- feat: use database for credentials + expiry (prototype) view
- feat: utils for database view
- feat: read options from database view
- start new design view
- update view
- solve merge conflict view
- update view
- WIP view
- merge master view
- fix: cookie + database fixes view
- UI layout changes view
- update working code view
- add multiple clustering positions view
- add pacmap dependency view
- update. sync. view
- code update view
- refactor module view
- refactor module view
- resolve merge conflict view
- sync view
- work in progress view
- progress update view
- add new file view
- various updates view
- add missing value ratio plot view
- update view
- cleanup view
- clean virtualenv folder view
- work in progress view
- change histogram view
- resolve merge conflicts view
- remove commented out view
- fix: umap different view
- fix: umap mismatch problem view
- test wizard in upload view
- feat: add modal wizard to the upload module view
- Dbg: add bslib components to test container overflow view
- upload_panel now sits in wizard container view
- temporary height calculation to fit tabs into wizard container view
- initial wizard styles on omicsplayground view
- improve button spacing view
- improve color style of navbar steps when steps succeed view
- feat: upload new data button now works view
- feat: upload button now has bigomics styles view
- improve styles of margins view
- improve button border color style view
- feat: disable upload tab and handle upload UI directly via modal calls view
- disable hardcoded height and width view
- fix typo view
- remove y parameter view
- feat: upload module can now be triggered via load dataset module button view
- clean up; style upload button in load module view
- pass new_upload to WelcomeBoard; refactor WelcomeBoard into inputs/ui/server standard view
- feat: modal upload can now be triggered by welcome board view
- feat: upload module is not triggered at startup view
- initial attempt to embed data preview tables in wizard view
- samples and contrasts table preview added to wizard view
- separate wizarrd steps for samples, counts and contrasts as a ui function view
- feat: Add legend and checklist to upload_table_preview_counts_ui via server rendering view
- replace fluidRow and column by flex components (via bslib) view
- add checklist to upload_table_preview_samples ui and server view
- add checklist to upload_table_preview_contrasts ui and server view
- attempt to render table server-side view
- Move tablemodule UI to server side view
- feat: dynamically render UI based on input of counts view
- remvove unused component view
- minor fix view
- remove unused component view
- feat: counts are now passing directly from counts_ui to checked_counts view
- feat: wizard can now be locked based on state of input file view
- clean up of unused observers; remove sample check at counts level view
- better organize upload_module_preview, placing functions at the end view
- add buttons for removing input and downloading example and move button UI to server side view
- dynamic UI of counts switch to listening to upload instead of widget input, so we can have better control with counts check; add style view
- feat: restyle buttons and load example counts when clicking load_example button view
- Refactor fileInput2 to fileInputArea view
- dynamically render remove_counts button view
- Refactor upload_table_preview_samples_ui and upload_table_preview_samples_server functions to accomodate new upload layout view
- Refactor upload_table_preview_samples_ui and upload_table_preview_sample_server functions to accomodate new upload layout view
- temporary style fix for width of fileInputArea and control buttons view
- attempt to pass wizard finished event to R: works in demo but not in OPG view
- add link targets for documentation view
- feat: logic for counts when other input files are uploaded view
- clean up unused components view
- disable navigation bar to switch steps; change text of final wizard button (submit) view
- feat: handle deletion of samples when contrasts are already uploaded view
- remove obsolete tabsetpanel tab control view
- rename step title for comparisons view
- remove unused logic view
- remove unused compute button in pgxcompute view
- remove browser; add todo view
- feat: contrast builder is embedded into contrasts_ui view
- feat: dynamically render contrast builder view
- contrast maker correctly responses to button input view
- remove bslib modal (conflict with bsutils) view
- fix typo view
- remove - from namespace view
- feat: wizard now sends message to compute and active step view
- feat: upload module now responds to wizard commands view
- fix issue with removing files (remove input button) view
- add print for dbg view
- temporarily skip informing user via modals that additional upstream files will be deleted view
- bring organism to computepgx view
- add basic logic to validate compute tab inputs and prevent missing inputs being accepted for computation view
- attempt to lock computer step view
- remove redundant styles view
- feat: rename compute tab and add an additional tab for review, to avoid the locking issues view
- move inputs to parent component in order to control the wizard (un)locking view
- fix reactivity in upload module, in order to pass computepgx results to main server view
- fix reactivity and add boilerplate to control (un)locking of Dataset description view
- attempt: control wizard contrast step via commands in upload-server (event listener not working) view
- minor fix in contrast logic (req assignment) view
- feat: contrasts step now (un)locks depending on modified_ct view
