search

obophenotype / planaria-ontology

PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
5 stars 6 forks source link

prepare_release attempt and fail #203

Closed srobb1 closed 2 years ago

srobb1 commented 2 years ago

@matentzn Trying to make a new release with odk 1.2.30 and adding a new term, nerve plexis. I have errors when running prepare_release

srobb1 commented 2 years ago

Here is my output: 


plana.Makefile:29: warning: overriding recipe for target 'plana.owl'
Makefile:501: warning: ignoring old recipe for target 'plana.owl'
if [ true  = true ] && [ true  = true ]; then curl -L http://purl.obolibrary.org/obo/go.owl --create-dirs -o mirror/go.owl --retry 4 --max-time 200 && robot --catalog catalog-v001.xml convert -i mirror/go.owl -o mirror/go.owl.tmp.owl && mv mirror/go.owl.tmp.owl mirror/go.owl; fi
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   316  100   316    0     0    532      0 --:--:-- --:--:-- --:--:--   534
100  125M  100  125M    0     0  4902k      0  0:00:26  0:00:26 --:--:-- 5944k
if [ true  = true ]; then touch ../patterns/data  ../patterns/data/default/plana_terms_immediately_deep_to.txt  ../patterns/data/default/cellTypes.txt  ../patterns/data/default/progenitorCellTypes.txt  ../patterns/data/default/plana_terms_part_of.txt  ../patterns/data/default/regeneratingFragment.txt  ../patterns/data/default/cellType_cellCycle.txt  ../patterns/data/default/plana_terms_immediately_superficial_to.txt  ../patterns/data/default/plana_terms.txt  ../patterns/data/default/lumenOfAnatomicalEntity.txt  ../patterns/data/default/plana_terms_produces_this.txt  ../patterns/data/default/plana_terms_existence_overlaps.txt  ../patterns/data/default/blastemaDevelopsIntoAnatomicalEntity.txt  ../patterns/data/default/anatomicalSpaceAndFragmentEntity.txt  ../patterns/data/default/plana_terms_existence_starts_during_or_after.txt  ../patterns/data/default/plana_terms_anterior_to.txt  ../patterns/data/default/plana_terms_produced_by.txt  ../patterns/data/default/fragment.txt  ../patterns/data/default/plana_terms_adjacent_to.txt  ../patterns/data/default/plana_terms_contained_in.txt  ../patterns/data/default/plana_terms_posterior_to.txt  ../patterns/data/default/primordiumCellTypes.txt  ../patterns/data/default/example.txt  ../patterns/data/default/anatomicalSpaceAndCellType.txt  ../patterns/data/default/plana_terms_develops_from.txt  ../patterns/data/default/anatomicalSpaceAndAnatomicalEntity.txt  ../patterns/data/default/plana_terms_luminal_space_of.txt  ../patterns/data/default/plana_terms_existence_ends_during_or_before.txt  ; fi
if [ true  = true ]; then touch ../patterns/data  ../patterns/data/default/plana_terms_immediately_deep_to.ofn  ../patterns/data/default/cellTypes.ofn  ../patterns/data/default/progenitorCellTypes.ofn  ../patterns/data/default/plana_terms_part_of.ofn  ../patterns/data/default/regeneratingFragment.ofn  ../patterns/data/default/cellType_cellCycle.ofn  ../patterns/data/default/plana_terms_immediately_superficial_to.ofn  ../patterns/data/default/plana_terms.ofn  ../patterns/data/default/lumenOfAnatomicalEntity.ofn  ../patterns/data/default/plana_terms_produces_this.ofn  ../patterns/data/default/plana_terms_existence_overlaps.ofn  ../patterns/data/default/blastemaDevelopsIntoAnatomicalEntity.ofn  ../patterns/data/default/anatomicalSpaceAndFragmentEntity.ofn  ../patterns/data/default/plana_terms_existence_starts_during_or_after.ofn  ../patterns/data/default/plana_terms_anterior_to.ofn  ../patterns/data/default/plana_terms_produced_by.ofn  ../patterns/data/default/fragment.ofn  ../patterns/data/default/plana_terms_adjacent_to.ofn  ../patterns/data/default/plana_terms_contained_in.ofn  ../patterns/data/default/plana_terms_posterior_to.ofn  ../patterns/data/default/primordiumCellTypes.ofn  ../patterns/data/default/example.ofn  ../patterns/data/default/anatomicalSpaceAndCellType.ofn  ../patterns/data/default/plana_terms_develops_from.ofn  ../patterns/data/default/anatomicalSpaceAndAnatomicalEntity.ofn  ../patterns/data/default/plana_terms_luminal_space_of.ofn  ../patterns/data/default/plana_terms_existence_ends_during_or_before.ofn  ; fi
robot --catalog catalog-v001.xml remove --input plana-edit.owl --select imports --trim false \
    merge   -i ../patterns/definitions.owl  -i components/obsolete.owl -o tmp/merged-plana-edit.owl
robot --catalog catalog-v001.xml query -f csv -i tmp/merged-plana-edit.owl --query ../sparql/terms.sparql tmp/pre_seed.txt.tmp &&\
cat tmp/pre_seed.txt.tmp | sort | uniq >  tmp/pre_seed.txt
