Merge pull request #107 from lz100/devel

prepare for 1.18 bug fix and changes

Author: lz100

..Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 3ee419e1-3a27-4c0f-864f-2fa23a0603d1
 
 RestoreWorkspace: No
 SaveWorkspace: No

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: systemPipeShiny
 Title: systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
-Version: 1.17.0
-Date: 2023-10-16
+Version: 1.17.1
+Date: 2025-04-10
 Authors@R: c(
     person(given = "Le", family = "Zhang", role = c("aut", "cre"), email = "le.zhang001@email.ucr.edu"),
     person(given = "Daniela", family = "Cassol", role = c("aut"), email = "danicassol@gmail.com"),
@@ -53,8 +53,8 @@ Suggests:
     BiocStyle,
     knitr, 
     rmarkdown,
-    systemPipeR (>= 2.2.0),
-    systemPipeRdata (>= 2.0.0),
+    systemPipeR (>= 2.12.0),
+    systemPipeRdata (>= 2.10.0),
     rhandsontable,
     zip,
     callr,
@@ -80,6 +80,6 @@ Encoding: UTF-8
 LazyData: true
 BugReports: https://github.com/systemPipeR/systemPipeShiny/issues
 URL: https://systempipe.org/sps, https://github.com/systemPipeR/systemPipeShiny
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3

NEWS.md

@@ -1,3 +1,20 @@
+# systemPipeShiny 1.18.0
+## Major Change
+- Update to systemPipeR 2.12 and systemPipeRdata 2.10
+- Add support for Single Cell RNAseq, BLAST, and Cheminformatics workflows
+  which are new in systemPipeR. 
+
+## Minor Change
+- use `esquisse_container` instead of `esquisseContainer` due to the new version of {esquisse}.
+
+## Bug Fix
+- Fix shiny 1.10 update that caused some buttons not working.
+- Fix welcome page logo animation not working, now remove the animation.
+- Fix checkModulePkgs_internal had wrong logic when all packages are installed.
+  Now return the correct value.
+
+
+
 # systemPipeShiny 1.9.04
 
 ## Major Change

R/spsCore.R

@@ -371,10 +371,7 @@ spsOptDefaults <- function(app_path = getwd()){
 #' @rdname spsOptDefaults
 #' @param show_legend bool, show the color legend?
 #' @importFrom crayon green blue make_style chr
-#'
-#' @return
 #' @export
-#'
 spsOptions <- function(app_path = getwd(), show_legend = TRUE){
     if(!file.exists(glue("{app_path}/config/sps_options.yaml"))) {
         spserror(glue("{app_path}/config/sps_options.yaml does not exist"))
@@ -590,16 +587,18 @@ checkModulePkgs_internal <- function(module_name, pkgs, mol_title){
                 BiocManager::install(c("{missing_str}"))\n
                 '
             ))
+            return(glue(
+                '
+                ```r
+                if (!requireNamespace("BiocManager", quietly=TRUE))
+                    install.packages("BiocManager")
+                BiocManager::install(c("{missing_str}"))
+                ```
+                '
+            ))
+        } else {
+            return(character(0))
         }
-        glue(
-        '
-        ```r
-        if (!requireNamespace("BiocManager", quietly=TRUE))
-            install.packages("BiocManager")
-        BiocManager::install(c("{missing_str}"))
-        ```
-        '
-        )
     } else NULL
 }
 

R/spsCoreServer.R

@@ -148,7 +148,6 @@ spsServer <- function(tabs, server_expr, mod_missings, sps_env, guide, mainUI) {
 #'
 #' @param session shiny session
 #' @noRd
-#' @return
 #' @importFrom shinyWidgets sendSweetAlert
 spsWarnings <- function(session, shared){
     sps_warnings <- list()

