Minor release, incorporate major bug fixes and recommendations from OHBM meeting.
- [FIX] unique already creates an index, unique made a repetitive index (#600) @jdkent
- [ENH] add base_study attribute (#599) @jdkent
- [FIX] ignore string if doi/pmid/name string is empty (#598) @jdkent
- [ENH] add conditions and weights to specification (#597) @jdkent
- [ENH] add studyset-references endpoint (#596) @jdkent
- chore(deps): bump @cypress/request and cypress in /compose/neurosynth-frontend (#595) @dependabot
- 197 display user icon name (#591) @nicoalee
- [ENH] add username and neurostore studyset script (#590) @jdkent
- [FIX] nick feedback (#589) @jdkent
- [ENH] add usernames to compose (#588) @jdkent
- [MAINT] update openapi to main branch (#586) @jdkent
- [ENH] bulk upload (#585) @jdkent
- 565 update the advanced search input (#583) @nicoalee
- [ENH] add username as resource attribute (#584) @jdkent
- 561 switch api from studies to abstract studies (#582) @nicoalee
- [FIX] id not showing up for info=true (#581) @jdkent
- [ENH] using an iterator over a list comprehension should be faster (#578) @jdkent
- [FIX] add data_type to base_study (#577) @jdkent
- [FIX] info query param behavior (#576) @jdkent
- [ENH] make it quicker to filter studies by whether they have images/points. (#574) @jdkent
- chore(deps): bump tough-cookie and @cypress/request in /compose/neurosynth-frontend (#569) @dependabot
Post-OHBM major release. Includes a wide array of major improvements, including
## What's Changed * feat: updated node and react scripts by @nicoalee in #352 * 307 refactor loading and http requests using react query by @nicoalee in #362 * feat: updated tests and removed old types by @nicoalee in #365 * feat: add create meta-analysis button by @nicoalee in #366 * feat: added redirect to created meta-analysis and unit tests by @nicoalee in #367 * 361 improve meta analysis summary page by @nicoalee in #368 * [TEST] skip tests if external service is not working by @jdkent in #353 * [ENH] add studyset link by @jdkent in #364 * 363 add ability to delete studies by @nicoalee in #373 * [FIX] data type both by @jdkent in #375 * [FIX] add httpx until schemathesis is fixed by @jdkent in #378 * 371 enhance study search view to add studysets that a study is part of with better study addremove functionality by @nicoalee in #377 * 356 add search for studysets by @nicoalee in #379 * [ENH] change workflow to incorporate data for frontend tests by @jdkent in #372 * [FIX] flask sqlalchemy by @jdkent in #385 * [MAINT] use tilde versioning on dependencies by @jdkent in #387 * [REF] neurosynth to compose by @jdkent in #386 * [ENH] add meta analysis provenance by @jdkent in #389 * [ENH] add project table by @jdkent in #393 * feat: added plausible by @nicoalee in #392 * [FIX] allow project to be null by @jdkent in #395 * [FIX] add annotations when analysis is added, not just study by @jdkent in #397 * Add/improve documentation by @jdkent in #333 * [ENH] Add upload process (celery) by @jdkent in #332 * [FIX] add new analysis annotation by @jdkent in #402 * [FIX] celery tests by @jdkent in #405 * [MAINT] delete compose packages by @jdkent in #409 * [FIX] add api in context of current app by @jdkent in #410 * [FIX] increase page size limit by @jdkent in #414 * [FIX] only debug when specified by @jdkent in #413 * [FIX] handled numeric input parse by @jdkent in #416 * [REF] list user args by @jdkent in #415 * [FIX] compose tests by @jdkent in #418 * [FIX] study unique query by @jdkent in #417 * [FIX] neurosynth ingestion by @jdkent in #419 * change to refactored openapi by @jdkent in #420 * [FIX] annotations not updating properly (again) by @jdkent in #421 * [FIX] POST meta-analysis with project by @jdkent in #424 * [ENH] upload neurostore table from results by @jdkent in #422 * [FIX] update openapi spec by @jdkent in #427 * [ENH] project public private by @jdkent in #428 * [FIX] create neurostore study when project is created by @jdkent in #439 * [FIX] compose bot by @jdkent in #440 * [FIX] junit tests by @jdkent in #441 * 381 restructure user experience with meta first