Merge branch 'main' of github.com:nlpsandbox/i2b2-phi-dataset into main

.env.example

@@ -12,5 +12,5 @@ SYNAPSE_TOKEN=yourtoken
 HOST_PORT=80
 
 # User-specified settings made visible to RStudio (APP_*)
-APP_NLPSANDBOX_SCHEMAS_VERSION=1.1.1
-APP_DATASET_VERSION=1.0.0
+APP_NLPSANDBOX_SCHEMAS_VERSION=1.1.2
+APP_DATASET_VERSION=1.1.0

README.md

@@ -80,7 +80,7 @@ If you decided to fork this repository, you will need to update the environment
 variables defined at the top of the [CI/CD workflow]. You also need to create
 the following [GitHub Secrets]:
 
-- `RSTUDIO_PASSWORD`: Simply use a random password.
+- `RSTUDIO_PASSWORD`: Random password.
 - `SYNAPSE_USERNAME`: Your [Synapse.org] username.
 - `SYNAPSE_TOKEN`: A [personal access token (PAT)] that has the permissions
   `View`, `Download` and `Modify`.

notebooks/generate-dataset.Rmd

@@ -493,6 +493,16 @@ noop <- lapply(names(datasets), function(dataset_name) {
       df <- physical_address_annotations[[dataset_name]]
       df <- df[df$noteId == noteId,]
       text_physical_address_annotations <- df %>% purrr::transpose()
+      
+      ## get contact annotations
+      df <- contact_annotations[[dataset_name]]
+      df <- df[df$noteId == noteId,]
+      text_contact_annotations <- df %>% purrr::transpose()
+      
+      ## get id annotations
+      df <- id_annotations[[dataset_name]]
+      df <- df[df$noteId == noteId,]
+      text_id_annotations <- df %>% purrr::transpose()
 
       annotation=list(
         annotationSource=list(
@@ -502,7 +512,9 @@ noop <- lapply(names(datasets), function(dataset_name) {
         ),
         textDateAnnotations=text_date_annotations,
         textPersonNameAnnotations=text_person_name_annotations,
-        textPhysicalAddressAnnotations=text_physical_address_annotations
+        textPhysicalAddressAnnotations=text_physical_address_annotations,
+        textContactAnnotations=text_contact_annotations,
+        textIdAnnotations=text_id_annotations
       )
 
       # create note bundle