improve instant UI

ChangeLog

@@ -1,6 +1,8 @@
 2018-08-16 Li Jianfeng <[email protected]>
 
 		* add pubmed search tool
+		* add geoquery instant plugin
+		* improve instant spack and code plugins
 
 2018-08-15 Li Jianfeng <[email protected]>
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioInstaller
 Title: Integrator of Bioinformatics Resources
-Version: 0.3.5.4000
+Version: 0.3.5.5000
 Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Maintainer: Jianfeng Li <[email protected]>
 Description:

inst/extdata/config/shiny/shiny.bioinstaller.parameters.toml

@@ -12,7 +12,7 @@ rcmd_last = """
 
 """
 progressbar_message = "Running BioInstaller functions."
-render_id = "bioinstaller_bioinstaller_input_box"
+render_id = "bioinstaller_input_box"
 
 #!!!!! input_ui_order required related section
 input_ui_order = ["single_input", "start_analysis"]
@@ -37,7 +37,7 @@ label = "Run"
 section_type = "output"
 rcmd_last = "BioInstaller::install.bioinfo(show.all.names = TRUE)[1:10]"
 render_type = "shiny::renderPrint"
-render_id = "bioinstaller_bioinstaller_output_text"
+render_id = "bioinstaller_output_text"
 output_type = "shiny::verbatimTextOutput"
 progressbar_message = "BioInstaller bioinstaller_output_text"
 
@@ -77,6 +77,6 @@ if (object_type != "all") {
 obj <- cbind(obj, resources_db)
 """
 render_type = "DT::renderDataTable"
-render_id = "bioinstaller_bioinstaller_output_table"
+render_id = "bioinstaller_output_table"
 output_type = "DT::dataTableOutput"
 progressbar_message = "BioInstaller bioinstaller_output_table"

inst/extdata/config/shiny/shiny.conda.parameters.toml

@@ -1,30 +1,63 @@
 [conda.ui.sections]
-order = ["readfiles", "outputFields"]
+order = ["conda_input_box", "conda_output_box_text", "conda_output_box_table"]
 [conda.ui.sections.ui_basic]
-readfiles = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
-outputFields = "title = 'Output of conda', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+conda_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+conda_output_box_text = "title = 'Output of conda (Text)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+conda_output_box_table = "title = 'Output of conda (Table)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 
-[conda.paramters.readfiles]
+[conda.paramters.conda_input_box]
 # For reading annovarR shiny APP conda tool input files  
 section_type = "input"
 rcmd_last = """
 
 """
 progressbar_message = "Running conda functions."
-render_id = "conda_readfiles"
+render_id = "conda_input_box"
 
 #!!!!! input_ui_order required related section
-input_ui_order = ["start_analysis"]
+input_ui_order = ["single_input", "start_analysis"]
 
-[conda.paramters.readfiles.input.start_analysis]
+[conda.paramters.conda_input_box.input.single_input]
+title = "Parameters:"
+title_control = "class = 'input-section-p'"
+varname = ["conda_sub_cmd", "conda_env_name", "conda_params"]
+input_id = ["input_conda_1", "input_conda_2", "input_conda_3"]
+type = ["shiny::selectInput", "shiny::selectInput", "shiny::textInput"]
+label = ["Conda subcommands", "Conda environment", "Conda parameters"]
+
+[conda.paramters.conda_input_box.input.single_input.choices]
+conda_sub_cmd = ["clean", "config", "create", "info", "install",
+                 "list", "package", "remove", "uninstall",
+                 "search", "update", "upgrade"]
+conda_env_name = "!!glue {BioInstaller::conda.env.list()[,1]}"
+[conda.paramters.conda_input_box.input.single_input.selected]
+conda_sub_cmd = "list"
+conda_env_name = "base"
+
+[conda.paramters.conda_input_box.input.start_analysis]
 input_id = "start_conda_analysis"
 type = "shiny::actionButton"
 label = "Run"
 
-[conda.paramters.outputFields]
+[conda.paramters.conda_output_box_text]
 section_type = "output"
-rcmd_last = "BioInstaller::conda.list()"
+rcmd_last = """
+conda_env_cmd <- sprintf("source activate %s;", conda_env_name)
+conda_params <- sprintf("%s %s", conda_sub_cmd, conda_params)
+cat(conda(conda_params, conda_env_cmd))
+"""
 render_type = "shiny::renderPrint"
 render_id = "conda_output"
 output_type = "shiny::verbatimTextOutput"
-progressbar_message = "conda ouput"
+progressbar_message = "conda ouput_box_text"
+
+[conda.paramters.conda_output_box_table]
+section_type = "output"
+rcmd_last = """
+if (conda_sub_cmd == 'list')
+conda.list(conda_env_name)
+"""
+render_type = "DT::renderDataTable"
+render_id = "conda_output_table"
+output_type = "DT::dataTableOutput"
+progressbar_message = "conda ouput_box_table"

