dmgaldi
commented
5 months ago - initial commit
- updates
- Fix logger calls.
- Exclude ancient log4j files.
- restructuring
- updates
- fixes
- no longer trying to use record types
- fixed call order with database initialization
- fixed option unwrap error on db port
- fixed test query (forgot oracle doesn't like trailing semicolons)
- updates
- added api doc endpoint
- sorted out raml
- request context for logger
- corrected log suppliers
- adjusted filter priorities
- fix log format
- logging
- logging
- added service dependency wrapper
- added unit tests
- tweaked schema
- auth filter
- updated health endpoint
- duration formatting
- duration formatting
- dockerfile & auth
- fix auth issue
- added prometheus metrics
- updated docker file, registered metrics filter
- Improved histogram buckets, added more logging.
- improved the auth annotation cache
- corrected filter priorities
- restructured raml
- corrected weird log quirk with RequestIdFilter
- corrected typo in readme
- removed unnecessary string.format in a log call
- fixed function name to camel case.
- optimized imports
- docs and minor cleanup
- documentation and cleanup
- updated docs
- unit tests and documentation
- more unit tests
- removed library code
- updates
- removed generated sources
- supports multiproject, testing with provider
- updates
- using user profile in post request
- updates
- updates
- user profile provider update
- updated HelloWorld
- working with user provider
- minor cleanup
- docs and minor code cleanup
- update example project based on meta repo updates
- Initial commit
- Commit generated copies of api.html to be consistent with derived projects
- updated dependencies and added GitHub packages to repos
- update to use newer gradle plugin
- add timezone info
- Initial commit
- Update to latest status of FgpUtil, container core, and build-utils/gradle plugin
- Add generated java sources for reference
- updates
- implementing
- updates
- updated
- working example
- don't rerun jobs we already know
- updates
- updates
- updates
- correct indent
- clear
- re-add
- regen jaxrs
- update API docs to include examples
- update to release version of platform lib
- clean up imports
- rm demo code
- add generated code to trim out of diff
- diff cleanup
- add kotlin files
- pull in changes from original branch
- log5j
- comments
- comments
- beta div plugin framework
- add basic beta div functionality
- added comments describing goals
- add access to PluginUtil type
- checkpoint: beta div draft plugin
- for now assume we need both metadata and statistics for beta div
- decided dont need stats endpoint for now
- get compiling
- first draft ranked abundance and alpha div
- get compiling again
- write metadata for alpha div and ranked abund
- get data in and out of rserve properly
- move beta div to slow queue for now
- typo
- require auth
- remove appdb
- Update generated files
- Update generated files
- update startup.sh
- update log4j2.yml
- log5j2
- Complete example plugin, including two API changes to ease plugin development + validation
- fix output
- add a simple statistic
- s3 https is now configurable
- s3 https is now configurable
- Move a lot of shared RAML to EdaCommon and use local EdaCommon checkout if present
- Use new metadata types and write methods
- Rework existing compute configs for easy access by data service and merge service and add stats objects
- Changes to add compute info to tabular requests
- Add plot reference for the example viz to read the computed column
- New generated docs
- Make sure column name format matches other column names
- write metadata from R
- Merge from main
- Add utilities to directly stream R command file results into the various plugin result files
- write data and meta results to file in rserve
- update example plugin
- update generated files
- update generated files
- Comply with new RAML and var metadata API
- Update generated docs
- update generated docs
- fix warning from Jersey
- refine imports
- generated files
- Add optional autostart query param to job submission/status endpoint (default still true)
- Comply with eda common upgrade
- Fix headers: should match subsetting service format (not merging)
- Add plot reference to computed var
- bugs
- draft add ancestor id cols to response
- Rename translated request body object since 'entity' has special meaning in EDA and check for presence of 'config' and nested 'outputEntityId' properties in request (throwing 400 if not present)
- some bugs and update docs
- silly bug
- update args to R for ranked abund and beta div
- Ensure deterministic hashing even when derived vars or subset props are missing
- update generated docs
- Allow compute configs to omit computed entity ID
- Upgrade deps
- Refine build process and upgrade to latest gradle plugin and EdaCommon
- cleanup imports
- check if job should be restarted before returning it
- fix for empty dotNotatedIdColumns
- replace distance with dissimilarity in beta div
- Compliance w/edaCommon + dep upgrades
- Dependency upgrades
- dep upgrades and small API compliance fix
- Update generated class
- Revert to EdaCommon generated from main
- Update compute service to comply with new derived vars APIs
- comply with new EdaCommon APIs
- Remove old generated types
- added diff abund plugin organization
- differential abundance plugin reachable
