in #291
• fix: crawling of seqauto inputs by @mehalter in #292
• Update template.html.j2 by @truemerrill in #294
• gzip uncompressed fastx files when processing incoming archive by @thecaffiend in #296
• bring manual demo changes into mainline by @thecaffiend in #307
• fix: update cape-frontend cognito settings by @mehalter in #308

New Contributors

• @truemerrill made their first contribution in #291

Full Changelog: 2025.02.11...2025.09.18

2025.02.11

What's Changed

• 126 refactor alb static app deployment acm cert stuff etc out to reusable place by @thecaffiend in #168
• Swapped out host-specific cert/key for wildcard version by @thecaffiend in #171
• 142 move dap api behind alb and route53 by @thecaffiend in #177
• limit static apps to top level domains by @thecaffiend in #181
• Add CapePy Python library across the infrastructure by @mehalter in #173
• Update public pulumi stack configuration by @github-actions in #170
• 61 get our openapi spec working for the data analysis pipeline api by @thecaffiend in #182
• Update public pulumi stack configuration by @github-actions in #183
• 172 deploy some kind of jupyter environment by @thecaffiend in #187
• 190 update default config file docs and values by @thecaffiend in #193
• Update public pulumi stack configuration by @github-actions in #189
• Refactor ETL semantics to operate on an arbitrary src/sink buckets by @mehalter in #194
• Update public pulumi stack configuration by @github-actions in #195
• 109 rework swimlane subnet definitions by @thecaffiend in #196

Full Changelog: 2024.10.14...2025.02.11

2024.10.14

What's Changed

• updated NOTICE.txt by @thecaffiend in #13
• Get to baseline of datalake demo with ResourceComponent architecture changes by @thecaffiend in #14
• Add Public stack for easy infrastructure creation by @mehalter in #20
• ci: add necessary permissions for pull request creation by @mehalter in #21
• Update public pulumi stack configuration by @github-actions in #23
• Add unit testing by @mehalter in #19
• Added README.md by @thecaffiend in #25
• docs: add configuration for prettier by @mehalter in #26
• fixed bad parental relations by @thecaffiend in #27
• First cut private VPC by @thecaffiend in #29
• Add descriptive tags and fix/shorten resource names by @thecaffiend in #35
• Update public pulumi stack configuration by @github-actions in #30
• Updates to get genomics tributary in by @thecaffiend in #36
• Update public pulumi stack configuration by @github-actions in #37
• Moved inline policy docs to module by @thecaffiend in #39
• added get_inline_role function by @thecaffiend in #42
• changed crawlers from event driven to scheduled by @thecaffiend in #43
• added sub readme for push vs pull queuing by @thecaffiend in #47
• 46 implement push based queuing for etl by @thecaffiend in #48
• changed genomics crawler to run hourly by @thecaffiend in #51
• Update public pulumi stack configuration by @github-actions in #44
• feat(private): add vm subnet by @mehalter in #53
• Modified swimlane VPCs for egress to internet by @thecaffiend in #56
• Update public pulumi stack configuration by @github-actions in #59
• start of simple api spec for data analysis pipelines by @thecaffiend in #60
• linked all TODOs in code to specific issues for tracking by @thecaffiend in #73
• Add AWS Batch Compute Environments by @mehalter in #74
• Update public pulumi stack configuration by @github-actions in #79
• chore: add .vscode with basic configuration by @mehalter in #82
• Markdown formatting by @mehalter in #83
• Implement a few new configuration options by @mehalter in #80
• foundation for job submission to head node by @thecaffiend in #90
• Update public pulumi stack configuration by @github-actions in #85
• 87 need to pass region into lambdas that need it as an env var by @edpg-cp-24 in #93
• feat(etl): add GPHL sequencing PDF ETL script by @mehalter in #52
• Update public pulumi stack configuration by @github-actions in #94
• updated etl (tnl, gphl-cre) scripts from their respective repos by @thecaffiend in #96
• Formalize our usage of the Pulumi configuration by @mehalter in #81
• added a config value for type of deployment by @thecaffiend in #91
• Update public pulumi stack configuration by @github-actions in #97
• fix(config): ignore keys that resolve to None by @mehalter in #98
• chore(vscode): configure pytest for project by @mehalter in #103
• Add testing badge by @mehalter in #104
• added private swimlane vpn by @thecaffiend in #102
• Update public pulumi stack configuration by @github-actions in #108
• ci: add release workflow by @mehalter in #110
• 107 separate tracked and non tracked assets by @thecaffiend in #111
• Update public pulumi stack configuration by @github-actions in #113
• Get AWS Batch working by @mehalter in #116
• use versioning for CI/CD by @mehalter in #117
• changed the default schedule for all crawlers to be 0200 daily by @thecaffiend in #121
• ci: add pre-commit configuration for safer development by @mehalter in #123
• fix(batch): update AMI environment ID by @mehalter in #124
• plumbing for private s3 hosted web forms by @thecaffiend in #119
• fix(batch): update image AMI for analysis pipeline by @mehalter in #137
• add baseline cape analysis UI application to repo by @thecaffiend in #139
• list pipelines api endpoint and api static app permissions by @thecaffiend in #140
• temporary handling of output s3 buckets for data analysis pipeline output by @thecaffiend in #149
• remove cape frontend from repo, will deploy manually by @mehalter in #154
• get nextflow head node running commands from lambda by @thecaffiend in #160
• add a second bactopia version for testing purposes by @mehalter in #157
• update bactopia pipeline parameters by @thecaffiend in #161
• fix: add support for v3.0.1 by @mehalter in #162
• EC2 Instance tagging for pipeline executors by @mehalter in #163
• fix integrationHttpMethod always showing change for options endpoints by @thecaffiend in #164
• implement real bactopia output etl by @thecaffiend in #165
• Update public pulumi stack configuration by @github-actions in #122

New Contributors

• @thecaffiend made their first contribution in #13
• @mehalter made their first contribution in #20
• @github-actions made their first contribution in #23
• @edpg-cp-24 made their first contribution in #93

Full Changelog: https://github.com/cape-ph/cape-cod/commits/2024.10.14