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_immediately_deep_to.tsv --template=../patterns/dosdp-patterns/plana_terms_immediately_deep_to.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_immediately_deep_to.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/cellTypes.tsv --template=../patterns/dosdp-patterns/cellTypes.yaml --obo-prefixes=true --outfile=../patterns/data/default/cellTypes.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/progenitorCellTypes.tsv --template=../patterns/dosdp-patterns/progenitorCellTypes.yaml --obo-prefixes=true --outfile=../patterns/data/default/progenitorCellTypes.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_part_of.tsv --template=../patterns/dosdp-patterns/plana_terms_part_of.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_part_of.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/regeneratingFragment.tsv --template=../patterns/dosdp-patterns/regeneratingFragment.yaml --obo-prefixes=true --outfile=../patterns/data/default/regeneratingFragment.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/cellType_cellCycle.tsv --template=../patterns/dosdp-patterns/cellType_cellCycle.yaml --obo-prefixes=true --outfile=../patterns/data/default/cellType_cellCycle.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_immediately_superficial_to.tsv --template=../patterns/dosdp-patterns/plana_terms_immediately_superficial_to.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_immediately_superficial_to.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms.tsv --template=../patterns/dosdp-patterns/plana_terms.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/lumenOfAnatomicalEntity.tsv --template=../patterns/dosdp-patterns/lumenOfAnatomicalEntity.yaml --obo-prefixes=true --outfile=../patterns/data/default/lumenOfAnatomicalEntity.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_produces_this.tsv --template=../patterns/dosdp-patterns/plana_terms_produces_this.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_produces_this.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_existence_overlaps.tsv --template=../patterns/dosdp-patterns/plana_terms_existence_overlaps.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_existence_overlaps.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/blastemaDevelopsIntoAnatomicalEntity.tsv --template=../patterns/dosdp-patterns/blastemaDevelopsIntoAnatomicalEntity.yaml --obo-prefixes=true --outfile=../patterns/data/default/blastemaDevelopsIntoAnatomicalEntity.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/anatomicalSpaceAndFragmentEntity.tsv --template=../patterns/dosdp-patterns/anatomicalSpaceAndFragmentEntity.yaml --obo-prefixes=true --outfile=../patterns/data/default/anatomicalSpaceAndFragmentEntity.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_existence_starts_during_or_after.tsv --template=../patterns/dosdp-patterns/plana_terms_existence_starts_during_or_after.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_existence_starts_during_or_after.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_anterior_to.tsv --template=../patterns/dosdp-patterns/plana_terms_anterior_to.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_anterior_to.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_produced_by.tsv --template=../patterns/dosdp-patterns/plana_terms_produced_by.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_produced_by.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/fragment.tsv --template=../patterns/dosdp-patterns/fragment.yaml --obo-prefixes=true --outfile=../patterns/data/default/fragment.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_adjacent_to.tsv --template=../patterns/dosdp-patterns/plana_terms_adjacent_to.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_adjacent_to.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_contained_in.tsv --template=../patterns/dosdp-patterns/plana_terms_contained_in.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_contained_in.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_posterior_to.tsv --template=../patterns/dosdp-patterns/plana_terms_posterior_to.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_posterior_to.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/primordiumCellTypes.tsv --template=../patterns/dosdp-patterns/primordiumCellTypes.yaml --obo-prefixes=true --outfile=../patterns/data/default/primordiumCellTypes.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/example.tsv --template=../patterns/dosdp-patterns/example.yaml --obo-prefixes=true --outfile=../patterns/data/default/example.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/anatomicalSpaceAndCellType.tsv --template=../patterns/dosdp-patterns/anatomicalSpaceAndCellType.yaml --obo-prefixes=true --outfile=../patterns/data/default/anatomicalSpaceAndCellType.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_develops_from.tsv --template=../patterns/dosdp-patterns/plana_terms_develops_from.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_develops_from.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/anatomicalSpaceAndAnatomicalEntity.tsv --template=../patterns/dosdp-patterns/anatomicalSpaceAndAnatomicalEntity.yaml --obo-prefixes=true --outfile=../patterns/data/default/anatomicalSpaceAndAnatomicalEntity.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_luminal_space_of.tsv --template=../patterns/dosdp-patterns/plana_terms_luminal_space_of.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_luminal_space_of.txt; fi
