implements #122

scripts/larvatagger.sh

@@ -204,8 +204,14 @@ eval $DOCKER_RUN
 
 	predict)
 
+if [ "$(basename "$(dirname "$1")")" = "**" ]; then
+parentdir=$(cd "$(dirname "$(dirname "$1")")"; pwd -P)
+data_file=$(basename "$(dirname "$1")")/$(basename "$1")
+else
 parentdir=$(cd "$(dirname "$1")"; pwd -P)
-data_file=$(basename "$1"); shift
+data_file=$(basename "$1")
+fi
+shift
 
 RUN_ARGS="$RUN_ARGS -v \"$parentdir\":/data"
 

src/cli_toolkit.jl

@@ -3,7 +3,7 @@ module Toolkit
 using DocOpt
 using Pkg
 using OrderedCollections
-using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Formats
+using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Formats, PlanarLarvae.Dataloaders
 
 include("Taggers.jl")
 using .Taggers
@@ -191,10 +191,14 @@ function main(args=ARGS; exit_on_error=true)
             if endswith(datapath, ".txt")
                 # assume that the file lists paths to data files to be processed;
                 # in this case, the path to the txt file is not relevant
+                @info "The listed data file paths are expected to be relative to current directory" cwd=pwd()
                 pwd()
             else
                 dirname(datapath)
             end
+        elseif occursin("*", datapath)
+            repository = Dataloaders.Repository(datapath)
+            repository.root
         else
             datapath
         end