Merge pull request #10 from EMSL-Computing/feature/map-upload

Feature/map upload
EMSL-Computing · Apr 23, 2024 · 01be8fa · 01be8fa
2 parents f7bd042 + 4b1f9dd
commit 01be8fa
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diff --git a/.gitignore b/.gitignore
@@ -30,15 +30,14 @@ vignettes/*.pdf
 tests/screenshots/*
 !tests/screenshots/info.txt
 tests/test_*/
-#packrat
-/packrat/*
-#random
-script_dump.R
-packrat/lib*/
-Data/
-untracked_resources
-cfg
+# config and renv
+cfg/*
 !cfg/minio_config_example.yml
 !cfg/minio_config_corems.yml
+!cfg/minio_config_map.yml
 renv
 !renv/settings.json
+#random
+script_dump.R
+Data/
+untracked_resources
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: FREDA
 Title: An app for the processing and visualization of Fourier-transform mass spectrometry data.
-Version: 1.1.1
+Version: 1.2.0
 Authors@R: c(person("Lisa", "Bramer", "[email protected]", role = "aut", "cre"),
     person("Daniel", "Claborne", "[email protected]", role = c("aut")))
 Description: A frontend application which exposes functionality of the ftmsRanalysis R package.  See 

diff --git a/Makefile b/Makefile
@@ -9,7 +9,12 @@ APP_REGISTRY="docker.artifactory.pnnl.gov/mscviz/freda"
 BASE_IMAGE_TAG="${APP_REGISTRY}/base:${BASE_VERSION}"
 IMAGE_TAG="${APP_REGISTRY}:${TOP_VERSION}"
 MAP_SHINYTEST=2
-PROFILE=local
+PROFILE=''
+DO_BUILD=false
+
+ifeq ($(DO_BUILD), true)
+  BUILD_TARGET=build_top
+endif
 
 .PHONY: build_base
 build_base:
@@ -30,8 +35,8 @@ build_top:
 build: build_base build_top
 
 .PHONY: run
-run:
-	docker compose up --build
+run: ${BUILD_TARGET}
+	docker compose --profile ${PROFILE} up
 
 .PHONY: login
 login:

diff --git a/Observers/startup_observers.R b/Observers/startup_observers.R
@@ -5,8 +5,93 @@ observe({
 
   # establish minio connection if we are pulling cloud resources
   if (any(names(query) %in% VALID_MINIO_HEADER_PARAMS)) {
-    cfg_location = if (Sys.getenv("MINIO_CONFIG_PATH") == "") "./cfg/minio_config.yml" else Sys.getenv("MINIO_CONFIG_PATH")
-    minio_con <<- mapDataAccess::map_data_connection(cfg_location)
+    isolate({
+      # store header params in a reactive variable
+      for (key in names(query)) {
+        header_params[[key]] <- query[[key]]
+        message(sprintf("INFO: stored parameter %s: %s", key, query[[key]]))
+      }
+
+      if ('corems-prefix' %in% names(query)) {
+        # get the appropriate minio config for retrieving CoreMS files
+        cfg_location = if (Sys.getenv("COREMS_MINIO_CONFIG_PATH") == "") "./cfg/minio_config_corems.yml" else Sys.getenv("COREMS_MINIO_CONFIG_PATH")
+        cms_minio_con <<- mapDataAccess::map_data_connection(cfg_location)
+
+        html(selector = "#loading-gray-overlay > div", html = "Loading Core-MS data...")
+
+        uris <- reticulate::iterate(
+          cms_minio_con$client$list_objects(
+            cms_minio_con$bucket,
+            prefix = header_params[['corems-prefix']],
+            recursive = TRUE),
+          function(x) x$object_name
+        )
+
+        if (length(uris) > 0) {
+          corems_upload_success <- tryCatch({
+            fpaths <- lapply(uris, function(uri) {
+              mapDataAccess::get_file(
+                cms_minio_con, id = uri, filename = file.path(tempfile(), basename(uri)),
+                use_dir = FALSE
+              )
+            })
+
+            modalmessage <- store_corems(fpaths)
+            TRUE
+
+          }, error = function(e) {
+            modalmessage <<- div(sprintf(info_text[["COREMS_UPLOAD_ERROR"]], e))
+            FALSE
+          })
+        } else {
+          corems_upload_success <- FALSE
+          modalmessage <- div(info_text[["COREMS_UPLOAD_NOSAMPS"]])
+        }
+
+        if (corems_upload_success) {
+          # defined in srv_ui_elements/corems_UI.R
+          showModal(corems_upload_success_modal(modalmessage)) 
+        } else {
+          showNotification(
+            modalmessage,
+            duration = NULL,
+            type = "error"
+          )
+        }
+      } else if ('map-object' %in% names(query)) {
+        # get the appropriate minio config for retrieving CoreMS files
+        cfg_location = if (Sys.getenv("MAP_MINIO_CONFIG_PATH") == "") "./cfg/minio_config_map.yml" else Sys.getenv("MAP_MINIO_CONFIG_PATH")
+        map_minio_con <<- mapDataAccess::map_data_connection(cfg_location)
+
+        html(selector = "#loading-gray-overlay > div", html = "Loading data from MAP...")
+
+        ftms_obj <- tryCatch({
+          mapDataAccess::get_data(map_minio_con, header_params[['map-object']])
+        }, error = function(e) {
+          NULL
+        })
+
+        valid_obj_types = c("project omic")
+
+        if (!inherits(ftms_obj, valid_obj_types)) {
+          showNotification(
+            HTML(sprintf("Something went wrong retrieving your data from MAP.  Your MAP object was not of the appropriate type.  Please confirm that the object is of types:  [%s]", valid_obj_types)),
+            duration = NULL,
+            type = "error"
+          )
+        } else {
+          # store in some reactive variable that e_data and e_meta....essentially check exists and use if so.
+          revals$map_project <- ftms_obj 
+        }
+      }
+    })
+
+  } else if (length(names(query)) > 0) {
+    showNotification(
+      sprintf("No valid header parameters found in query string.  Found parameters: (%s).  Valid header parameters: (%s).  Presenting manual upload dialog.", paste(names(query), collapse = ", "), paste(VALID_MINIO_HEADER_PARAMS, collapse = ", ")),
+      duration = NULL,
+      type = 'error'
+    ) 
   }
 