if [ true  = true ]; then dosdp-tools terms --infile=../patterns/data/default/plana_terms_existence_ends_during_or_before.tsv --template=../patterns/dosdp-patterns/plana_terms_existence_ends_during_or_before.yaml --obo-prefixes=true --outfile=../patterns/data/default/plana_terms_existence_ends_during_or_before.txt; fi
if [ true  = true ]; then rm -f ../patterns/dosdp-patterns/*.yaml.1 || true; fi
if [ true  = true ] && [ -s ../patterns/dosdp-patterns/external.txt ]; then wget -i ../patterns/dosdp-patterns/external.txt --backups=1 -P ../patterns/dosdp-patterns; fi
if [ true  = true ]; then rm -f ../patterns/dosdp-patterns/*.yaml.1 || true; fi
simple_pattern_tester.py ../patterns/dosdp-patterns/
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/anatomicalSpaceAndAnatomicalEntity.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/anatomicalSpaceAndCellType.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/anatomicalSpaceAndFragmentEntity.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/blastemaDevelopsIntoAnatomicalEntity.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/cellType_cellCycle.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/cellTypes.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/example.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/fragment.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/lumenOfAnatomicalEntity.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_adjacent_to.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_anterior_to.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_contained_in.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_develops_from.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_existence_ends_during_or_before.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_existence_overlaps.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_existence_starts_during_or_after.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_immediately_deep_to.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_immediately_superficial_to.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_luminal_space_of.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_part_of.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_posterior_to.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_produced_by.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/plana_terms_produces_this.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/primordiumCellTypes.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/progenitorCellTypes.yaml
  warnings.warn("Checking %s" % pattern_doc)
/tools/simple_pattern_tester.py:99: UserWarning: Checking ../patterns/dosdp-patterns/regeneratingFragment.yaml
  warnings.warn("Checking %s" % pattern_doc)
if [ true  = true ]; then dosdp-tools prototype --obo-prefixes true --template=../patterns/dosdp-patterns --outfile=../patterns/pattern.owl; fi
if [ true  = true ]; then robot --catalog catalog-v001.xml query --use-graphs true -f csv -i ../patterns/pattern.owl --query ../sparql/terms.sparql ../patterns/pattern_owl_seed.txt; fi
if [ true  = true ]; then cat ../patterns/data/default/plana_terms_immediately_deep_to.txt ../patterns/data/default/cellTypes.txt ../patterns/data/default/progenitorCellTypes.txt ../patterns/data/default/plana_terms_part_of.txt ../patterns/data/default/regeneratingFragment.txt ../patterns/data/default/cellType_cellCycle.txt ../patterns/data/default/plana_terms_immediately_superficial_to.txt ../patterns/data/default/plana_terms.txt ../patterns/data/default/lumenOfAnatomicalEntity.txt ../patterns/data/default/plana_terms_produces_this.txt ../patterns/data/default/plana_terms_existence_overlaps.txt ../patterns/data/default/blastemaDevelopsIntoAnatomicalEntity.txt ../patterns/data/default/anatomicalSpaceAndFragmentEntity.txt ../patterns/data/default/plana_terms_existence_starts_during_or_after.txt ../patterns/data/default/plana_terms_anterior_to.txt ../patterns/data/default/plana_terms_produced_by.txt ../patterns/data/default/fragment.txt ../patterns/data/default/plana_terms_adjacent_to.txt ../patterns/data/default/plana_terms_contained_in.txt ../patterns/data/default/plana_terms_posterior_to.txt ../patterns/data/default/primordiumCellTypes.txt ../patterns/data/default/example.txt ../patterns/data/default/anatomicalSpaceAndCellType.txt ../patterns/data/default/plana_terms_develops_from.txt ../patterns/data/default/anatomicalSpaceAndAnatomicalEntity.txt ../patterns/data/default/plana_terms_luminal_space_of.txt ../patterns/data/default/plana_terms_existence_ends_during_or_before.txt ../patterns/pattern_owl_seed.txt | sort | uniq > ../patterns/all_pattern_terms.txt; else robot --catalog catalog-v001.xml query --use-graphs true -f csv -i ../patterns/definitions.owl --query ../sparql/terms.sparql ../patterns/all_pattern_terms.txt; fi
if [ true  = true ]; then cat tmp/pre_seed.txt  ../patterns/all_pattern_terms.txt  | sort | uniq > tmp/seed.txt; fi
if [ true  = true ]; then cat tmp/seed.txt imports/go_terms.txt | grep -v ^# | sort | uniq >  imports/go_terms_combined.txt; fi
if [ true  = true ]; then robot --catalog catalog-v001.xml query -i mirror/go.owl --update ../sparql/preprocess-module.ru \