inst/extdata/config/shiny/shiny.config.yaml

@@ -46,10 +46,11 @@ shiny_tools:
   pipeline: easy_project
   instant:
       - bioinstaller
-      - conda
       - spack
+      - conda
       - datasets2tools
       - pubmed 
+      - geoquery
       - maftools
 shiny_tools_params:
     require:
@@ -62,6 +63,7 @@ shiny_tools_params:
       pubmed:
           - rentrez
           - XML
+      geoquery: GEOquery
       maftools: maftools
 shiny_upload:
   upload_dir: ~/.BioInstaller/upload

inst/extdata/config/shiny/shiny.datasets2tools.parameters.toml

@@ -20,9 +20,11 @@ for (i in input_params) {
 json_dat <- getForm(url, .params=datasets2tools_params)
 json_dat <- jsonlite::fromJSON(json_dat)
 json_dat <- as.data.frame(json_dat)
-for(i in 1:ncol(json_dat)) {
-  if (typeof(json_dat[,i]) == "list") {
-    json_dat[,i] <- unlist(lapply(json_dat[,i], function(x) {paste0(x, collapse = ", ")}))
+if (length(json_dat) > 0) {
+  for(i in 1:ncol(json_dat)) {
+    if (typeof(json_dat[,i]) == "list") {
+      json_dat[,i] <- unlist(lapply(json_dat[,i], function(x) {paste0(x, collapse = ", ")}))
+    }
   }
 }
 """
@@ -42,7 +44,7 @@ input_id = ["input_datasets2tools_1", "input_datasets2tools_2",
 type = ["shiny::selectInput", "shiny::textInput", "shiny::textInput", "shiny::textInput", "shiny::textInput",
        "shiny::textInput", "shiny::textInput", "shiny::numericInput"]
 label = ["Query type", "Key Words", "Dataset Accession (e.g. GSE775)", "Tool name", "Disease name", 
-         "Canned nalysis Cccession", "Geneset", "Page size"]
+         "Canned nalysis Cccession", "Geneset", "Counts"]
 
 [datasets2tools.paramters.dataset2tools_input_box.input.single_input.choices]
 object_type = ["canned_analysis", "dataset", "tool"]
@@ -53,7 +55,7 @@ page_size = 100
 [datasets2tools.paramters.dataset2tools_input_box.input.start_analysis]
 input_id = "start_datasets2tools_analysis"
 type = "shiny::actionButton"
-label = "Submit"
+label = "Run"
 
 [datasets2tools.paramters.dataset2tools_out_box]
 section_type = "output"

inst/extdata/config/shiny/shiny.geoquery.parameters.toml

@@ -0,0 +1,59 @@
+[geoquery.ui.sections]
+order = ["geoquery_input_box", "geoquery_output_text_1", "geoquery_output_table_1"]
+[geoquery.ui.sections.ui_basic]
+geoquery_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+geoquery_output_text_1 = "title = 'Output of geoquery', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+geoquery_output_table_1 = "title = 'Output of geoquery (Table)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+
+[geoquery.paramters.geoquery_input_box]
+# For reading annovarR shiny APP geoquery tool input files  
+section_type = "input"
+rcmd_last = """
+gds <- ""
+gsm <- ""
+if (gds_file != "") gds <- getGEO(filename=gds_file)
+if (gsm_file != "") gsm <- getGEO(filename=gsm_file)
+"""
+progressbar_message = "Running geoquery functions."
+render_id = "geoquery_input_box"
+
+#!!!!! input_ui_order required related section
+input_ui_order = ["single_input", "start_analysis"]
+
+[geoquery.paramters.geoquery_input_box.input.single_input]
+title = "Parameters:"
+title_control = "class = 'input-section-p'"
+varname = ["gds_file", "gsm_file"]
+input_id = ["input_geoquery_1", "input_geoquery_2"]
+type = ["shiny::selectInput", "shiny::selectInput"]
+label = ["GDS File", "GSE File"]
+
+[geoquery.paramters.geoquery_input_box.input.single_input.choices]
+gds_file = "!!glue {c(system.file('extdata', 'GDS507.soft.gz', package = 'GEOquery'), featch_files()$file_path, '')}"
+gsm_file = "!!glue {c(system.file('extdata', 'GSM11805.txt.gz', package = 'GEOquery'), featch_files()$file_path, '')}"
+[geoquery.paramters.geoquery_input_box.input.single_input.selected]
+gds_file = ""
+gsm_file = ""
+
+[geoquery.paramters.geoquery_input_box.input.start_analysis]
+input_id = "start_geoquery_analysis"
+type = "shiny::actionButton"
+label = "Run"
+
+[geoquery.paramters.geoquery_output_text_1]
+section_type = "output"
+rcmd_last = "head(Meta(gsm))"
+render_type = "shiny::renderPrint"
+render_id = "geoquery_output_text_1"
+output_type = "shiny::verbatimTextOutput"
+progressbar_message = "GEOquery geoquery_output_text_1"
+
+[geoquery.paramters.geoquery_output_table_1]
+section_type = "output"
+rcmd_last = """
+Table(gsm)
+"""
+render_type = "DT::renderDataTable"
+render_id = "geoquery_output_table_1"
+output_type = "DT::dataTableOutput"
+progressbar_message = "GEOquery geoquery_output_table_1"

inst/extdata/config/shiny/shiny.pubmed.parameters.toml

@@ -86,7 +86,7 @@ if (!is.null(objs) && (max_n_items >= 500)){
 colnames(result) <- c("PMID", "DOI", "Title", "Abstract", "PublishDate", "JournalName", "BookName")
 """
 progressbar_message = "Running pubmed functions."
-render_id = "pubmed_pubmed_input_box"
+render_id = "pubmed_input_box"
 