   on.exit({
@@ -15,49 +100,17 @@ observe({
   })
 
   isolate({
-    # store header params in a reactive variable
-    for (key in names(query)) {
-      header_params[[key]] <- query[[key]]
-      message(sprintf("INFO: stored parameter %s: %s", key, query[[key]]))
-    }
-
-    if ('corems-prefix' %in% names(query)) {
-      html(selector = "#loading-gray-overlay > div", html = "Loading Core-MS data...")
-
-      uris <- reticulate::iterate(
-        minio_con$client$list_objects(
-          minio_con$bucket,
-          prefix = header_params[['corems-prefix']],
-          recursive = TRUE),
-        function(x) x$object_name
-      )
-
-      if (length(uris) > 0) {
-        tryCatch({
-          fpaths <- lapply(uris, function(uri) {
-            mapDataAccess::get_file(
-              minio_con, id = uri, filename = file.path(tempfile(), basename(uri)),
-              use_dir = FALSE
-            )
-          })
-
-          modalmessage <- store_corems(fpaths)
-
-        }, error = function(e) {
-          modalmessage <<- div(sprintf(info_text[["COREMS_UPLOAD_ERROR"]], e))
-        })
-      } else {
-        modalmessage <- div(info_text[["COREMS_UPLOAD_NOSAMPS"]])
-      }
-
-      # defined in srv_ui_elements/corems_UI.R
-      showModal(corems_upload_success_modal(modalmessage))
-    }
-
-    # if we're not coming from minio, ask whether they have multiple CoreMS files to upload.
-    # if they don't automatically insert the Core
-    if (length(corems_revals[['combined_tables']]) == 0) {
+    # if we're not coming from minio (CoreMS files or MAP project object), ask whether they have multiple CoreMS files to upload or a single unified file.
+    if ((length(corems_revals[['combined_tables']]) == 0) && is.null(revals$map_project)) {
       showModal(upload_type_modal())
+    } else if (!is.null(revals$map_project)) {
+      insertTab(
+        "top_page",
+        target = "Welcome",
+        tab = upload_tab(),
+        position = "after"
+      )
+      showModal(map_upload_modal())
     } else {
       insertTab(
         "top_page",
@@ -81,6 +134,24 @@ upload_type_modal <- function() {
   )
 }
 
+#' Modal which informs the user that a MAP object was uploaded correctly (or incorrectly)
+map_upload_modal <- function() {
+  modalDialog(
+    title = "Data Uploaded from MAP",
+    tags$p("Your data has been uploaded from the Multi-Omics Analysis Portal.  Your data will be pre-populated on the Upload tab"),
+    footer = tagList(
+      actionButton("map_modal_goto_upload", "Go to Upload tab"),
+      modalButton("Dismiss")
+    )
+  )
+}
+
+#' observer for above modal actionbutton
+observeEvent(input$map_modal_goto_upload, {
+  updateTabsetPanel(inputId = "top_page", selected="Upload")
+  removeModal()
+})
+
 #' @details Insert the manual CoreMS upload tab
 observeEvent(input$upload_type_modal_multiple, {
   insertTab(

diff --git a/Observers/upload_observers.R b/Observers/upload_observers.R
@@ -1,3 +1,17 @@
+# MAP Upload.  Disable the two file upload widgets if we've loaded data from MAP.
+observeEvent(input$top_page, {
+  req(input$top_page == "Upload")
+
+  if (!is.null(revals$map_project)) {
+    edata_placeholder_content = revals$map_project$Data$e_data_filename
+    emeta_placeholder_content = revals$map_project$Data$e_meta_filename
+
+    mimic_fileinput_upload(id = "file_edata", progress_content="Uploaded from MAP", placeholder_content = edata_placeholder_content)
+    mimic_fileinput_upload(id = "file_emeta", progress_content="Uploaded from MAP", placeholder_content = emeta_placeholder_content)
+  }
+
+})
+
 # Main:  Create peakData when upload button or preprocess button clicked
 observeEvent(input$upload_click, {
   # prevent multiple clicks
@@ -208,12 +222,12 @@ observeEvent(Edata(), {
 })
 
