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use hotfix for cladetime #176

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merged 3 commits into from
Nov 25, 2024
Merged

use hotfix for cladetime #176

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bfbd8a4
use hotfix for cladetime
zkamvar Nov 25, 2024
7ff594d
use correct schema
zkamvar Nov 25, 2024
8ec1f46
missed one :see_no_evil:
zkamvar Nov 25, 2024
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2 changes: 1 addition & 1 deletion src/get_clades_to_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
# /// script
# requires-python = ">=3.11"
# dependencies = [
# "cladetime@git+https://github.com/reichlab/cladetime",
# "cladetime@git+https://github.com/reichlab/cladetime@elr/use_metadata_url",
# "polars",
# ]
# ///
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8 changes: 8 additions & 0 deletions src/make_round_config.R
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Expand Up @@ -46,6 +46,7 @@ get_latest_clade_file <- function(hub_dir) {
#' @param hub_root Character vector. The full path to the hub's root directory.
#' @returns A round object.
create_new_round <- function(hub_root) {
the_schema <- "v3.0.1"
this_round_clade_file <- get_latest_clade_file(hub_root)
this_round_clade_list <- fromJSON(this_round_clade_file$clade_file)$clades
this_round_date <- this_round_clade_file$round_id
Expand All @@ -57,15 +58,18 @@ create_new_round <- function(hub_root) {
hubAdmin::create_model_task(
task_ids = hubAdmin::create_task_ids(
hubAdmin::create_task_id("nowcast_date",
schema = the_schema,
required = list(this_round_date),
optional = NULL
),
hubAdmin::create_task_id("target_date",
schema = the_schema,
required = NULL,
## target date is nowcast_date and the three prior weeks
optional = as.character(seq(as.Date(this_round_date) - 31, as.Date(this_round_date) + 10, by = "day"))
),
hubAdmin::create_task_id("location",
schema = the_schema,
required = NULL,
optional = c(
"AL", "AK", "AZ", "AR", "CA", "CO",
Expand All @@ -80,18 +84,21 @@ create_new_round <- function(hub_root) {
)
),
hubAdmin::create_task_id("clade",
schema = the_schema,
required = this_round_clade_list,
optional = NULL
)
),
output_type = hubAdmin::create_output_type(
hubAdmin::create_output_type_mean(
schema = the_schema,
is_required = FALSE,
value_type = "double",
value_minimum = 0L,
value_maximum = 1L
),
hubAdmin::create_output_type_sample(
schema = the_schema,
is_required = FALSE,
output_type_id_type = "character",
max_length = 15L,
Expand All @@ -104,6 +111,7 @@ create_new_round <- function(hub_root) {
),
target_metadata = hubAdmin::create_target_metadata(
hubAdmin::create_target_metadata_item(
schema = the_schema,
target_id = "clade prop",
target_name = "Daily nowcasted clade proportions",
target_units = "proportion",
Expand Down