diff --git a/README.md b/README.md index 1859efdd7..901da9c1d 100644 --- a/README.md +++ b/README.md @@ -42,6 +42,12 @@ This expects the Jena tools to be available in your $PATH. e.g. `export PATH="$J ./convertToOneTurtle.sh -p uniprot ``` +An other option is to build the inbuild converter and use that. + +```bash +mvn package +java -jar target/sparql-examples-util-1.0.0-SNAPSHOT-uber.jar -i examples/ -p all -f jsonld +``` # Querying for queries diff --git a/convertToOneTurtle.sh b/convertToOneTurtle.sh index d0c7c7676..39e7ac861 100755 --- a/convertToOneTurtle.sh +++ b/convertToOneTurtle.sh @@ -35,14 +35,10 @@ if [ -f examples_${project}.ttl ] then rm examples_${project}.ttl fi -echo "# baseURI: http://sparql.${project}.org/.well-known/sparql-examples#" > examples_${project}.ttl -echo "# imports: http://purl.uniprot.org/core/ " >> examples_${project}.ttl -echo "# prefix: ex" >> examples_${project}.ttl - if which riot then - cat prefixes.ttl $project/*.ttl | riot --syntax=turtle --formatted=turtle > examples_${project}.ttl + cat examples/prefixes.ttl examples/$project/*.ttl | riot --syntax=turtle --formatted=turtle > examples_${project}.ttl else - rapper -q -i turtle <(cat ${project}/[1-9]*.ttl prefixes.ttl) -o turtle > examples_${project}.ttl + rapper -q -i turtle <(cat examples/prefixes.ttl examples/${project}/*.ttl) -o turtle > examples_${project}.ttl fi diff --git a/convertToRDFXml.sh b/convertToRDFXml.sh deleted file mode 100755 index b3eec64f2..000000000 --- a/convertToRDFXml.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/bash -riot --formatted=rdfxml *.ttl | xz > examples.rdf.xz - diff --git a/bgee/1.ttl b/examples/bgee/1.ttl similarity index 100% rename from bgee/1.ttl rename to examples/bgee/1.ttl diff --git a/bgee/10.ttl b/examples/bgee/10.ttl similarity index 100% rename from bgee/10.ttl rename to examples/bgee/10.ttl diff --git a/bgee/11-a.ttl b/examples/bgee/11-a.ttl similarity index 100% rename from bgee/11-a.ttl rename to examples/bgee/11-a.ttl diff --git a/bgee/11.ttl b/examples/bgee/11.ttl similarity index 100% rename from bgee/11.ttl rename to examples/bgee/11.ttl diff --git a/bgee/12-a.ttl b/examples/bgee/12-a.ttl similarity index 100% rename from bgee/12-a.ttl rename to examples/bgee/12-a.ttl diff --git a/bgee/12.ttl b/examples/bgee/12.ttl similarity index 100% rename from bgee/12.ttl rename to examples/bgee/12.ttl diff --git a/bgee/13.ttl b/examples/bgee/13.ttl similarity index 100% rename from bgee/13.ttl rename to examples/bgee/13.ttl diff --git a/bgee/14.ttl b/examples/bgee/14.ttl similarity index 100% rename from bgee/14.ttl rename to examples/bgee/14.ttl diff --git a/bgee/15.ttl b/examples/bgee/15.ttl similarity index 100% rename from bgee/15.ttl rename to examples/bgee/15.ttl diff --git a/bgee/2.ttl b/examples/bgee/2.ttl similarity index 100% rename from bgee/2.ttl rename to examples/bgee/2.ttl diff --git a/bgee/3.ttl b/examples/bgee/3.ttl similarity index 100% rename from bgee/3.ttl rename to examples/bgee/3.ttl diff --git a/bgee/4.ttl b/examples/bgee/4.ttl similarity index 100% rename from bgee/4.ttl rename to examples/bgee/4.ttl diff --git a/bgee/5.ttl b/examples/bgee/5.ttl similarity index 100% rename from bgee/5.ttl rename to examples/bgee/5.ttl diff --git a/bgee/6.ttl b/examples/bgee/6.ttl similarity index 100% rename from bgee/6.ttl rename to examples/bgee/6.ttl diff --git a/bgee/7.ttl b/examples/bgee/7.ttl similarity index 100% rename from bgee/7.ttl rename to examples/bgee/7.ttl diff --git a/bgee/8-a.ttl b/examples/bgee/8-a.ttl similarity index 100% rename from bgee/8-a.ttl rename to examples/bgee/8-a.ttl diff --git a/bgee/8-b.ttl b/examples/bgee/8-b.ttl similarity index 100% rename from bgee/8-b.ttl rename to examples/bgee/8-b.ttl diff --git a/bgee/8.ttl b/examples/bgee/8.ttl similarity index 100% rename from bgee/8.ttl rename to examples/bgee/8.ttl diff --git a/bgee/9.ttl b/examples/bgee/9.ttl similarity index 100% rename from bgee/9.ttl rename to examples/bgee/9.ttl diff --git a/bgee/prefixes.ttl b/examples/bgee/prefixes.ttl similarity index 100% rename from bgee/prefixes.ttl rename to examples/bgee/prefixes.ttl diff --git a/glyconnect/.gitkeep b/examples/glyconnect/.gitkeep similarity index 100% rename from glyconnect/.gitkeep rename to examples/glyconnect/.gitkeep diff --git a/glyconnect/1.ttl b/examples/glyconnect/1.ttl similarity index 100% rename from glyconnect/1.ttl rename to examples/glyconnect/1.ttl diff --git a/glyconnect/2.ttl b/examples/glyconnect/2.ttl similarity index 100% rename from glyconnect/2.ttl rename to examples/glyconnect/2.ttl diff --git a/glyconnect/3.ttl b/examples/glyconnect/3.ttl similarity index 100% rename from glyconnect/3.ttl rename to examples/glyconnect/3.ttl diff --git a/glyconnect/4.ttl b/examples/glyconnect/4.ttl similarity index 100% rename from glyconnect/4.ttl rename to examples/glyconnect/4.ttl diff --git a/glyconnect/5.ttl b/examples/glyconnect/5.ttl similarity index 100% rename from glyconnect/5.ttl rename to examples/glyconnect/5.ttl diff --git a/hamap/1.ttl b/examples/hamap/1.ttl similarity index 100% rename from hamap/1.ttl rename to examples/hamap/1.ttl diff --git a/hamap/2.ttl b/examples/hamap/2.ttl similarity index 100% rename from hamap/2.ttl rename to examples/hamap/2.ttl diff --git a/hamap/3.ttl b/examples/hamap/3.ttl similarity index 100% rename from hamap/3.ttl rename to examples/hamap/3.ttl diff --git a/hamap/4.ttl b/examples/hamap/4.ttl similarity index 100% rename from hamap/4.ttl rename to examples/hamap/4.ttl diff --git a/nextprot/NXQ_00001.ttl b/examples/nextprot/NXQ_00001.ttl similarity index 100% rename from nextprot/NXQ_00001.ttl rename to examples/nextprot/NXQ_00001.ttl diff --git a/nextprot/NXQ_00002.ttl b/examples/nextprot/NXQ_00002.ttl similarity index 100% rename from nextprot/NXQ_00002.ttl rename to examples/nextprot/NXQ_00002.ttl diff --git a/nextprot/NXQ_00003.ttl b/examples/nextprot/NXQ_00003.ttl similarity index 100% rename from nextprot/NXQ_00003.ttl rename to examples/nextprot/NXQ_00003.ttl diff --git a/nextprot/NXQ_00004.ttl b/examples/nextprot/NXQ_00004.ttl similarity index 100% rename from nextprot/NXQ_00004.ttl rename to examples/nextprot/NXQ_00004.ttl diff --git a/nextprot/NXQ_00005.ttl b/examples/nextprot/NXQ_00005.ttl similarity index 100% rename from nextprot/NXQ_00005.ttl rename to examples/nextprot/NXQ_00005.ttl diff --git a/nextprot/NXQ_00006.ttl b/examples/nextprot/NXQ_00006.ttl similarity index 100% rename from nextprot/NXQ_00006.ttl rename to examples/nextprot/NXQ_00006.ttl diff --git a/nextprot/NXQ_00007.ttl b/examples/nextprot/NXQ_00007.ttl similarity index 100% rename from nextprot/NXQ_00007.ttl rename to examples/nextprot/NXQ_00007.ttl diff --git a/nextprot/NXQ_00008.ttl b/examples/nextprot/NXQ_00008.ttl similarity index 100% rename from nextprot/NXQ_00008.ttl rename to examples/nextprot/NXQ_00008.ttl diff --git a/nextprot/NXQ_00009.ttl b/examples/nextprot/NXQ_00009.ttl similarity index 100% rename from