    extract -T imports/go_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
    query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
    annotate --ontology-iri http://purl.obolibrary.org/obo/plana/imports/go_import.owl annotate -V http://purl.obolibrary.org/obo/plana/releases/2021-10-19/imports/go_import.owl --annotation owl:versionInfo 2021-10-19 --output imports/go_import.owl.tmp.owl && mv imports/go_import.owl.tmp.owl imports/go_import.owl; fi
if [ true  = true ] && [ true  = true ]; then curl -L http://purl.obolibrary.org/obo/iao.owl --create-dirs -o mirror/iao.owl --retry 4 --max-time 200 && robot --catalog catalog-v001.xml convert -i mirror/iao.owl -o mirror/iao.owl.tmp.owl && mv mirror/iao.owl.tmp.owl mirror/iao.owl; fi
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   356  100   356    0     0    506      0 --:--:-- --:--:-- --:--:--   506
100  547k  100  547k    0     0   337k      0  0:00:01  0:00:01 --:--:-- 1973k
if [ true  = true ]; then cat tmp/seed.txt imports/iao_terms.txt | grep -v ^# | sort | uniq >  imports/iao_terms_combined.txt; fi
if [ true  = true ]; then robot --catalog catalog-v001.xml query -i mirror/iao.owl --update ../sparql/preprocess-module.ru \
    extract -T imports/iao_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
    query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
    annotate --ontology-iri http://purl.obolibrary.org/obo/plana/imports/iao_import.owl annotate -V http://purl.obolibrary.org/obo/plana/releases/2021-10-19/imports/iao_import.owl --annotation owl:versionInfo 2021-10-19 --output imports/iao_import.owl.tmp.owl && mv imports/iao_import.owl.tmp.owl imports/iao_import.owl; fi
if [ true  = true ] && [ true  = true ]; then curl -L http://purl.obolibrary.org/obo/ro.owl --create-dirs -o mirror/ro.owl --retry 4 --max-time 200 && robot --catalog catalog-v001.xml convert -i mirror/ro.owl -o mirror/ro.owl.tmp.owl && mv mirror/ro.owl.tmp.owl mirror/ro.owl; fi
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   337  100   337    0     0    836      0 --:--:-- --:--:-- --:--:--   836
100  616k  100  616k    0     0   621k      0 --:--:-- --:--:-- --:--:-- 1652k
if [ true  = true ]; then cat tmp/seed.txt imports/ro_terms.txt | grep -v ^# | sort | uniq >  imports/ro_terms_combined.txt; fi
if [ true  = true ]; then robot --catalog catalog-v001.xml query -i mirror/ro.owl --update ../sparql/preprocess-module.ru \
    extract -T imports/ro_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
    query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
    annotate --ontology-iri http://purl.obolibrary.org/obo/plana/imports/ro_import.owl annotate -V http://purl.obolibrary.org/obo/plana/releases/2021-10-19/imports/ro_import.owl --annotation owl:versionInfo 2021-10-19 --output imports/ro_import.owl.tmp.owl && mv imports/ro_import.owl.tmp.owl imports/ro_import.owl; fi
if [ true  = true ] && [ true  = true ]; then curl -L http://purl.obolibrary.org/obo/bspo.owl --create-dirs -o mirror/bspo.owl --retry 4 --max-time 200 && robot --catalog catalog-v001.xml convert -i mirror/bspo.owl -o mirror/bspo.owl.tmp.owl && mv mirror/bspo.owl.tmp.owl mirror/bspo.owl; fi
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   359  100   359    0     0   1225      0 --:--:-- --:--:-- --:--:--  1229
100  620k  100  620k    0     0   578k      0  0:00:01  0:00:01 --:--:-- 1108k
if [ true  = true ]; then cat tmp/seed.txt imports/bspo_terms.txt | grep -v ^# | sort | uniq >  imports/bspo_terms_combined.txt; fi
if [ true  = true ]; then robot --catalog catalog-v001.xml query -i mirror/bspo.owl --update ../sparql/preprocess-module.ru \
    extract -T imports/bspo_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
    query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
    annotate --ontology-iri http://purl.obolibrary.org/obo/plana/imports/bspo_import.owl annotate -V http://purl.obolibrary.org/obo/plana/releases/2021-10-19/imports/bspo_import.owl --annotation owl:versionInfo 2021-10-19 --output imports/bspo_import.owl.tmp.owl && mv imports/bspo_import.owl.tmp.owl imports/bspo_import.owl; fi
if [ true  = true ] && [ true  = true ]; then robot --catalog catalog-v001.xml convert -I http://purl.obolibrary.org/obo/pato/pato-simple.owl -o mirror/pato.owl.tmp.owl && mv mirror/pato.owl.tmp.owl mirror/pato.owl; fi
[Fatal Error] :6:3: The element type "hr" must be terminated by the matching end-tag "</hr>".
org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://purl.obolibrary.org/obo/pato/pato-simple.owl
Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation.
The following parsers were tried:
1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@a3d9978
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@5d5f10b2
3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@69653e16
4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4983159f
6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@6b44435b
16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@77a98a6a
17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@68b6f0d6
18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d

Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@a3d9978
    Stack trace:
org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=1:column=7] Expecting rdf:RDF element.        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
[line=1:column=7] Expecting rdf:RDF element.        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451)
        org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201)
        com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
        com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
        com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl$NSContentDriver.scanRootElementHook(XMLNSDocumentScannerImpl.java:613)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3132)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:852)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
        com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@5d5f10b2
    Stack trace:
org.xml.sax.SAXParseException; systemId: http://purl.obolibrary.org/obo/pato/pato-simple.owl; lineNumber: 6; columnNumber: 3; The element type "hr" must be terminated by the matching end-tag "</hr>".        org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:70)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
The element type "hr" must be terminated by the matching end-tag "</hr>".        com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
        com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
        com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
        com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
        com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1473)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1749)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2967)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
        com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@69653e16
    Stack trace:
Encountered " <FULLIRI> "<html> "" at line 1, column 1.
Was expecting one of:
    "Ontology" ...
    "Prefix" ...
     (Line 0)        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:94)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Encountered " <FULLIRI> "<html> "" at line 1, column 1.
Was expecting one of:
    "Ontology" ...
    "Prefix" ...
            org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.generateParseException(OWLFunctionalSyntaxParser.java:3443)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.jj_consume_token(OWLFunctionalSyntaxParser.java:3363)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.Ontology(OWLFunctionalSyntaxParser.java:192)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.parse(OWLFunctionalSyntaxParser.java:171)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:92)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
    Stack trace:
org.openrdf.rio.RDFParseException: Relative URI 'html' cannot be resolved using the opaque base URI 'urn:default:baseUri:' [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Relative URI 'html' cannot be resolved using the opaque base URI 'urn:default:baseUri:' [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
        org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
        org.openrdf.rio.turtle.TurtleParser.reportError(TurtleParser.java:1355)
        org.openrdf.rio.helpers.RDFParserBase.resolveURI(RDFParserBase.java:412)
        org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:982)
        org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
        org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
        org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4983159f
    Stack trace:
Encountered '<html>' at line 1 column 1.  Expected either 'Ontology:' or 'Prefix:' (Line 1)        org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:120)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
    Stack trace:
org.openrdf.rio.RDFParseException: Not a valid (absolute) URI: html [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Not a valid (absolute) URI: html [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737)
        org.openrdf.rio.ntriples.NTriplesParser.reportFatalError(NTriplesParser.java:659)
        org.openrdf.rio.helpers.RDFParserBase.createURI(RDFParserBase.java:433)
        org.openrdf.rio.ntriples.NTriplesParser.createURI(NTriplesParser.java:566)
        org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:337)
        org.openrdf.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:123)
        org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:102)
        org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:60)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
Not a valid (absolute) URI: html        org.openrdf.model.impl.URIImpl.setURIString(URIImpl.java:79)
        org.openrdf.model.impl.URIImpl.<init>(URIImpl.java:68)
        org.openrdf.model.impl.ValueFactoryImpl.createURI(ValueFactoryImpl.java:50)
        org.openrdf.rio.helpers.RDFParserBase.createURI(RDFParserBase.java:430)
        org.openrdf.rio.ntriples.NTriplesParser.createURI(NTriplesParser.java:566)
        org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:337)
        org.openrdf.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:123)
        org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:102)
        org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:60)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
    Stack trace:
org.openrdf.rio.RDFParseException: Found IOException during parsing [line 1, column 2]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Found IOException during parsing [line 1, column 2]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