approach by @nicoalee in #399 * [FIX] upload key name by @jdkent in #442 * chore(deps): bump @sideway/formula from 3.0.0 to 3.0.1 in /compose/neurosynth-frontend by @dependabot in #404 * chore(deps): bump json5 from 1.0.1 to 1.0.2 in /compose/neurosynth-frontend by @dependabot in #398 * [FIX] celery context by @jdkent in #445 * feat: prevent scroll from changing number input, better support for e… by @nicoalee in #444 * chore(deps): bump webpack from 5.74.0 to 5.83.1 in /compose/neurosynth-frontend by @dependabot in #443 * [FIX] schemas by @jdkent in #446 * [FIX] show diagnostic table at endpoint by @jdkent in #447 * chore(deps-dev): bump jsonwebtoken from 8.5.1 to 9.0.0 in /compose/neurosynth-frontend by @dependabot in #396 * chore(deps): bump decode-uri-component from 0.2.0 to 0.2.2 in /compose/neurosynth-frontend by @dependabot in #394 * chore(deps): bump loader-utils from 2.0.2 to 2.0.4 in /compose/neurosynth-frontend by @dependabot in #391 * feat: set the same order for all analyses - alphabetically by analysi… by @nicoalee in #448 * feat: add default studyset name and description by @nicoalee in #454 * feat: added more info for selecting a study by @nicoalee in #456 * feat: updated save button sitting below annotations by @nicoalee in #460 * 434 coordinate editing ability to add more than one row at a time by @nicoalee in #463 * feat: removed autofill name for meta analysis by @nicoalee in #464 * feat: made links clickable for study display by @nicoalee in #466 * [FIX] swagger ui fix with prance by @jdkent in #467 * [ENH] results endpoint improvements by @jdkent in #462 * [FIX] null results by @jdkent in #468 * [FIX] add new fields to point by @jdkent in #469 * [FIX] update openapi spec by @jdkent in #470 * [FIX] make value a float by @jdkent in #471 * 436 proposal for coordinate table organization by @nicoalee in #472 * [ENH] make the studies endpoint query faster by @jdkent in #474 * [ENH] add order to Points object by @jdkent in #475 * [FIX] add order and status by @jdkent in #477 * [FIX] try to catch more errors on analysis creation by @jdkent in #478 * [FIX] allow bot to add analysis to study owned by user by @jdkent in #479 * [FIX] neurostore analysis upload by @jdkent in #481 * [FIX] make analysis upload a task by @jdkent in #482 * [ENH] use outerjoins to display studies by @jdkent in #483 * 455 upload workflow post meta analysis run by @nicoalee in #491 * chore(deps): bump fast-xml-parser from 4.0.12 to 4.2.4 in /compose/neurosynth-frontend by @dependabot in #484 * feat: added semantic scholar to provide full text by @nicoalee in #492 * 488 make sample size a default metadata key when the user owns the study by @nicoalee in #493 * [ENH] abstract study by @jdkent in #486 * [ENH] switch missing names to base_studies by @jdkent in #495 * [ENH] Add sqltap by @jdkent in #496 * [FIX] fix the study search endpoint by @jdkent in #497 * [FIX] search capabilities by @jdkent in #498 * feat: finished user improvements from feedback by @nicoalee in #499 * feat: updated links for navbar docs and neurovault by @nicoalee in #501 * bugfix: save tags by @nicoalee in #504 * bugfix: handled non prisma case for exclusion selector popup by @nicoalee in #506 * [ENH] allow multiword queries by @jdkent in #512 * [ENH] add load_testing config by @jdkent in #523 * [ENH] misc performance by @jdkent in #526 * feat: added handling of expired tokens and handling of updates betwee… by @nicoalee in #511 * chore(deps): bump fast-xml-parser from 4.2.4 to 4.2.5 in /compose/neurosynth-frontend by @dependabot in #524 * chore(deps): bump semver from 6.3.0 to 6.3.1 in /compose/neurosynth-frontend by @dependabot in #525 * Enh/add caching by @jdkent in #527 * [FIX] bump gunicorn workers and change nested back to subquery by @jdkent in #528 * [FIX] nested query by @jdkent in #529 * [FIX] studyset nested by @jdkent in #530 * feat: removed mark all as complete button if all are complete by @nicoalee in #531 * fix: resolved bugs with out of sync curation, resolved issue with mis… by @nicoalee in #533 * [FIX] switch caching strategy to redis by @jdkent in #532 * feat: put specification details last when creating spec, improved int… by @nicoalee in #534 * [ENH] add info and flat query parameters by @jdkent in #535 * feat: add flat by @nicoalee in #538 * feat: set cloned study annotations to be included by default by @nicoalee in #540 * [ENH] ACE Ingestion by @jdkent in #536 * feat: remove alpha from site and add to labels by @nicoalee in #555 * [FIX] flake8 errors by @jdkent in #568 * feat: add google analytics by @nicoalee in #560 * feat: added neurosynth logo as favicon and change default text by @nicoalee in #558 * chore(deps): bump word-wrap from 1.2.3 to 1.2.4 in /compose/neurosynth-frontend by @dependabot in #542 * codespell: config, workflow + typos fixed by @yarikoptic in #541 * [MAINT] update openapi by @jdkent in #571 * [FIX/ENH] usernames by @jdkent in #570 * [FIX] ignore sample_text by @jdkent in #572
## New Contributors * @yarikoptic made their first contribution in #541
Full Changelog: https://github.com/neurostuff/neurostore/compare/v0.1...v0.2
This is the first versioned release of neurostore. The main items implemented are: - backend for storing coordinate/image based studies (neurostore.org) - backend for creating meta-analyses (compose.neurosynth.org) - frontend for interfacing with both backends This release represents a functional website for using previously ingested studies to create studysets, specify meta-analyses and run those meta-analyses on a google collab notebook.
- [REF] Set up docker-compose, and other boilerplate by @adelavega in #3
- [REF] Move to Python 3.8, add tests by @adelavega in #8
- [REF] Drop Flask-Restful by @adelavega in #9
- [ENH] Remove initialization of database by @jdkent in #16
- [FIX] DockerTestConfig by @jdkent in #15
- [ENH] Add OpenAPI Specification by @jdkent in #19
- [ENH, FIX] Deploy behind nginx-proxy by @tyarkoni in #24
- [ENH] post/get datasets by @jdkent in #29
- [REF] use id's only instead of IRIs by @jdkent in #26
- [STY] run black and check style with flake8 by @jdkent in #30
- [ENH] add login by @jdkent in #33
- [ENH] Add cloning functionality by @jdkent in #36
- [FIX] neurovault ingestion by @jdkent in #39
- [ENH] Add Condition POST by @jdkent in #40
- [FIX] minor fixes by @jdkent in #57
- [FIX] reference original parent when cloning by @jdkent in #58
- [FIX] conform test cases to openapi standard by @jdkent in #61
- [REF] use Auth0 for authentication by @jdkent in #67
- [ENH] pagination by @jdkent in #72
- [FIX] urls in example_config by @jdkent in #78
- [FIX] cloning studies with images by @jdkent in #80
- [REF] add query parameters and filters to display only original studies by @jdkent in #82
- [ENH] New neurosynth format by @jdkent in #86
- [REF] merge the frontend with the backend by @nicoalee in #88
- [FIX] Do no include id in PUT requests by @jdkent in #90
- [REF] database changes by @jdkent in #93
- [ENH] Ingestion by @jdkent in #95
- [TST] add tests by @nicoalee in #97
- [FIX] public/private distinction by @jdkent in #96
- [MAINT] update spec by @jdkent in #103
- [MAINT] upgrade react materials to MUI V5 by @nicoalee in #105
- [ENH] add pagination by @nicoalee in #106
- [ENH] run frontend by @jdkent in #108
- [ENH] basic search filtering by @nicoalee in #109
- [ENH] edit enhancements by @nicoalee in #114
- [MNT] update staging by @jdkent in #115
- [FIX] add try_file in nginx by @jdkent in #118
- [TST] add frontend tests by @jdkent in #116
- [MAINT] updated gitignore with postgres py migration files and added e… by @nicoalee in #120
- [DOC] added build steps for dev and staging and updated readme by @nicoalee in #123
- [FIX] code review improvements by @nicoalee in #125
- [ENH] datasets & annotations by @jdkent in #126
- [REF] docker compose init procedure by @jdkent in #135
- [FIX] images add date by @jdkent in #137
- [REF] restructure code by @jdkent in #139
- [ENH] add analyses to study view by @nicoalee in #143
- [ENH] cloning a study will redirect to that study, log out bug fixed by @nicoalee in #150
- [FIX] map port 80 again by @jdkent in #153
- [ENH] study analyses editing by @nicoalee in #156
