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adding connectome sideloading #26

Merged
merged 16 commits into from
Mar 21, 2022
Merged

adding connectome sideloading #26

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a02de24
https://github.com/VirtualFlyBrain/Management/issues/295
hkir-dev Dec 20, 2021
344fa5a
adding connectome
Robbie1977 Jan 25, 2022
bf87c8a
building vfb_sideloading
Robbie1977 Jan 25, 2022
d50dccc
build all branches
Robbie1977 Jan 25, 2022
bbb20f2
external ontologies support added #24
hkir-dev Jan 31, 2022
201a39c
rename fields #24
hkir-dev Jan 31, 2022
0f1fb33
only region connectivity needed
Robbie1977 Feb 1, 2022
a7b3fb1
owlery doesn't need the merge
Robbie1977 Feb 1, 2022
4d37c43
moving debug
Robbie1977 Feb 1, 2022
0582f74
passing memory options to java also
Robbie1977 Feb 1, 2022
950f1cf
adding fixed log to output
Robbie1977 Feb 1, 2022
0c7981a
adding time
Robbie1977 Feb 1, 2022
97672bf
removing reasoning from pdb csv step
Robbie1977 Feb 7, 2022
d58ae90
new jar
Robbie1977 Feb 7, 2022
5163e84
Merge branch 'vfb_sideloading' into unique_facets
Robbie1977 Feb 14, 2022
ad7fdc3
Merge pull request #22 from VirtualFlyBrain/unique_facets
Robbie1977 Feb 14, 2022
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4 changes: 2 additions & 2 deletions .github/workflows/docker-image.yml
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Expand Up @@ -2,7 +2,7 @@ name: Docker Image CI

on:
push:
branches: [ master ]
branches: '**'
pull_request:
branches: [ master ]

Expand All @@ -15,7 +15,7 @@ jobs:
steps:
- name: Checkout
uses: actions/checkout@v1
- run: docker build . --file Dockerfile --tag vfb-pipeline-dumps:latest
- run: docker build . --file Dockerfile --tag vfb-pipeline-dumps:${GITHUB_REF#refs/heads/}
- name: Dockerize
if: success()
uses: manusa/[email protected]
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11 changes: 7 additions & 4 deletions dumps.Makefile
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Expand Up @@ -65,7 +65,7 @@ $(FINAL_DUMPS_DIR)/solr.json: $(FINAL_DUMPS_DIR)/obographs.json $(RAW_DUMPS_DIR)
# 2. create new sparql query in sparql/, naming it 'construct_name.sparql', e.g. sparql/construct_image_names.sparql
# Note that non-sparql goals, like 'inferred_annotation', need to be added separately
DUMPS_SOLR=all preferred_roots deprecation_label image_names has_image
DUMPS_PDB=all preferred_roots deprecation_label has_image has_neuron_connectivity has_region_connectivity
DUMPS_PDB=all preferred_roots deprecation_label has_image
DUMPS_OWLERY=all
CSV_IMPORTS="$(FINAL_DUMPS_DIR)/csv_imports"
OWL2NEOCSV="$(SCRIPTS_DIR)/owl2neo4jcsv.jar"
Expand All @@ -76,11 +76,14 @@ $(CSV_IMPORTS):
$(FINAL_DUMPS_DIR)/obographs.json: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DUMPS_SOLR)) $(RAW_DUMPS_DIR)/inferred_annotation.owl
$(ROBOT) merge $(patsubst %, -i %, $^) convert -f json -o $@ $(STDOUT_FILTER)

$(FINAL_DUMPS_DIR)/pdb.owl: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DUMPS_PDB)) $(RAW_DUMPS_DIR)/inferred_annotation.owl
PDB_EXTERNAL_ONTS=connectome_fafb.owl connectome_l1em.owl connectome_hemibrain.owl
$(FINAL_DUMPS_DIR)/pdb.owl: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DUMPS_PDB)) $(RAW_DUMPS_DIR)/inferred_annotation.owl $(patsubst %, $(RAW_DUMPS_DIR)/%, $(PDB_EXTERNAL_ONTS))
$(ROBOT) merge $(patsubst %, -i %, $^) -o $@ $(STDOUT_FILTER)

$(FINAL_DUMPS_DIR)/owlery.owl: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DUMPS_OWLERY))
$(ROBOT) filter -i $< --axioms "logical" --preserve-structure true annotate --ontology-iri "http://virtualflybrain.org/data/VFB/OWL/owlery.owl" -o $@ $(STDOUT_FILTER)
OWLERY_EXTERNAL_ONTS=connectome_fafb.owl connectome_l1em.owl connectome_hemibrain.owl
$(FINAL_DUMPS_DIR)/owlery.owl: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DUMPS_OWLERY)) $(patsubst %, $(RAW_DUMPS_DIR)/%, $(OWLERY_EXTERNAL_ONTS))
$(ROBOT) merge $(patsubst %, -i %, $^) \
filter --axioms "logical" --preserve-structure true annotate --ontology-iri "http://virtualflybrain.org/data/VFB/OWL/owlery.owl" -o $@ $(STDOUT_FILTER)

pdb_csvs: $(FINAL_DUMPS_DIR)/pdb.owl | $(CSV_IMPORTS)
java $(ROBOT_ARGS) -jar $(OWL2NEOCSV) $< "$(VFB_CONFIG)" $(CSV_IMPORTS)