From 5c80650a5866cd71e165f0edbb122d7e092488bd Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Mon, 7 Aug 2023 20:15:10 +0300
Subject: [PATCH 1/2] Update hp.Makefile

---
 src/ontology/hp.Makefile | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/ontology/hp.Makefile b/src/ontology/hp.Makefile
index 286dde4d6..0d0fc3d93 100644
--- a/src/ontology/hp.Makefile
+++ b/src/ontology/hp.Makefile
@@ -636,3 +636,18 @@ $(TMPDIR)/hp-%-merged.owl: hp-base.owl tmp/%.owl
 
 mappings: 
 	$(MAKE_FAST) ../mappings/hp-snomed.lexmatch.sssom.tsv
+
+export ROBOT_PLUGINS_DIRECTORY := $(PWD)/tmp/pluginsTest
+
+
+
+update-plugins: $(ROBOT_PLUGINS_DIRECTORY)/monarch.jar
+
+$(ROBOT_PLUGINS_DIRECTORY)/monarch.jar:
+	mkdir -p $(ROBOT_PLUGINS_DIRECTORY)
+	cp ~/ws/robot-phenotype-toolkit/target/robot-plugins-0.0.1-SNAPSHOT.jar $(ROBOT_PLUGINS_DIRECTORY)/monarch.jar
+
+export ROBOT_PLUGINS_DIRECTORY=$(PWD)/tmp/plugins
+
+hp-eq.owl: | tmp/plugins/monarch.jar
+	$(ROBOT) monarch:upheno-augment -i hp-edit.owl --relation has_phenotype_affecting  -o $@

From c61ff7b9252bf3ee7ceea4d3c4c4137a7ccb27e0 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Tue, 8 Aug 2023 16:26:15 +0300
Subject: [PATCH 2/2] Update hp.Makefile

---
 src/ontology/hp.Makefile | 32 ++++++++++++++++++++++++--------
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/src/ontology/hp.Makefile b/src/ontology/hp.Makefile
index 0d0fc3d93..924f5d795 100644
--- a/src/ontology/hp.Makefile
+++ b/src/ontology/hp.Makefile
@@ -132,8 +132,15 @@ reports/hp_xrefs.csv: $(SRC)
 ###### SKIP DEFAULTS #############
 ##################################
 
+$(EDIT_PREPROCESSED): $(SRC)
+	# Instead of making the prepare-robot-plugins a dependency, we just call the goal
+	# to update the plugins when we need it
+	$(MAKE) prepare-robot-plugins
+	$(ROBOT) monarch:upheno-augment -i $< --relation has_phenotype_affecting  \
+		convert --format ofn --output $@
+
 # We overwrite the .owl release to be, for now, a simple merged version of the editors file.
-$(ONT).owl: $(SRC)
+$(ONT).owl: $(EDIT_PREPROCESSED)	
 	$(ROBOT) merge --input $< \
 		annotate --ontology-iri $(URIBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ \
 		convert -o $@.tmp.owl && mv $@.tmp.owl $@
@@ -637,17 +644,26 @@ $(TMPDIR)/hp-%-merged.owl: hp-base.owl tmp/%.owl
 mappings: 
 	$(MAKE_FAST) ../mappings/hp-snomed.lexmatch.sssom.tsv
 
-export ROBOT_PLUGINS_DIRECTORY := $(PWD)/tmp/pluginsTest
+###########################################
+### Testing new custom plugin system ######
+###########################################
+
+# Make sure ROBOT knows where to find plugins
+export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins
 
+# List of "repository plugins" (plugins permanently installed in top-level plugins directory, entirely managed by users)
+ROBOT_REPOSITORY_PLUGINS=$(wildcard ../../plugins/*.jar)
 
+# Standard rule to create symlinks in $(TMPDIR)/plugins, so that the repository plugins
+# are visible to ROBOT
+prepare-robot-plugins:
+	for plugin in $(ROBOT_REPOSITORY_PLUGINS) ; do ln $plugin $(TMPDIR)/plugins ; done
 
-update-plugins: $(ROBOT_PLUGINS_DIRECTORY)/monarch.jar
+# in the custom.Makefile, users can simply attach any custom plugins they need
+# as dependencies to the prepare-robot-plugins goal
+prepare-robot-plugins: $(ROBOT_PLUGINS_DIRECTORY)/monarch.jar
 
 $(ROBOT_PLUGINS_DIRECTORY)/monarch.jar:
 	mkdir -p $(ROBOT_PLUGINS_DIRECTORY)
+	# Ignore this obviously this will be replaced by a download step
 	cp ~/ws/robot-phenotype-toolkit/target/robot-plugins-0.0.1-SNAPSHOT.jar $(ROBOT_PLUGINS_DIRECTORY)/monarch.jar
-
-export ROBOT_PLUGINS_DIRECTORY=$(PWD)/tmp/plugins
-
-hp-eq.owl: | tmp/plugins/monarch.jar
-	$(ROBOT) monarch:upheno-augment -i hp-edit.owl --relation has_phenotype_affecting  -o $@