nextprot/NXQ_00009.ttl rename to examples/nextprot/NXQ_00009.ttl diff --git a/nextprot/NXQ_00010.ttl b/examples/nextprot/NXQ_00010.ttl similarity index 100% rename from nextprot/NXQ_00010.ttl rename to examples/nextprot/NXQ_00010.ttl diff --git a/nextprot/NXQ_00011.ttl b/examples/nextprot/NXQ_00011.ttl similarity index 100% rename from nextprot/NXQ_00011.ttl rename to examples/nextprot/NXQ_00011.ttl diff --git a/nextprot/NXQ_00012.ttl b/examples/nextprot/NXQ_00012.ttl similarity index 100% rename from nextprot/NXQ_00012.ttl rename to examples/nextprot/NXQ_00012.ttl diff --git a/nextprot/NXQ_00013.ttl b/examples/nextprot/NXQ_00013.ttl similarity index 100% rename from nextprot/NXQ_00013.ttl rename to examples/nextprot/NXQ_00013.ttl diff --git a/nextprot/NXQ_00014.ttl b/examples/nextprot/NXQ_00014.ttl similarity index 100% rename from nextprot/NXQ_00014.ttl rename to examples/nextprot/NXQ_00014.ttl diff --git a/nextprot/NXQ_00015.ttl b/examples/nextprot/NXQ_00015.ttl similarity index 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similarity index 100% rename from nextprot/NXQ_00021.ttl rename to examples/nextprot/NXQ_00021.ttl diff --git a/nextprot/NXQ_00022.ttl b/examples/nextprot/NXQ_00022.ttl similarity index 100% rename from nextprot/NXQ_00022.ttl rename to examples/nextprot/NXQ_00022.ttl diff --git a/nextprot/NXQ_00023.ttl b/examples/nextprot/NXQ_00023.ttl similarity index 100% rename from nextprot/NXQ_00023.ttl rename to examples/nextprot/NXQ_00023.ttl diff --git a/nextprot/NXQ_00024.ttl b/examples/nextprot/NXQ_00024.ttl similarity index 100% rename from nextprot/NXQ_00024.ttl rename to examples/nextprot/NXQ_00024.ttl diff --git a/nextprot/NXQ_00025.ttl b/examples/nextprot/NXQ_00025.ttl similarity index 100% rename from nextprot/NXQ_00025.ttl rename to examples/nextprot/NXQ_00025.ttl diff --git a/nextprot/NXQ_00026.ttl b/examples/nextprot/NXQ_00026.ttl similarity index 100% rename from nextprot/NXQ_00026.ttl rename to examples/nextprot/NXQ_00026.ttl diff --git a/nextprot/NXQ_00027.ttl 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similarity index 100% rename from nextprot/NXQ_00058.ttl rename to examples/nextprot/NXQ_00058.ttl diff --git a/nextprot/NXQ_00059.ttl b/examples/nextprot/NXQ_00059.ttl similarity index 100% rename from nextprot/NXQ_00059.ttl rename to examples/nextprot/NXQ_00059.ttl diff --git a/nextprot/NXQ_00060.ttl b/examples/nextprot/NXQ_00060.ttl similarity index 100% rename from nextprot/NXQ_00060.ttl rename to examples/nextprot/NXQ_00060.ttl diff --git a/nextprot/NXQ_00061.ttl b/examples/nextprot/NXQ_00061.ttl similarity index 100% rename from nextprot/NXQ_00061.ttl rename to examples/nextprot/NXQ_00061.ttl diff --git a/nextprot/NXQ_00062.ttl b/examples/nextprot/NXQ_00062.ttl similarity index 100% rename from nextprot/NXQ_00062.ttl rename to examples/nextprot/NXQ_00062.ttl diff --git a/nextprot/NXQ_00063.ttl b/examples/nextprot/NXQ_00063.ttl similarity index 100% rename from nextprot/NXQ_00063.ttl rename to examples/nextprot/NXQ_00063.ttl diff --git a/nextprot/NXQ_00064.ttl 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a/nextprot/NXQ_00070.ttl b/examples/nextprot/NXQ_00070.ttl similarity index 100% rename from nextprot/NXQ_00070.ttl rename to examples/nextprot/NXQ_00070.ttl diff --git a/nextprot/NXQ_00072.ttl b/examples/nextprot/NXQ_00072.ttl similarity index 100% rename from nextprot/NXQ_00072.ttl rename to examples/nextprot/NXQ_00072.ttl diff --git a/nextprot/NXQ_00073.ttl b/examples/nextprot/NXQ_00073.ttl