R/tab_vs_esq.R

@@ -116,7 +116,7 @@ vs_esqUI <- function(id) {
                         esquisse::esquisse_ui(
                             id = ns("esq"),
                             header = FALSE,
-                            container = esquisse::esquisseContainer(height = "700px")
+                            container = esquisse::esquisse_container(height = "700px")
                         )
                     ),
                     div(

R/tab_wf_setup.R

@@ -75,10 +75,18 @@ wf_setupUI <- function(id){
                     selectizeInput(
                         inputId = ns("choose_wf"),
                         label = "Choose a workflow template",
-                        choices = c(Example="eg", RNAseq="rnaseq", Varseq="varseq",
-                                    Riboseq="riboseq", Chipseq="chipseq", `Empty workflow (start from scratch)`="new",
-                                    `Upload custom workflows`="exist"
-                                    ),
+                        choices = c(
+                            Example="eg",
+                            RNAseq="rnaseq",
+                            Varseq="varseq",
+                            Riboseq="riboseq",
+                            Chipseq="chipseq",
+                            `Single Cell RNAseq`="SPscrna",
+                            BLAST="SPblast",
+                            `Cheminformatics Drug Similarity`="SPcheminfo",
+                            `Empty workflow (start from scratch)`="new",
+                            `Upload custom workflows`="exist"
+                        ),
                         options = list(style = "btn-primary")
                     )
                 ),
@@ -153,8 +161,8 @@ wf_setupUI <- function(id){
                         If the required command
                         line tools are not installed, the workflow will fail. Please
                         make sure you install them and the path is exported."),
-                HTML("<li>Current version of SPS (>= 1.6) is compatible with the latest
-                     SPR (>= 2.2.0) and SPRdata (>=1.24.0). Make sure you install the
+                HTML("<li>Current version of SPS (>= 1.17) is compatible with the latest
+                     SPR (>= 2.12.0) and SPRdata (>=2.10.0). Make sure you install the
                      correct versions.
                      </li>")
             ),
@@ -350,6 +358,7 @@ wf_setupServer <- function(id, shared){
                 "new" = normalizePath(file.path(final_env_path, "targets.txt")),
                 "exist" = wf_targets_path(),
                 "eg" = normalizePath(file.path(final_env_path, "targets.txt")),
+                "SPblast" = normalizePath(file.path(final_env_path, "targets_blast.txt")),
                 normalizePath(file.path(final_env_path, "targetsPE.txt"))
             ), blocking_level = "error")
             updateProgressBar(session, "gen_wf_pg", 4, 6, title = "update project info - workflow file")
@@ -359,6 +368,9 @@ wf_setupServer <- function(id, shared){
                 "varseq" = normalizePath(file.path(final_env_path, "systemPipeVARseq.Rmd")),
                 "riboseq" = normalizePath(file.path(final_env_path, "systemPipeRIBOseq.Rmd")),
                 "chipseq" = normalizePath(file.path(final_env_path, "systemPipeChIPseq.Rmd")),
+                "SPscrna" = normalizePath(file.path(final_env_path, "SPscrna.Rmd")),
+                "SPblast" = normalizePath(file.path(final_env_path, "SPblast.Rmd")),
+                "SPcheminfo" = normalizePath(file.path(final_env_path, "SPcheminfo.Rmd")),
                 "exist" = wf_wf_path(),
                 "eg" = normalizePath(file.path(final_env_path, "systemPipeExample.Rmd")),
                 "new" = normalizePath(file.path(final_env_path, "new.Rmd"))
@@ -406,6 +418,19 @@ wf_setupServer <- function(id, shared){
         observeEvent(input$confirm_next, {
             req(input$confirm_next)
             shinyjs::runjs("$('#wf-wf_panel-1-heading > h4').trigger('click');")
+            if (input$choose_wf %in% c("SPscrna", "SPcheminfo")) {
+                shinyWidgets::sendSweetAlert(
+                    session = session,
+                    type = "info",
+                    title = "No need of targets",
+                    html = TRUE,
+                    text = h4(
+                        tags$b("Single Cell and Cheminformatics workflows"),
+                        " do not require a targets file. You can directly click
+                        'Add to task' to skip the targets preparation step."
+                    )
+                )
+            }
         })
     }
     moduleServer(id, module)