 #!!!!! input_ui_order required related section
 input_ui_order = ["single_input", "start_analysis"]

inst/extdata/config/shiny/shiny.spack.parameters.toml

@@ -1,29 +1,44 @@
 [spack.ui.sections]
-order = ["readfiles", "outputFields"]
+order = ["spack_input_box", "spack_output_box_text"]
 [spack.ui.sections.ui_basic]
-readfiles = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
-outputFields = "title = 'Output of spack', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+spack_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+spack_output_box_text = "title = 'Output of spack', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 
-[spack.paramters.readfiles]
+[spack.paramters.spack_input_box]
 # For reading annovarR shiny APP spack tool input files  
 section_type = "input"
-rcmd_last = """
-
-"""
+rcmd_last = ""
 progressbar_message = "Running spack functions."
-render_id = "spack_readfiles"
+render_id = "spack_input_box"
 
 #!!!!! input_ui_order required related section
-input_ui_order = ["start_analysis"]
+input_ui_order = ["single_input", "start_analysis"]
+
+[spack.paramters.spack_input_box.input.single_input]
+title = "Parameters:"
+title_control = "class = 'input-section-p'"
+varname = ["spack_sub_cmd", "spack_params"]
+input_id = ["input_spack_1", "input_spack_2"]
+type = ["shiny::selectInput", "shiny::textInput"]
+label = ["spack subcommands", "spack parameters"]
+
+[spack.paramters.spack_input_box.input.single_input.choices]
+spack_sub_cmd = ["list", "info", "find", "install", "uninstall",
+                 "spec", "load",
+                 "module", "unload",
+                 "view", "create", "edit",
+                 "arch", "compilers"]
+[spack.paramters.spack_input_box.input.single_input.selected]
+spack_sub_cmd = "find"
 
-[spack.paramters.readfiles.input.start_analysis]
+[spack.paramters.spack_input_box.input.start_analysis]
 input_id = "start_spack_analysis"
 type = "shiny::actionButton"
 label = "Run"
 
-[spack.paramters.outputFields]
+[spack.paramters.spack_output_box_text]
 section_type = "output"
-rcmd_last = "cat(BioInstaller::spack('find'))"
+rcmd_last = "cat(BioInstaller::spack(sprintf('%s %s', spack_sub_cmd, spack_params)))"
 render_type = "shiny::renderPrint"
 render_id = "spack_output"
 output_type = "shiny::verbatimTextOutput"

inst/extdata/shiny/server_download.R

@@ -70,7 +70,7 @@ download_section_server <- function(input, output) {
   output$conda_installer_ui <- renderUI({
     conda_envs <- BioInstaller::conda.env.list()[,1]
     HTML(
-    paste0(shiny::selectInput("installer_conda_sub_command", "Sub command of conda",
+    paste0(shiny::selectInput("installer_conda_sub_command", "Conda subcommands",
                        c("clean", "config", "create",
                          "info", "install",
                          "list", "package",
@@ -80,8 +80,8 @@ download_section_server <- function(input, output) {
     shiny::selectInput("installer_conda_env_name", label = "Conda environment",
                        choices = conda_envs,
                        selected = "base"),
-    shiny::textAreaInput("installer_conda_parameters", label = "Parameters"),
-    actionButton("installer_conda_run", label = "Run")
+    shiny::textAreaInput("installer_conda_parameters", label = "Conda parameters"),
+    actionButton("installer_conda_run", label = "Submit")
     ), collapse = "\n")
   })
 
@@ -97,7 +97,7 @@ download_section_server <- function(input, output) {
                                   "arch", "compilers"),
                                 selected = "find"),
              shiny::textAreaInput("installer_spack_parameters", label = "Parameters"),
-             actionButton("installer_spack_run", label = "Run")
+             actionButton("installer_spack_run", label = "Submit")
       ), collapse = "\n")
   })
 

inst/extdata/shiny/ui_body_download.R

@@ -35,7 +35,7 @@ get_download_tabItem_ui <- function(){
                                                             "save.to.db", "overwrite")
                                             ),
                 shiny::textInput("extra.paramters", "Extra parameters", "list()"),
-                actionButton("install_run", "Run")
+                actionButton("install_run", "Submit")
               ),
               box(
                 title = "Conda",