similarity index 100% rename from nextprot/NXQ_00073.ttl rename to examples/nextprot/NXQ_00073.ttl diff --git a/nextprot/NXQ_00074.ttl b/examples/nextprot/NXQ_00074.ttl similarity index 100% rename from nextprot/NXQ_00074.ttl rename to examples/nextprot/NXQ_00074.ttl diff --git a/nextprot/NXQ_00075.ttl b/examples/nextprot/NXQ_00075.ttl similarity index 100% rename from nextprot/NXQ_00075.ttl rename to examples/nextprot/NXQ_00075.ttl diff --git a/nextprot/NXQ_00076.ttl b/examples/nextprot/NXQ_00076.ttl similarity index 100% rename from nextprot/NXQ_00076.ttl rename to 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rename from uniprot/43_patents_used_in_uniprot_granted_twenty_years_in_the_past.ttl rename to examples/uniprot/43_patents_used_in_uniprot_granted_twenty_years_in_the_past.ttl diff --git a/uniprot/44_rhea_interpro_union_in_uniprot.ttl b/examples/uniprot/44_rhea_interpro_union_in_uniprot.ttl similarity index 100% rename from uniprot/44_rhea_interpro_union_in_uniprot.ttl rename to examples/uniprot/44_rhea_interpro_union_in_uniprot.ttl diff --git a/uniprot/45_drugs_targeting_human_sterol_metabolism_enzymes.ttl b/examples/uniprot/45_drugs_targeting_human_sterol_metabolism_enzymes.ttl similarity index 100% rename from uniprot/45_drugs_targeting_human_sterol_metabolism_enzymes.ttl rename to examples/uniprot/45_drugs_targeting_human_sterol_metabolism_enzymes.ttl diff --git a/uniprot/46_duck_pictures_via_eepa_and_taxonomy.ttl b/examples/uniprot/46_duck_pictures_via_eepa_and_taxonomy.ttl similarity index 100% rename from uniprot/46_duck_pictures_via_eepa_and_taxonomy.ttl rename to examples/uniprot/46_duck_pictures_via_eepa_and_taxonomy.ttl diff --git a/uniprot/47_protein_with_transmembrane_region_with_close_by_alanine.ttl b/examples/uniprot/47_protein_with_transmembrane_region_with_close_by_alanine.ttl similarity index 100% rename from uniprot/47_protein_with_transmembrane_region_with_close_by_alanine.ttl rename to examples/uniprot/47_protein_with_transmembrane_region_with_close_by_alanine.ttl diff --git a/uniprot/48_glycosylation_sites_and_glycans.ttl b/examples/uniprot/48_glycosylation_sites_and_glycans.ttl similarity index 100% rename from uniprot/48_glycosylation_sites_and_glycans.ttl rename to examples/uniprot/48_glycosylation_sites_and_glycans.ttl diff --git a/uniprot/49_tissues_where_genes_metabolizing_cholestrol_are_expressed.ttl b/examples/uniprot/49_tissues_where_genes_metabolizing_cholestrol_are_expressed.ttl similarity index 100% rename from uniprot/49_tissues_where_genes_metabolizing_cholestrol_are_expressed.ttl rename to examples/uniprot/49_tissues_where_genes_metabolizing_cholestrol_are_expressed.ttl diff --git a/uniprot/4_uniprot_mnemonic_id.ttl b/examples/uniprot/4_uniprot_mnemonic_id.ttl similarity index 100% rename from uniprot/4_uniprot_mnemonic_id.ttl rename to examples/uniprot/4_uniprot_mnemonic_id.ttl diff --git a/uniprot/50_tissues_where_genes_sphingosines_are_expressed.ttl b/examples/uniprot/50_tissues_where_genes_sphingosines_are_expressed.ttl similarity index 100% rename from uniprot/50_tissues_where_genes_sphingosines_are_expressed.ttl rename to examples/uniprot/50_tissues_where_genes_sphingosines_are_expressed.ttl diff --git a/uniprot/51_all_proteins_linked_to_arachidonate.ttl b/examples/uniprot/51_all_proteins_linked_to_arachidonate.ttl similarity index 100% rename from uniprot/51_all_proteins_linked_to_arachidonate.ttl rename to examples/uniprot/51_all_proteins_linked_to_arachidonate.ttl