Commit wrapper

data_curation/README.md

@@ -18,7 +18,7 @@ Make sure that you have installed:
 - [Nextflow](https://nextflow.io)
 
 ```sh
-./import_datasets.sh ~/.spt_db.config.local --drop-first moldoveanu
+./import_dataset.sh ~/.spt_db.config.local --drop-first moldoveanu
 ```
 
 - `~/.spt_db.config.local` is an example name of a [database configuration file](https://github.com/nadeemlab/SPT/blob/main/spatialprofilingtoolbox/workflow/assets/.spt_db.config.template).

data_curation/import_dataset.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+source convenience_scripts/verifications_and_configurations.sh
+source convenience_scripts/import_functions.sh
+
+dbconfigargument=$1
+dbconfig=$(handle_dbconfig_argument $dbconfigargument)
+
+drop_first=$( if [[ "$2" == "--drop-first" ]]; then echo "yes"; else echo "no" ; fi; )
+
+one_inclusion="$3"
+
+available_datasets=$(get_available_dataset_handles)
+configured_datasets=$(get_configured_run_handles)
+if [[ ! "$available_datasets" == "$configured_datasets" ]];
+then
+    bash convenience_scripts/configure_all_imports.sh "$dbconfigargument" "$one_inclusion"
+    var=$?
+    if [ $var -ne 0 ];
+    then
+        echo "Configuration had some error. $var"
+        exit 1
+    fi
+fi
+
+SECONDS=0
+if [[ "$one_inclusion" == "" ]];
+then
+    configured_datasets=$(get_configured_run_handles)
+else
+    configured_datasets=$(get_configured_run_handles | grep -o "$one_inclusion")
+fi
+echo "Will import from configured run directories:"
+echo "$configured_datasets" | sed 's/  /\n  /g'
+echo "Command: import_datasets '$configured_datasets' $PWD $drop_first $dbconfig"
+import_datasets "$configured_datasets" "$PWD" "$drop_first" "$dbconfig"
+echo "Dataset import took $SECONDS seconds ("$(( SECONDS / 60 ))" minutes)."