        org.openrdf.rio.rdfjson.RDFJSONParser.reportFatalError(RDFJSONParser.java:155)
        org.openrdf.rio.rdfjson.RDFJSONParser.parse(RDFJSONParser.java:96)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
    Stack trace:
org.openrdf.rio.RDFParseException: Relative URI 'html' cannot be resolved using the opaque base URI 'urn:default:baseUri:' [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Relative URI 'html' cannot be resolved using the opaque base URI 'urn:default:baseUri:' [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
        org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
        org.openrdf.rio.turtle.TurtleParser.reportError(TurtleParser.java:1355)
        org.openrdf.rio.helpers.RDFParserBase.resolveURI(RDFParserBase.java:412)
        org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:982)
        org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        org.openrdf.rio.trig.TriGParser.parseGraph(TriGParser.java:132)
        org.openrdf.rio.trig.TriGParser.parseStatement(TriGParser.java:119)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
    Stack trace:
org.openrdf.rio.RDFParseException: Not a valid (absolute) URI: html [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Not a valid (absolute) URI: html [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737)
        org.openrdf.rio.ntriples.NTriplesParser.reportFatalError(NTriplesParser.java:659)
        org.openrdf.rio.helpers.RDFParserBase.createURI(RDFParserBase.java:433)
        org.openrdf.rio.ntriples.NTriplesParser.createURI(NTriplesParser.java:566)
        org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:337)
        org.openrdf.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:280)
        org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:191)
        org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:130)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
Not a valid (absolute) URI: html        org.openrdf.model.impl.URIImpl.setURIString(URIImpl.java:79)
        org.openrdf.model.impl.URIImpl.<init>(URIImpl.java:68)
        org.openrdf.model.impl.ValueFactoryImpl.createURI(ValueFactoryImpl.java:50)
        org.openrdf.rio.helpers.RDFParserBase.createURI(RDFParserBase.java:430)
        org.openrdf.rio.ntriples.NTriplesParser.createURI(NTriplesParser.java:566)
        org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:337)
        org.openrdf.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:280)
        org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:191)
        org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:130)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
    Stack trace:
org.openrdf.rio.RDFParseException: File does not contain a binary RDF document        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
File does not contain a binary RDF document        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:424)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:693)
        org.openrdf.rio.binary.BinaryRDFParser.parse(BinaryRDFParser.java:87)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
    Stack trace:
org.openrdf.rio.RDFParseException: Could not parse JSONLD        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Could not parse JSONLD        com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:69)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
Unexpected character ('<' (code 60)): expected a valid value (number, String, array, object, 'true', 'false' or 'null')
 at [Source: (BufferedReader); line: 1, column: 2]        com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1798)
        com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:663)
        com.fasterxml.jackson.core.base.ParserMinimalBase._reportUnexpectedChar(ParserMinimalBase.java:561)
        com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1892)
        com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:747)
        com.github.jsonldjava.utils.JsonUtils.fromReader(JsonUtils.java:107)
        com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:88)
        com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:68)
        com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:65)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
    Stack trace:
org.openrdf.rio.RDFParseException: Relative URI 'html' cannot be resolved using the opaque base URI 'urn:default:baseUri:' [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Relative URI 'html' cannot be resolved using the opaque base URI 'urn:default:baseUri:' [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
        org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
        org.openrdf.rio.turtle.TurtleParser.reportError(TurtleParser.java:1355)
        org.openrdf.rio.helpers.RDFParserBase.resolveURI(RDFParserBase.java:412)
        org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:982)
        org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
        org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
        org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
    Stack trace:
org.openrdf.rio.RDFParseException: unqualified property element <head> not allowed [line 2, column 14]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
unqualified property element <head> not allowed [line 2, column 14]        org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
        org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
        org.openrdf.rio.rdfxml.RDFXMLParser.reportError(RDFXMLParser.java:1269)
        org.openrdf.rio.rdfxml.RDFXMLParser.processPropertyElt(RDFXMLParser.java:770)