- Add expiration endpoint
- functional differential abundance
- Remove requirement on native var in example plugin so we can test derived vars
- Update to latest edacommon
- comments
- Fix differential abundance raml and enable compute controller to handle more specific response types
- Add configurable authorization key to expiration endpoint
- Change name from key to token so value is not obscured in pconf
- avoid race condition
- Revert "avoid race condition"
- avoid race condition
- add diff abund stats raml and cleanup
- Get expiration endpoint working with auth param
- avoid race condition
- Fix comment
- Add job-id option to expiration endpoint
- Change procedural endpoint name to a verb, read config file correctly, and fix misplaced comment
- user comparator methods
- cleanup
- update generated files
- Clear out some local memory before allocating more- may help a little because some collections have up to 70k vars
- Fix result file bug; Consumer
!= StreamingOutput - generated code
- Use parallel stream to look up job attributes (independent operations)
- Add log line telling how many jobs were expired (and echoing request) in case apache returns 502 due to timeout
- Use custom threadpool with 10 'threads' since performance is IO bound
- gen code for correlation plugin
- added correlation plugin
- functional correlation app
- update api for diff abund to allow cont variables
- use variable data shape
- cleanup
- Upgrade edacommon to latest DV-compatible version
- Upgrade edacommon to latest DV-compatible version
- Dependency upgrades
- use LabeledRange and common getRBinListAsString
- Update generated code
- fix typos
- Use latest EDACommon
- remove temporary rounding
- Use latest eda-common
- Use latest EdaCommon
- use beta edacommon
- make sure raml is updated
- support maaslin for diff abund
- update docs and generated classes
- use updated edacommon
- update diff abund api
- update generated docs
- wip
- update generated docs
- use edacommon beta4
- some new stuff
- received correlation response with two abundances
- Add data constraints to compute plugins
- fixed collectionSpec error
- get sample metadata
- successful metadata correlation computations
- cleanup correlation plugin
- cleanup correlation provider
- update generated files
- Add comment
- fix correlation repsonse raml
- update generated classes
- fix response delegate
- add pvalue floor to diff abund
- make pvaluefloor optional
- add generated files
- use old edacommon for now
- break correlation request into multiple types
- cleanup
- Fetching variables from ancestor entities
- remove ids from continuous metadata variables list
- correlation assay assay wiring
- stub for correlation assay assay
- update correlation assay assay stream specs
- update stream spec validation and use two streams
- get the data in R
- build AbundanceData and run correlation
- remove completed todo
- add some kinda lame constraints to correlation assay assay
- meh comment constraints i suppose
- update generated docs
- add some new generated classes
- clean up
- use new correlation api
- typo
- Add internal endpoints
- Enable auth
- allow ud in correlation metadata app
- clean and comment
- restrict correlation to integers and numbers
- revert restrict correlation to integers and numbers
- update plugins to reflect new correlations api
- update generated docs
- add generated classes for correlation prefilter thresholds
- clean up logic for grabbing correlation metadata
- factor out correlation metadata filter into private method
- update correlation plugins to respect prefilter options
- correlation prefilters are optional
- rescale values to be non-negative
- review feedback
- draft correlation assay self plugin
- wire in correlation assay self plugin
- update generated docs
- explicitly call selfCorrelation R fxn
- correlation method now in utils rather than mbio R package
- draft support for eigengenes
- forgotten import
- compiling issues
- update edacommon version
- update correlation assay self to know about eigengenes
- couple little bugs
- properly order incoming data tables and pass only numeric cols to correlation fxns
- cleanup comments and logic
- make test for eigengene case insensitive
- Commit latest code-gen
- Upgrade to oauth version of container core
- whitespace and generated files
- Don't need user auth in expiration controller, only @AdminRequired
- use refactored mbio r packages
- very rough draft correlations plugins refactor
- remove now deprecated plugins
- update compute controller
- update generated classes
- update plugin to revised correlation api
- update generated docs
- some bugs
- collectionVariable not optional for selfcorrelation... for now
- add some clarifying comments
- add names to abundancedata objects
- switch eigengenes in correlations plugins to use new CollectionWithMetadata R class
- define constant metadata collection
- translate compute to rserve api for diff abund
- expand correlation input types
- fix conditional for metadata input check
- reinstate hasSecondCollection
- rough draft supporting metadata as first data arg for assay X metadata
- fix some compile issues
- update generated docs
- update to reflect recent r refactor
- typo
- clarify some logic
- Mono-eda rename
- Merge DataService changes for correlations-refactor