Sage-Bionetworks · danlu1 · Apr 28, 2022 · Apr 28, 2022 · Apr 28, 2022 · Apr 28, 2022
diff --git a/R/mod-validator.R b/R/mod-validator.R
@@ -31,26 +31,26 @@ validator_ui <- function(id, species_list, assay_templates,
         get_study_ui(ns("study")),
 
         # Species
-        div(
-          class = "result",
-          div(
-            class = "wide",
-            shinyjs::disabled(
-              radioButtons(
-                ns("species"),
-                "Species",
-                species_list
-              )
-            )
-          ),
-          popify(
-            tags$a(icon(name = "question-circle"), href = "#"),
-            "Information",
-            "Select the species used in the study.",
-            placement = "left",
-            trigger = "hover"
-          )
-        ),
+        #div(
+          #class = "result",
+          #div(
+          # class = "wide",
+           # shinyjs::disabled(
+           #   radioButtons(
+            #    ns("species"),
+            #    "Species",
+            #    species_list
+            #  )
+          #  )
+         # ),
+         # popify(
+         #   tags$a(icon(name = "question-circle"), href = "#"),
+         #   "Information",
+         #   "Select the species used in the study.",
+         #   placement = "left",
+          #  trigger = "hover"
+         # )
+       # ),
 
         # Biospecimen type
         if (include_biospecimen_type) {
@@ -83,26 +83,26 @@ validator_ui <- function(id, species_list, assay_templates,
         },
 
         # Assay name
-        div(
-          class = "result",
-          div(
-            class = "wide",
-            shinyjs::disabled(
-              selectInput(
-                ns("assay_name"),
-                "Assay type",
-                names(assay_templates)
-              )
-            )
-          ),
-          popify(
-            tags$a(icon(name = "question-circle"), href = "#"),
-            "Information",
-            "Select the type of assay that matches your assay metadata.", # nolint
-            placement = "left",
-            trigger = "hover"
-          )
-        ),
+        #div(
+         # class = "result",
+         # div(
+          #  class = "wide",
+          #  shinyjs::disabled(
+           #   selectInput(
+           #     ns("assay_name"),
+           #     "Assay type",
+           #     names(assay_templates)
+          #    )
+          #  )
+         # ),
+         # popify(
+         #   tags$a(icon(name = "question-circle"), href = "#"),
+         #   "Information",
+        #    "Select the type of assay that matches your assay metadata.", # nolint
+         #   placement = "left",
+        #    trigger = "hover"
+        #  )
+       # ),
 
         # Files to be validated
         conditionalPanel(
@@ -114,7 +114,7 @@ validator_ui <- function(id, species_list, assay_templates,
               shinyjs::disabled(
                 fileInput(
                   ns("indiv_meta"),
-                  "Individual metadata file (.csv)",
+                  "1kD_standardized_demographic_data file (.csv)",
                   width = NULL,
                   accept = c(
                     "text/csv",
@@ -127,7 +127,7 @@ validator_ui <- function(id, species_list, assay_templates,
             popify(
               tags$a(icon(name = "question-circle"), href = "#"),
               "Information",
-              "Select the individual metadata file. This file should have one row per individual, with data about each individual in the experiment. If adding a new dataset to an existing dataset, please include all previous individuals.", # nolint
+              "Select the 1kD_standardized_demographic_data file. This file should have one row per individual, with data about each individual in the experiment. If adding a new dataset to an existing dataset, please include all previous individuals.", # nolint
               placement = "left",
               trigger = "hover"
             )
@@ -159,31 +159,31 @@ validator_ui <- function(id, species_list, assay_templates,
             trigger = "hover"
           )
         ),
-        div(
-          class = "result",
-          div(
-            class = "wide",
-            shinyjs::disabled(
-              fileInput(
-                ns("assay_meta"),
-                "Assay metadata file (.csv)",
-                width = NULL,
-                accept = c(
-                  "text/csv",
-                  "text/comma-separated-values,text/plain",
-                  ".csv"
-                )
-              )
-            )
-          ),
-          popify(
-            tags$a(icon(name = "question-circle"), href = "#"),
-            "Information",
-            "Select the assay metadata file. Depending on the assay, this file should have one row per specimen or one row per individual (indicated in the template), with data about the assay performed on each specimen or individual in the experiment. If adding a new dataset to an existing dataset, please include all previous assay specimens or individuals. Please be sure to choose the correct assay type from the drop-down above, as well.", # nolint
-            placement = "left",
-            trigger = "hover"
-          )
-        ),
+       # div(
+         # class = "result",
+         # div(
+         #   class = "wide",
+         #   shinyjs::disabled(
+         #     fileInput(
+          #      ns("assay_meta"),
+          #      "Assay metadata file (.csv)",
+          #      width = NULL,
+           #     accept = c(
+           #       "text/csv",
+           #       "text/comma-separated-values,text/plain",
+           #       ".csv"
+           #     )
+           #   )
+           # )
+          #),
+        #  popify(
+         #   tags$a(icon(name = "question-circle"), href = "#"),
+         #   "Information",
+          #  "Select the assay metadata file. Depending on the assay, this file should have one row per specimen or one row per individual (indicated in the template), with data about the assay performed on each specimen or individual in the experiment. If adding a new dataset to an existing dataset, please include all previous assay specimens or individuals. Please be sure to choose the correct assay type from the drop-down above, as well.", # nolint
+          #  placement = "left",
+          #  trigger = "hover"
+         # )
+        #),
         div(
           class = "result",
           div(

diff --git a/app.R b/app.R
@@ -2,7 +2,7 @@
 # To deploy, run: rsconnect::deployApp()
 # Or use the blue button on top of this file
 