- fix comparisons locking when user deleted manually all comparisons in comparison builder view
- wizard partially locks based on inputs from dataset description fields view
- add upload_name to dataset description unlocking requirements view
- Refactor input variable names in upload_module_computepgx.R view
- add upload_name to observer in order to lock/unlock wizard view
- clean up view
- fix issue with req inhibiting the locking of wizard when user removes input variables (name, description...); minor fix when state of variable is "" and not null view
- attempt to refactor options for better ui view
- refactor compute/options to layout grid and cards to avoid conflicts view
- fix issue with fillCol layout not assigning correct display sizes to compute/options view
- bs alert now does not affect compute/options view
- bypass upload_module_outliers (crashing) in order to test computation; clean up view
- minor style fix in contrast command buttons (remove div of remove_contrasts) view
- fix buttons alignining all to the right view
- comparisons buttons now separate left (cancel) and right (other buttons) view
- disable bsalert until we find a solution for the height adjustment (server side issue) view
- minor fix view
- feat: block new uploads if we already have a processx computation running view
- remove example data multi-species view
- fix for passing reactVals to params object: some variables were not treated as reactVal view
- minor fix in variable assignment in params.RData view
- fix merging conflict view
- fix merge issue where a missing component was left behind view
- bring process_counter to parent component so it can be used to block new wizard upload when a computation is active view
- improve styling of wizard buttons to match load board styles view
- improve style of run comparison builder view
- move run_contrasts to the left, in order to make the load and document button standard across all steps view
- test a different modal type view
- attempt to add shinyvalidate to computepgx text input view
- feat: shinyvalidate now works! view
- clean up view
- attempt to bring back countstats to review step in wizard view
- feat: countsstats is displays correctly and checkTables deprecated input removed view
- Add upload_plot_phenostats module to board.upload, remove deprecated checkTables view
- add contraststats to review in wizard step; attempt to fix display units issue view
- stat plots: disable download and maximize, as it has modal conflicts view
- add basic text output for user review before computing view
- split the plots from text input (paralel column via fluidRow) view
- convert text output to html view
- feat: manage to render the plots in correct size (with a lot of flickering) view
- display text inputs as columns, display on top of plots view
- add vertical space between input recep and plots view
- install wizardR view
- feat: initial prototype of wizard reset view
- install bsutils with fix view
- feat: wizard reset on new upload view
- remove reset button view
- reset inputs upon wizard reset (new upload) view
- fix issue with unlocking wizard when inputs are selected view
- temporarily remove shinyvalidate (conflicts with wizard) view
- update base to v3; change repo of wizardR for faster testing orutine view
- force install latest bsutils to add fix for wizard view
- force wizard install view
- remove shinyvalidate in auth to test wizard view
- remove shinyalert pop up in home to test wizard view
- temporarily disable shinyalert at auth view
- bring back bsutils modal as there is no conflict with bootstrap 5 view
- feat: wizard works without conflicts with shinyvalidate and shinyalert (preventing re-initialization) view
- reduce height slightly view
- remove review panel (revisit needed) view
- restore shinyalert modals to alert user that counts.samples, contrasts will be deleted if a previous file is deleted view
- fix minor issue that removed input files when users opted not to view
- bring comparison builder reactive to parent component for better control and reset; clean up view
- remove unused pcaplot; add samples as template for selectInput (dbg) view
- feat: pass wizard controls to fire updateSelectInput exactly when contrast builder is triggered view
- remove browser view
- remove print statement view
- remove merge issue with startup modal (now defined server-side) view
- create a single menu item for datasets (loading datasets page) view
- removed unused startupmodal.scss view
- #TODO identify why newuploadbutton if being triggered when dataset computation is finished view
- minor fix for test deployment: keep old left sidebar structure to avoid conflicts view
- feat: validate dataset name is not at upload_server level for better wizard control view
- remove unnecessary control (wizard server control already checks for description input) view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- minor comment fix view
- revert shinyvalidate as there is no longer conflicts with wizard view
- bring back custom genesets incompatibility alert (no more conflicts with wizard) view
- move wizard download to stable repo (bigomics) view
- feat: end of computation does not trigger new wizard upload view
- attempt to edit the left sidebar menu (failed) view
- fix: unload sidebar correctly view
- fix issue with samples/contrast tables not displaying correct values in columns view
- remove obsolete code view
- add filename check for counts, so count has to be present in filename view
- minor fix; log2 detection needs review (move to pgx checks or to parent server?) view
- fix issue where counts with errors were not shown in counts preview view