R/tab_wf_wf.R

@@ -93,9 +93,9 @@ wf_wfUI <- function(id){
                         br(), br(), br(), spsHr(other_color = "rgb(2, 117, 216, 0.5)"),
                         div(
                             class = 'step-box-control',
-                            tags$button(class="fa fa-undo-alt shiny-bound-input action-button", id=ns("step_undo"), style="color: #3c8dbc") %>%
+                            actionButton(ns("step_undo"), "", icon = icon("undo-alt"), style="color: #3c8dbc", class = "") %>%
                                 bsTip("Undo", placement = "bottom"),
-                            tags$button(class="fa fa-redo-alt shiny-bound-input action-button", id=ns("step_redo"), style="color: #3c8dbc") %>%
+                            actionButton(ns("step_redo"), "", icon = icon("redo-alt"), style="color: #3c8dbc") %>%
                                 bsTip("Redo", placement = "bottom"),
                             div(
                                 class = "wf-history-panel",
@@ -105,11 +105,11 @@ wf_wfUI <- function(id){
                                     tags$tr(tags$td("Next history:"), tags$td("3"))
                                 )
                             ),
-                            tags$i(class="fa fa-plus shiny-bound-input action-button", id=ns("step_new"), style="color: #5cb85c;") %>%
+                            actionButton(ns("step_new"), "", icon = icon("plus"), style="color: #5cb85c;") %>%
                                 bsTip("Add a new step", placement = "bottom", status = "success"),
-                            div(id=ns("step_trash"), class="step-trash", tags$span(), tags$i()) %>%
+                            div(id = ns("step_trash"), class="step-trash", tags$span(), tags$i()) %>%
                                 bsTip("Drag here to delete a step", placement = "bottom", status = "danger"),
-                            tags$button(class="fa fa-save shiny-bound-input action-button", id=ns("totask"))%>%
+                            actionButton(ns("totask"), "", icon = icon("save"), style="color: black;")%>%
                                 bsPop("Add to SPS task", placement = "bottom",
                                       "Send the workflow to SPS workflow module manager so you can run it.")
                         )

inst/app/www/css/sps_welcome.css

@@ -13,16 +13,6 @@
     transform: translate(-15px, -50px);
 }
 
-#sps_header_logo > g{
-  position: relative;
-  transition: filter 500ms;
-}
-
-#sps_header_logo > g:hover {
-  transform: scale(1.3);
-  filter: blur(1px);
-}
-
 .welcome-header .card {
   height: calc(20vw - 50px);
   width: calc(20vw - 50px);

inst/app/www/css/sps_wf_wf.css

@@ -109,11 +109,20 @@
 
 .step-box-control > button {
     width: 4rem;
-    margin: -5px 0;
+    margin: -20px 0;
     font-size: 4rem;
     top: 0;
     border: none;
-    background-color: transparent;
+    background-color: transparent !important;
+    &:active {
+        box-shadow: unset;
+        -webkit-box-shadow: unset;
+        -moz-box-shadow: unset;
+        -o-box-shadow: unset;
+    }
+    &:focus-visible, &:focus {
+        outline: none !important;
+    }
 }
 
 .step-box-control > button[disabled] {

inst/app/www/js/sps_welcome.js

@@ -7,13 +7,7 @@ $(function(){
     });
     var svg = $("#welcome-svg > svg");
     svg.removeAttr("height").removeAttr("width");
-    //$("#sps_header_logo").fadeIn(2000);
-    //hoverLogo(document.querySelector("#sps_header_logo"));
-    VanillaTilt.init(document.querySelector("#sps_header_logo > g"), {
-      "full-page-listening": true,
-      glare: true,
-      max: 45
-    });
+    $("#sps_header_logo").fadeIn(2000);
   })();