        org.openrdf.rio.rdfxml.RDFXMLParser.startElement(RDFXMLParser.java:531)
        org.openrdf.rio.rdfxml.SAXFilter.reportDeferredStartElement(SAXFilter.java:334)
        org.openrdf.rio.rdfxml.SAXFilter.startElement(SAXFilter.java:257)
        com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
        com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
    Stack trace:
org.openrdf.rio.RDFParseException: The element type "hr" must be terminated by the matching end-tag "</hr>". [line 6, column 3]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
The element type "hr" must be terminated by the matching end-tag "</hr>". [line 6, column 3]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737)
        org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123)
        org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90)
        org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
The element type "hr" must be terminated by the matching end-tag "</hr>".        com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
        com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
        com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
        com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
        com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1473)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1749)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2967)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
        com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
        com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@6b44435b
    Stack trace:
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <INTEGER> "307 "" at line 2, column 14.
Was expecting:
    "." ...
            org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:105)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Encountered " <INTEGER> "307 "" at line 2, column 14.
Was expecting:
    "." ...
            org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1548)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1430)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:151)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:98)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@77a98a6a
    Stack trace:
LINENO: 1 - Could not find tag separator ':' in line.
LINE: <html>        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
LINENO: 1 - Could not find tag separator ':' in line.
LINE: <html>        org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1465)
        org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:861)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:503)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:496)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderFrame(OBOFormatParser.java:480)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:345)
        org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:307)
        org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:259)
        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76)
        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@68b6f0d6
    Stack trace:
org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" "<html> "" at line 1, column 1.
Was expecting:
    <EOF>
            org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:289)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
Encountered " ">" "<html> "" at line 1, column 1.
Was expecting:
    <EOF>
            org.semanticweb.owlapi.krss2.parser.KRSS2Parser.generateParseException(KRSS2Parser.java:3187)
        org.semanticweb.owlapi.krss2.parser.KRSS2Parser.jj_consume_token(KRSS2Parser.java:3040)
        org.semanticweb.owlapi.krss2.parser.KRSS2Parser.parse(KRSS2Parser.java:141)
        org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:286)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
    Stack trace:
org.openrdf.rio.RDFParseException: org.xml.sax.SAXParseException; lineNumber: 6; columnNumber: 3; The element type "hr" must be terminated by the matching end-tag "</hr>".        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:491)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:543)
org.xml.sax.SAXParseException; lineNumber: 6; columnNumber: 3; The element type "hr" must be terminated by the matching end-tag "</hr>".        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:111)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
org.xml.sax.SAXParseException; lineNumber: 6; columnNumber: 3; The element type "hr" must be terminated by the matching end-tag "</hr>".        org.semarglproject.rdf.rdfa.RdfaParser.processException(RdfaParser.java:1141)
        org.semarglproject.source.XmlSource.process(XmlSource.java:50)
        org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
The element type "hr" must be terminated by the matching end-tag "</hr>".        com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1239)
        org.semarglproject.source.XmlSource.process(XmlSource.java:48)
        org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
make: *** [Makefile:325: mirror/pato.owl] Error 1
rm imports/iao_terms_combined.txt imports/go_terms_combined.txt imports/bspo_terms_combined.txt imports/ro_terms_combined.txt```
matentzn commented 2 years ago

Hey @srobb1 this has nothing to do with ODK, but the problem is truly puzzling.

If you get no response in a few days ping me again. Workaround:

use the raw.github URL in your plana-odk.yaml file instead the PURL, the sh run.sh make update_repo (twice) then try again.

srobb1 commented 2 years ago

Thanks @matentzn. I am always excited to find weird little bugs :)