- fix: clean sidebar when loading welcome board view
- clean: not necessary double cleaning view
- remove unnecessary insanity check (handled at check level) view
- refactor contrast builder so we store the conditions in a reactive value view
- minor improvements view
- feat: reset conditions when user add contrast view
- feat: prevent updateTextInput newname observer to change upon reset of builder view
- fix Error in if: argument is of length zero: input$contrast had invalid condition check view
- remove dbg statements; clean up view
- reset comparison name when adding contrast view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- add checks for samples/counts/contrasts in filename; return error if grep if false view
- feat: shinyvalidate does not need to to be triggered at page trigger view
- feat: improve ux by warning user that a locked button was clicked view
- snapshot review view
- move wizard reset to observer that trigger wizard; add integration with re-analize dataset view
- clean up view
- clean up and remove reset_upload, a deprecated reactive view
- minor fix in logic to trigger new upload when a dataset is re-computed view
- fix issue with display height and width: add fill container attributes view
- fix additional tabs display h/w view
- bring back bottom margin between tables and buttons; clean up view
- clean up and fix issue with v/h alignment of fileInputArea form-group view
- fix minor issue with fill container in contrasts step view
- rename contrasts to comparisons; rename contrast builder button view
- add switch screen to contrasts, giving user option to build online or upload contrasts view
- align buttons; add logic for page switch and debug statements view
- fix minor issue; remove dbg statements view
- add message to user on how to proceed with online or upload contrast options view
- improve styles view
- reset dataset name and description to empty values when wizard resets view
- include steps in upload navbar titles view
- rename "Load" to "Analyze" datasets in several modules view
- Fix missing load dataset naming view
- fix issue where clicking "analyze dataset" without any dataset selected crashed the platform view
- remove unused code view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- fix merge conflict view
- change labels of comparison redirect button view
- adjust style of comparison redirect buttons view
- add step number to dataset description; update controls for the step view
- fix issue with comparison builder not showing sample phenotypes view
- avoid pgx overwrite if dataset name matches a previous pgx file (raise error and invalidate new dataset name) view
- add icons that match button description in contrast navigation view
- improve UI; match color/style of contrast builder button across entire upload view
- improve style of comparison upload widget text view
- add buttons to comparison builder to match other steps view
- only show buttons if comparison builder is selected view
- move auto detect ui button to wizard step level view
- connect logic of wizard step addcontrast button to makecontrast view
- minor fix: replace contrast with comparison view
- fix uppercase in Check documentation; rename auto detect comparison button view
- switch navbar from progress to dots; increase wizard size slightly view
- rename buttons to reset computation and pop up to warn user only one computation is allowed view
- fix issue with comparison in the filename triggering invalid input view
- feat: centralize all warnings to give real-time feedback to use (in alerts, embed in wizard...) view
- feat: add shinyalert with error message only view
- fix crash when summary checks does not have any error view
- minor fix and refactoring for when there are no error in summary view
- fix typo: bring back alert message for error summary; remove browser view
- minor fix for cases with mixed warnings/errors view
- add alert when summary is not length 0 but we have only warnings as checks view
- update view
- change layout/design in new upload view
- add file view
- rename checked_samples; return both crosschecked counts and samples view
- refactor checked_contrasts view
- refactor check_samples calls view
- fix issue with phenotypes not appearing in comparison builder view
- clean up view
- layout changes: buttons & add bs_alert view
- layout changes: buttons & add bs_alert view
- layout changes: buttons & add bs_alert view
- layout changes: buttons & add bs_alert view
- remove margin to allow exit button to sit on the right side view
- cleanup view
- attempt to replace wizard tracking from title to assigned id view
- fix missing refactoring in makecontrast view
- improvement in alert message when step is incomplete view
- add dash view
- fix flex item issue in bs_alert view
- edit dash width view
- add fill item to bs_alert view
- fix alignment issue in samples/contrasts view
- attempt to improve bs_alert layout view
- apply layout styles to samples/comparisons view
- minor fix to samples layout style view
- attempt to refactor computation description fields view
- improve styles of description step view
- attempt to adjust options cards view
- fix issue with options cards displaying next to the description input fields view
- attempt to set description layout to two columns view
- adjust order of columns view
- improve style of computation options view
- align computation options text in center view
- add margin; reduce height of computation options view
- add margin bottom to description title view
- improve spacing between computation options; reorder description inputs view
- increase gap between description inputs view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- cleanup: no_sharing duplicated code view