 # Files Selected?
-observeEvent(c(input$top_page, input$file_edata, input$file_emeta), {
+observeEvent(c(input$top_page, input$file_edata, input$file_emeta, revals$map_project), {
   req(input$top_page == "Upload")
-  toggleCssClass("js_file_edata", "suggest-upload", is.null(input$file_edata))
-  toggleCssClass("js_file_emeta", "suggest-upload", is.null(input$file_emeta))
+  toggleCssClass("js_file_edata", "suggest-upload", is.null(input$file_edata) && is.null(revals$map_project))
+  toggleCssClass("js_file_emeta", "suggest-upload", is.null(input$file_emeta) && is.null(revals$map_project))
 
-  if (!is.null(input$file_edata) & !is.null(input$file_emeta)) {
+  if ((!is.null(input$file_edata) & !is.null(input$file_emeta)) || !is.null(revals$map_project)) {
     revals$warningmessage_upload$upload <- NULL
   }
 

diff --git a/Reactive_Variables/upload_revals.R b/Reactive_Variables/upload_revals.R
@@ -2,12 +2,14 @@
 Edata <- reactive({
   # Handle scenario where we made edata from another source.
   if (!is.null(revals$uploaded_data) & is.null(input$file_edata$datapath)) {
-    return(revals$uploaded_data$e_data %>%
-      dplyr::select(-dplyr::one_of(
-        ftmsRanalysis::getEDataColName(revals$uploaded_data)
-      )))
+    return(revals$uploaded_data$e_data)
   }
 
+  # If we uploaded from a MAP file
+  if (!is.null(revals$map_project)) {
+    return(revals$map_project$Data$e_data)
+  }
+
   # Error handling: Need file_edata path
   req(input$file_edata$datapath)
 
@@ -28,6 +30,10 @@ edata_cnames <- reactive({
 
 # Object: Get e_meta from file input
 Emeta <- reactive({
+  # If we uploaded from a MAP file
+  if (!is.null(revals$map_project)) {
+    return(revals$map_project$Data$e_meta)
+  }
   # Error handling: Need file_emeta to be valid
   req(input$file_emeta$datapath)
   # Load file

diff --git a/cfg/minio_config_corems.yml b/cfg/minio_config_corems.yml
@@ -0,0 +1,8 @@
+type: minio
+endpoint: minio-freda:9000
+access_key: minioadmin
+secret_key: minioadmin
+bucket: corems-freda
+secure: False
+python_venv: /venv
+verbose: true
diff --git a/cfg/minio_config_map.yml b/cfg/minio_config_map.yml
@@ -0,0 +1,8 @@
+type: minio
+endpoint: minio-freda:9000
+access_key: minioadmin
+secret_key: minioadmin
+bucket: map
+secure: False
+python_venv: /venv
+verbose: true
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -3,20 +3,23 @@
 version: "3" 
 services:
     freda:
+        profiles: ['']
         image: "docker.artifactory.pnnl.gov/mscviz/freda:${TOP_VERSION:-latest}"
         container_name: freda
         ports:
             - "${PORT:-3838}:3838"
         volumes:
-            - "./cfg/minio_config_corems_docker.yml:/srv/shiny-server/FREDA/cfg/minio_config.yml"
+            - "${COREMS_MINIO_CONFIG_PATH:-./cfg/minio_config_corems.yml}:/srv/shiny-server/FREDA/cfg/minio_config_corems.yml"
+            - "${MAP_MINIO_CONFIG_PATH:-./cfg/minio_config_map.yml}:/srv/shiny-server/FREDA/cfg/minio_config_map.yml"
         environment:
             - RETICULATE_PYTHON=/venv/bin/python
     minio:
+        profiles: ['', 'minio']
         image: minio/minio
         container_name: minio-freda
         ports:
-            - "9002:9000"
-            - "9003:9001"
+            - "9000:9000"
+            - "9001:9001"
         command: server --console-address ":9001" /data
 
 networks:

diff --git a/global.R b/global.R
@@ -56,7 +56,7 @@ info_text = list(
 )
 
 # cloud/minio resources
-VALID_MINIO_HEADER_PARAMS = c("corems-prefix")
+VALID_MINIO_HEADER_PARAMS = c("corems-prefix", "map-object")
 
 #' @SECTION Variables for selectors/inputs ##