CHANGELOG.md

v3.4.0 (2024-06-19)

• 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

v3.3.4 (2024-04-29)

• 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