- reduce gap between description fields view
- fix sharing_alert view
- add rv to store gx/gset methods in parent env view
- minor fix view
- move alert to upload_server view
- remove unnecessary comma view
- trigger observer when rv is null view
- refactor; clean up view
- fix typo view
- minor improvement in message view
- attempt to display comparison builder first view
- minor fix in comparison builder: restart wizard with builder active view
- keep expression correction; move log detection to check counts view
- warn user that expression was converted back to intensities view
- attempt to add log transformation warning logic view
- update shinyalert and fix minor issues view
- minor improvements in message view
- clean up view
- attempt to rewrite ref$df from counts_log_correction namespace view
- attempt to fix reactivity issue caused by shinyalert view
- attempt to refactor shinyalert warning view
- demote shinyalert for now view
- comment req view
- minor fix view
- remove dbg statement view
- add (temporary) message to inform user log reverse correction has been applied view
- add button to redirect to batch correction view
- minor fix in button layout view
- add basic template for batch correction in counts step view
- minor fix view
- fix conflict between remove_counts and batch correction buttons view
- move batch correction to comparison step view
- move logic of BC to comparison view
- move show BC button and observer to comparison step; initial prototype working view
- fix issue with double UI view
- add margin bottom to avoid BC getting too close with buttons view
- prevent BC from being called without any contrast view
- adjust message; remove dbg statements view
- fix issue with BC button not triggering when data fed via upload and not builder view
- feat: add default step layout to batch correction module view
- tag v3.4.4 && update changelog view
- add option to leave BC; reset BC state when wizard resets; improve leave BC button view
- edit: rename usersettings to appsettings view
- fix issue with compute button not working; fix crash at pgx name crash view
- add batch correction module to wizard upload view
- add overflow that respects limits of button div view
- disable batch correction panel view
- update shinyalert messages for each input view
- simplify code view
- minor fix to message; minor typo fixed view
- review: snapshots reviewed view
- fix: move specific packages after playbase installation view
- temp fix: to be removed after deploying new base image view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- report branch at initialization view
- snapshot review view
- feat: option to color or not (up/down reg) volcano plots view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- feat: echo playbase branch view
- fix: show info text when no geneset is selected view
- test: to be removed view
- test: pass build arg to docker build view
- test: pass correct argument view
- test: use a non GITHUB_* variable view
- test: inject HEAD_REF view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- test: reviewed snapshots view
- fix: remove test -- workflow is now fixed view
- test: update duration view
- revert: test duration view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snapshot review view
- fix: use pgx geneset genes view
- test: increase duration view
- increase idle threshold (so it does not timeout during idle) view
- run gha in test docker view
- install plsRcox with Matrix == 1.6.0 view
- add rat orgdb view
- ad missing packages to main docker view
- install plsRcox before playbase view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- review snapshots view
- build docker from opg:latest view
- minor fix in passing arguments to params object view
- fix incorrect declaration of steps view
- install orthogene and missing dependencies view
- test: add subtabs to the snapshots view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- test: add more time for connectivity tab view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- test: change input for enrichment tab view
- test: add extra wait for enrichment view
- test: move fdr change view
- minor fix for cases when samples_counts crosscheck fails (declare vairables) view
- test: more wait time view
- check if files are csv (in case of drag and drop) view
- feat: aux function to check if user in DB view
- feat: if user in DB use it, otherwise use user folder OPTIONS view
- fix: remove browser view
- fix: remove unused values view
- test: reviewed timings view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- review: snapshots view
- test: remove connectivity board view
- test: increase timer view
- test: use timeout argument + bring back connectivity view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- test: add 3 sec duration view
- test: more time for connectivity view
- fix: remove unused wait view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- fix: extra time + connectivity more duration view
- feat: extra duration for clustering board view
- snapshot review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- test: upper threshold view
- fix: threshold view
- test: bigger enrichment time view
- unfinished merge view
- add ssh to github actions view
- test: open ssh view
- test: remove ssh view
- snapshot review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- review: snapshots + threshold back to 10 view
- attempt to fix seurat install view
- do not upgrade dependencies when installing seurat view
- Revert "do not upgrade dependencies when installing seurat" view
- annothub installs view
