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Cleaning up makefile #3028

Merged
merged 53 commits into from
Aug 23, 2023
Merged

Cleaning up makefile #3028

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b01a116
Delete commented out code.
gouttegd Jul 19, 2023
3b49bbd
Remove Travis-specific code and comments.
gouttegd Jul 19, 2023
85192ee
Remove 'tmp/core.owl' intermediate product.
gouttegd Jul 19, 2023
b65fe5b
Clean up "step 2".
gouttegd Jul 19, 2023
2d76a28
Remove unnecessary intermediate products.
gouttegd Jul 19, 2023
e50dd88
Remove obsolete comment about reflexivity axioms.
gouttegd Jul 19, 2023
e6e1b17
Add FIXME tag to the rule that create basic.owl.
gouttegd Aug 10, 2023
4b462a5
Remove rule to produce uberon.yaml.
gouttegd Aug 10, 2023
ff0de2a
Merge branch 'master' into cleaning-up-makefile
gouttegd Aug 10, 2023
87e5cdb
Remove custom rule for mirroring BSPO.
gouttegd Aug 10, 2023
0d13d64
Remove old rule about ENVO import.
gouttegd Aug 10, 2023
27d0a0c
Merge branch 'master' into cleaning-up-makefile
gouttegd Aug 11, 2023
9cee90b
Remove the custom 'ext' product.
gouttegd Aug 11, 2023
7f143f1
Fix special rule for the RO mirror.
gouttegd Aug 11, 2023
dd30ff3
Remove hacking of ZFA mirror.
gouttegd Aug 12, 2023
235ccb5
Replace Owltools by ROBOT to create mirror/emapa.owl.
gouttegd Aug 12, 2023
c6d75ea
Remove unused fix to ehdaa2.
gouttegd Aug 12, 2023
435fe2e
Explain hacked mirrors.
gouttegd Aug 12, 2023
21fefc4
Re-organise and re-comment the section on imports.
gouttegd Aug 12, 2023
fd37d15
Remove obsolete rules for individual import modules.
gouttegd Aug 12, 2023
64da3e9
Create a section for "unreleased products".
gouttegd Aug 14, 2023
094e00e
Regroup all report-generating rules in the REPORTS section.
gouttegd Aug 15, 2023
123aa4c
Remove dependency to GO.xrf_abbs.
gouttegd Aug 15, 2023
ff6450c
Regroup all bridge-generation rules in the BRIDGES section.
gouttegd Aug 15, 2023
9630664
Remove the bridge to EMAP.
gouttegd Aug 15, 2023
62840c4
Remove rule to generate uberon-ext-bridge-to-zfa.
gouttegd Aug 15, 2023
2d1747c
Regroup subset-generating rules in the SUBSETS & VIEWS section.
gouttegd Aug 16, 2023
10b87bb
Re-organise the "bridge checks" section.
gouttegd Aug 16, 2023
775d824
Fixing the bridge checks (part 1).
gouttegd Aug 17, 2023
2370209
Amend the lists of bridge checks.
gouttegd Aug 17, 2023
3751a00
Fixing the BFO bridge checks.
gouttegd Aug 17, 2023
3f6f476
Remove the "failed" bridge checks.
gouttegd Aug 17, 2023
0d18f9d
Remove the ext-merged-%.owl unreleased product.
gouttegd Aug 17, 2023
bf30ae0
Simplify the composite stages section.
gouttegd Aug 17, 2023
ea39a1d
Remove the bundled-%.owl rule.
gouttegd Aug 17, 2023
c95e313
Arrange the composite anatomy section.
gouttegd Aug 17, 2023
e9fdef5
Remove FBbt-nd.
gouttegd Aug 18, 2023
364f31a
Cleanup RELEASE & RELEASE DEPLOYMENT section.
gouttegd Aug 18, 2023
f1e3c06
Do not exclude composite-metazoan-dv.txt.
gouttegd Aug 18, 2023
8bc44b9
Move some views to the appropriate section.
gouttegd Aug 18, 2023
327d198
Move the Allen rules to the LOCAL IMPORTS section.
gouttegd Aug 18, 2023
827b849
Move some lost checks to the REPORTS section.
gouttegd Aug 18, 2023
6b335f4
Re-format the XML CATALOG section.
gouttegd Aug 18, 2023
d7bcf70
Centralise the definition of test suites.
gouttegd Aug 18, 2023
69c5a08
Amend comments in the section about the main pipeline.
gouttegd Aug 18, 2023
9b5fc7f
Rename "ROBOT PATTERNS AND TEMPLATES".
gouttegd Aug 18, 2023
0bba7b4
Remove the entire DOSDP section.
gouttegd Aug 18, 2023
2cae55a
Make the composite-* stuff explicitly depend on update-stages.
gouttegd Aug 18, 2023
04e2c1e
Move the rule to generate external-disjoints.owl.
gouttegd Aug 18, 2023
6e5e3c5
Move the quick-qc test to the right section.
gouttegd Aug 18, 2023
9e7c84c
Moving last stuff around.
gouttegd Aug 18, 2023
7cee50e
Move variables closer to where they are used.
gouttegd Aug 18, 2023
a719af2
Merge branch 'master' into cleaning-up-makefile
gouttegd Aug 18, 2023
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11 changes: 1 addition & 10 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.

FORMATS = $(sort owl obo json owl)
FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic ext basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )

# ----------------------------------------
# Top-level targets
Expand Down Expand Up @@ -668,12 +668,6 @@ $(ONT)-basic.json: $(ONT)-basic.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
mv [email protected] $@
ext.obo: ext.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
ext.json: ext.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
mv [email protected] $@
basic.obo: basic.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
basic.json: basic.owl
Expand Down Expand Up @@ -781,9 +775,6 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
reduce -r ELK \
$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@

ext.owl:
echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false

basic.owl:
echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false

Expand Down
2 changes: 1 addition & 1 deletion src/ontology/bridge/collected-drosophila.owl
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Expand Up @@ -32,6 +32,6 @@
</rdfs:comment>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon/fbbt-nd.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/fbbt.owl"/>
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</owl:Ontology>
</rdf:RDF>
1 change: 0 additions & 1 deletion src/ontology/uberon-odk.yaml
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Expand Up @@ -20,7 +20,6 @@ release_artefacts:
- full
- simple
- basic
- custom-ext
- custom-basic
- custom-composite-metazoan
- custom-composite-metazoan-basic
Expand Down
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