diff --git a/.env.example b/.env.example index fb06317..5d9bf7e 100644 --- a/.env.example +++ b/.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 \ No newline at end of file +APP_NLPSANDBOX_SCHEMAS_VERSION=1.1.2 +APP_DATASET_VERSION=1.1.0 \ No newline at end of file diff --git a/README.md b/README.md index 785a1e9..21fc1c4 100644 --- a/README.md +++ b/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`. diff --git a/notebooks/generate-dataset.Rmd b/notebooks/generate-dataset.Rmd index f2238d7..6852770 100644 --- a/notebooks/generate-dataset.Rmd +++ b/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