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NEVER MERGE: ROBOT plugin testing #9952

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NEVER MERGE: ROBOT plugin testing #9952

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5c80650
Update hp.Makefile
matentzn Aug 7, 2023
c61ff7b
Update hp.Makefile
matentzn Aug 8, 2023
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33 changes: 32 additions & 1 deletion src/ontology/hp.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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This may be preferable to putting it into the dependencies (as it is a phony goal). The symlinks are very fast, and the other plugins are only updated when the make cache is invalidated first.

$(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 [email protected] && mv [email protected] $@
Expand Down Expand Up @@ -636,3 +643,27 @@ $(TMPDIR)/hp-%-merged.owl: hp-base.owl tmp/%.owl

mappings:
$(MAKE_FAST) ../mappings/hp-snomed.lexmatch.sssom.tsv

###########################################
### 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
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This does not throw an error when the ../../plugins directory does not exist, which is good.

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But this will throw an error if there are some plugins in the ../../plugins directory but the destination directory ($(TMPDIR)/plugins) does not exist. We need a mkdir -p $(TMPDIR)/plugins before attempting to create the symlinks.

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Thank you! Just unix 101: what happens if a file is deleted in ../../plugins/*.jar after this is run? Does the seem link disappear as well?

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No. We’re creating a normal link here, not a symbolic one (or a “hard” link instead of a “soft” one) – my mistake in the previous comment for calling them “symlinks” out of habit.

If the original file in ../../plugins/ is deleted, the newly added link in $(TMPDIR)/plugins will still be there, and will still point to the same contents (technically the same inode) on the disk.

(FYI: The reason we are creating normal links instead of symbolic links is that for some reasons, from within the ODK ROBOT would not be able to correctly follow the symlinks, even if both the symlinks and the files they are pointing to are both visible from the container – I’ve tried.)

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I’ll be curious to see whether this works as expected on Windows, though. AFAIK Windows has no such concepts as links and inodes, so I don’t know how Docker on Windows will handle that…


# 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
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renamed the goal a bit. Similar to test goal, custom Makefile extenders can simply attach the custom modules to that goal if they need to


$(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
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