- attempt to fix orthogene install view
- install Matrix.utils (required for orthogene) view
- minor fix for docker opg view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- split module_preview files view
- feat: colo up/down MA plot view
- fix: add plot options view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snapshot review view
- fix not responsive close button view
- simplify installation view
- fix: robust file extension detection view
- install rgeos, print steps to stdout view
- fix dependency issue view
- add base update target in Makefile (do not build entire base) view
- add required installs for base.update view
- attempt to fix multiple install issues view
- fix for Seurat: namespace ‘Matrix’ 1.6-0 is being loaded, but >= 1.6.3 is required view
- clean up docker file view
- fix Matrix version view
- attempt to fix [processx.1:stderr] Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : [processx.1:stderr] function 'as_cholmod_sparse' not provided by package 'Matrix' view
- feat: act matrix with plotly view
- remove obsolete updateSelectInput in upload server view
- remove unnecessary filter for ensembl db in biomart view
- ifelse on mart column view
- add left=NULL parameter view
- feat: disable legen on small plot view
- fix: detect colored columns after modifying
df
view - Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snapshot review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snap review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snap review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snap review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snap review view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snap review view
- fix: change drugconnect color scale + order view
- feat: drugconnect actmatrix change color gradient view
- feat: pathway actmatrix change color ramp view
- feat: pathway invert y axis view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- snap review view
- fix: do not check user on credentials on this auth metdho view
- fix: use db when logged with cookie view
- clean view
- fix: if no labels matched return plain wikipath view
- v3.3.5 view
- update version view
- fix: use mail variable, not reactive view
- fix: use dir variable, not reactive view
- fix: use req with a logic condition view
- edit VERSION view
- fix: plot tissue csv view
- fix: plot barplot csv view
- fix: plot decisiontree csv view
- fix: plot boxplot csv view
- fix: plot heatmap csv view
- fix: plot correlation csv view
- fix: plot volcanomethods csv view
- adding an invite button in menu bar view
- working view
- add file view
- Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
- v3.3.0: out of beta view
- set target blank to open a new tab view
- swag page does not exist, redirect to opg standard page view
- update view
- fix: Partial correlation network csv download view
- fix: Mechanism of action csv download view
- fix: Activation matrix csv download view
- fix: Similarity scores csv download view
- fix: upload files check view
- fix: singlecell broken csv download (removed them) view
- fix: Enrichment analysis csv download view
- fix: Frequency in top gene sets csv download view
- replace chirp button with Reddit; remove shinyChatR dependency view
- fix: Differential expression analysis csv download view
- fix: Dataset abundance of major gene types csv download view
- fix: Abundance of major gene types per group csv download view
- refactor code as InviteFriend shiny module view
- fix: Contrast table csv download view
- fix: Correlation scatter plots csv download view
- add email checks view
- add number of succesfull registered view
- add number of succesfull registered view
- cleanup view
- app test review view
- v3.3.1: adding invite/referral button view
- fix: abort invite if no mail server view
- fix: abort invite if no mail server view
- change already subscribed message view
- fix modal-title right margin view
- fix modal-title right margin view
- update names in credits view
- update names in credits view
- update names in credits view
- fix: Expression of top differentially expressed genes csv download view
- fix: Gene in comparisson csv download view
- rename file to match function names view
- clustersamples pca now has legends - but subplot needs to be deactivated view
- fix axis title names for single plots (subplot still erases titles) view
- add invite message view
- fix: QC tab not appearing view
- v3.3.2: fix Sample QC tab view
- redesign title of highlight popup view
- change capitalization view
- fix: use custom genelist when selected view
- install sf package on requirements and in docker opg build view
- edit messages view
- edit messages view
- fix: unresponsive close button in modal view
- remove dbg message view
- remove dbg message view
- remove dbg message view
- fix: sending invite view
- change: simplify invite message view
- change: simplify invite message view
- add personal email check for invite view
- add personal email check for invite view
- new: add detection of mobile and show warning view
- version 3.3.3 view
- add shinybrowser to dependencies view
- refactor invite click view
- remove gadget code view
- new version: v3.3.4 view
- version: v3.3.4.9001 view
- revert to v3.3.4 view
- fix: reactivity feature map plots view
- add indentation view
- edit view
- fix: show all contrasts view
- testing featuremap server view
- testing featuremap server view
- fix: react on contrasts missing in pgx view
- v4.4.3 view
- pin stable on v3.3.4. now on v3.3.4.9001 view
- edit default OPTIONS view
- change: add numpgx and maxpgx in error message view
- update view
- edit storage fullmessage view