-Sys.setenv(R_CONFIG_ACTIVE = "default") # Replace "default" with your config
+Sys.setenv(R_CONFIG_ACTIVE = "1kD") # Replace "default" with your config
 pkgload::load_all()
 options("golem.app.prod" = TRUE)
 dccvalidator::run_app() # add parameters here (if any)
diff --git a/inst/config.yml b/inst/config.yml
@@ -280,69 +280,68 @@ veoibd:
 
 1kD:
   app_url: "https://shinypro.synapse.org/users/danlu/dccvalidator_1kD/"
-  parent: "syn21763123"
+  parent: "syn27605292"
   path_to_markdown: "inst/using-the-dccvalidator-1kD.Rmd"
-  study_table: "syn20968992"
-  samples_table: "syn22175287"
-  annotations_table: "syn20981788"
-  annotations_link: "https://www.synapse.org/#!Synapse:syn20729790"
-  templates_link: "https://www.synapse.org/#!Synapse:syn20729790"
+  study_table: "syn27610007"
+  samples_table: "syn27817789"
+  annotations_table: "syn27806892"
+  annotations_link: "https://www.synapse.org/#!Synapse:syn27817580"
+  templates_link: "https://www.synapse.org/#!Synapse:syn27817580"
   docs_tab:
-    include_tab: TRUE
+    include_tab: FALSE
     include_upload_widget: FALSE
     tab_name: "Study Documentation"
     path_to_docs_markdown: "inst/study-documentation-1kD.Rmd"
   teams:
-    - "3323356"
-  include_biospecimen_type: TRUE
+    - "3433360"  # 1kD_admin
+    - "3436722"  # 1kD_Connectome
+    - "3436721"  # 1kD_InfantNaturalStatistics
+    - "3436720"  # 1kD_BRAINRISE
+    - "3436718"  # 1kD_KHULA
+    - "3436509"  # 1kD_MicrobiomeBrainDevelopment
+    - "3436717"  # 1kD_M4EFaD_LABS
+    - "3436716"  # 1kD_Assembloids
+    - "3436713"  # 1kD_DyadicSociometrics_NTU
+    - "3466183"  # 1kD_DyadicSociometrics_Cambridge
+    - "3436714"  # 1kD_First1000Daysdatabase
+    - "3458847"  # 1kD_M4EFaD_BMT team
+    - "3464137"  # 1kD_Stanford_Yeung team
+    - "3460645"  # 1kD_M4EFaD_Auckland
+  include_biospecimen_type: FALSE
   templates:
-    manifest_template: "syn20782058"
+    manifest_template: "syn27832372"
     individual_templates:
-      human: "syn20781820"
-      animal: "syn21053116"
+      human: "syn29358381"
     biospecimen_templates:
-      human:
-        in vivo, postmortem, other: "syn20768131"
-        in vitro: "syn26011297"
-      other mouse or animal model:
-        in vivo, postmortem, other: "syn20768131"
-        in vitro: "syn26011297"
-    assay_templates:
-      ATACSeq: "syn20768526"
-      bisulfiteSeq: "syn23017098"
-      ChIPSeq: "syn21861858"
-      HI-C: "syn21680758"
-      immunoassay: "syn25805392"
-      methylationArray: "syn25805391"
-      rnaSeq: "syn20768650"
-      snpArray: "syn21680759"
-      STARRSeq: "syn26011215"
-      TMT quantitation: "syn21680761"
-      wholeGenomeSeq: "syn20980993"
-  species_list:
-    - "human"
-    - "animal model"
+      human: "syn29358373"
   complete_columns:
     manifest:
-      - "consortium"
-      - "study"
-      - "grant"
-      - "fileFormat"
-      - "parent"
       - "path"
+      - "parent"
+      - "fileFormat"
+      - "program"
+      - "project"
+      - "study"
+      - "resourceType"
     individual:
+      - "program"
+      - "project"
+      - "study"
       - "individualID"
-      - "individualIdSource"
-      - "species"
-      - "reportedGender"
-      - "postmortem"
-      - "primaryDiagnosis"
+      - "householdID"
+      - "person"
+      - "sex"
+      - "noOfChildren"
+      - "noOfAdults"
+      - "spokenLanguage"
     biospecimen:
+      - "program"
+      - "project"
+      - "study"
+      - "person"
       - "individualID"
       - "specimenID"
-      - "organ"
-      - "tissue"
-      - "nucleicAcidSource"
-    assay:
-      - "specimenID"
-  contact_email: "[email protected]"
+      - "specimenType"
+      - "samplingAge"
+      - "samplingAgeUnits"
+  contact_email: "[email protected]"
diff --git a/inst/study-documentation-1kD.Rmd b/inst/study-documentation-1kD.Rmd
@@ -0,0 +1,21 @@
+---
+title: "1kD Study Documentation"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{pec-study-documentation}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+# Submit your Study and Assay Documentation to Synapse
+
+This information should be similar to a materials and methods section in a paper. 
+
+[Follow this link](https://www.synapse.org/#!Synapse:syn25150011){target="_blank"} to submit your documentation.