- [ENH] add delete operation to all endpoints by @jdkent in #165
- [ENH] implement datasets by @nicoalee in #174
- [FIX] add health command for postgres by @jdkent in #177
- [MAINT] update spec by @jdkent in #179
- [ENH] add export option to annotations by @jdkent in #181
- [MAINT] annotations/tests by @jdkent in #188
- [MAINT] change openapi branch to main by @jdkent in #189
- [MAINT] installation by @jdkent in #190
- [ENH] study year by @jdkent in #192
- [FIX] userview by @jdkent in #199
- [MAINT] add ipython to command flask shell by @jdkent in #200
- [FIX] public private by @jdkent in #201
- [ENH] Coordinate/Image search by @jdkent in #202
- [FIX] update annotations when adding study to dataset by @jdkent in #208
- [ENH] annotation key by @jdkent in #212
- [FEAT] Add Annotations Page by @jdkent in #193
- [ENH] add neurosynth2 by @jdkent in #218
- [FIX] maint by @jdkent in #222
- [FIX] spec conformance by @jdkent in #223
- [FIX] initialize annotation with empty notes by @jdkent in #224
- [ENH] added appzi feedback widget by @nicoalee in #229
- [REF] moved neurosynth-frontend to synth folder by @nicoalee in #230
- [FIX] removed notes property from payload by @nicoalee in #233
- [ENH] 234 add owner column to annotations by @nicoalee in #240
- [TST] point test by @jdkent in #246
- [ENH] make nested queries faster by @jdkent in #239
- [ENH] convert datasets to studysets by @jdkent in #242
- [FIX] missing change from dataset to studyset by @jdkent in #250
- [MAINT] update openapi spec by @jdkent in #251
- [Fix] entity by @jdkent in #256
- [FIX] change kwargs to metadata in schemas by @jdkent in #257
- [ENH] study editor: add/remove/update conditions by @jdkent in #244
- [REF] 258 integrate sdk into frontend and cicd pipeline by @nicoalee in #260
- [ENH] update spec by @jdkent in #272
- [ENH] ingest neurostore data by @jdkent in #273
- [FIX] neurosynth endpoint by @jdkent in #274
- [TST] schemathesis robustness by @jdkent in #276
- [FIX] add missing fields specification schema by @jdkent in #278
- [DOC] include documentation for the neurosynth spec by @jdkent in #282
- [ENH] add frontend config by @jdkent in #249
- [REF] Split nimads by @jdkent in #287
- [ENH] 113 edit enhancements involving addremoveupdate points by @nicoalee in #290
- [FIX] Remove unused function by @jdkent in #289
- [REF] prepare compose.neurosynth.org by @jdkent in #294
- [ENH] 292 rework landing page and improve performance by @nicoalee in #297
- [FIX] fix: resolved bug with ids set to same id by @nicoalee in #302
- [FIX] nginx GZIP javascript content by @jdkent in #301
- [ENH] 292 rework landing page and improve performance by @nicoalee in #303
- [DOCS] Mkdoc/neurosynth by @jdkent in #304
- [ENH] 292 rework landing page and improve performance by @nicoalee in #306
- [FIX] add explicit indices and remove subquery load from analysis-conditions by @jdkent in #324
- [ENH] feat: added add button to studypage and refactored code to move study set add/update logic to studysetpopupmenu component by @nicoalee in #336
- [ENH] create tour by @jdkent in #334
- [ENH] feat: made logo clickable by @nicoalee in #337
- [FIX] 312 handle situation when authenticated user tries to update studies studysets meta analyses that are not theirs by @nicoalee in #338
- [FIX] feat: allowed viewport to shrink more without turning into hamburger menu, moved drawer to right side by @nicoalee in #339
- [ENH] 309 add ability to delete study from studyset by @nicoalee in #340
- [ENH] feat: added studies link for empty studysets by @nicoalee in #342
- [ENH] feat: not found page implemented by @nicoalee in #344
- [ENH] 310 create protected routes for edit pages by @nicoalee in #346
- [ENH] 329 add warning are you sure prompt if the user tries to clone a cloned study by @nicoalee in #347
- [REF] use nimads repo by @jdkent in #348
- [ENH] 231 search improvements by @nicoalee in #349
- [ENH] add release drafter action and template by @jdkent in #354
## New Contributors * @adelavega made their first contribution in #3 * @tyarkoni made their first contribution in #24 * @nicoalee made their first contribution in #88