diff --git a/uniprot/52_drugs_targeting_sterol_metabolism.ttl b/examples/uniprot/52_drugs_targeting_sterol_metabolism.ttl similarity index 100% rename from uniprot/52_drugs_targeting_sterol_metabolism.ttl rename to examples/uniprot/52_drugs_targeting_sterol_metabolism.ttl diff --git a/uniprot/53_mouse_homologs_of_sterol_enzymes_via_omabrowser.ttl b/examples/uniprot/53_mouse_homologs_of_sterol_enzymes_via_omabrowser.ttl similarity index 100% rename from uniprot/53_mouse_homologs_of_sterol_enzymes_via_omabrowser.ttl rename to examples/uniprot/53_mouse_homologs_of_sterol_enzymes_via_omabrowser.ttl diff --git a/uniprot/54_binding_sites_for_ligands_similar_to_heme_sachem.ttl b/examples/uniprot/54_binding_sites_for_ligands_similar_to_heme_sachem.ttl similarity index 100% rename from uniprot/54_binding_sites_for_ligands_similar_to_heme_sachem.ttl rename to examples/uniprot/54_binding_sites_for_ligands_similar_to_heme_sachem.ttl diff --git a/uniprot/55_metal_or_sulphur_cluster_binding_sites_experimental.ttl b/examples/uniprot/55_metal_or_sulphur_cluster_binding_sites_experimental.ttl similarity index 100% rename from uniprot/55_metal_or_sulphur_cluster_binding_sites_experimental.ttl rename to examples/uniprot/55_metal_or_sulphur_cluster_binding_sites_experimental.ttl diff --git a/uniprot/56_enzymes_that_have_a_known_allosteric_effect.ttl b/examples/uniprot/56_enzymes_that_have_a_known_allosteric_effect.ttl similarity index 100% rename from uniprot/56_enzymes_that_have_a_known_allosteric_effect.ttl rename to examples/uniprot/56_enzymes_that_have_a_known_allosteric_effect.ttl diff --git a/uniprot/57_map_pdb_identifiers_plus_chains_to_uniprot.ttl b/examples/uniprot/57_map_pdb_identifiers_plus_chains_to_uniprot.ttl similarity index 100% rename from uniprot/57_map_pdb_identifiers_plus_chains_to_uniprot.ttl rename to examples/uniprot/57_map_pdb_identifiers_plus_chains_to_uniprot.ttl diff --git a/uniprot/58_uniprot_to_HGNC_and_symbols.ttl b/examples/uniprot/58_uniprot_to_HGNC_and_symbols.ttl similarity index 100% rename from uniprot/58_uniprot_to_HGNC_and_symbols.ttl rename to examples/uniprot/58_uniprot_to_HGNC_and_symbols.ttl diff --git a/uniprot/59_all_isoforms_for_a_given_proteome.ttl b/examples/uniprot/59_all_isoforms_for_a_given_proteome.ttl similarity index 100% rename from uniprot/59_all_isoforms_for_a_given_proteome.ttl rename to examples/uniprot/59_all_isoforms_for_a_given_proteome.ttl diff --git a/uniprot/5_mapping_to_PDB.ttl b/examples/uniprot/5_mapping_to_PDB.ttl similarity index 100% rename from uniprot/5_mapping_to_PDB.ttl rename to examples/uniprot/5_mapping_to_PDB.ttl diff --git a/uniprot/60_enzymes_working_on_substrate_with_Cholestene_backbone.ttl b/examples/uniprot/60_enzymes_working_on_substrate_with_Cholestene_backbone.ttl similarity index 100% rename from uniprot/60_enzymes_working_on_substrate_with_Cholestene_backbone.ttl rename to examples/uniprot/60_enzymes_working_on_substrate_with_Cholestene_backbone.ttl diff --git a/uniprot/61_Gene_Protein_Reaction_sets.ttl b/examples/uniprot/61_Gene_Protein_Reaction_sets.ttl similarity index 100% rename from uniprot/61_Gene_Protein_Reaction_sets.ttl rename to examples/uniprot/61_Gene_Protein_Reaction_sets.ttl diff --git a/uniprot/6_cross_ref_in_category_3D.ttl b/examples/uniprot/6_cross_ref_in_category_3D.ttl similarity index 100% rename from uniprot/6_cross_ref_in_category_3D.ttl rename to examples/uniprot/6_cross_ref_in_category_3D.ttl diff --git a/uniprot/7_swissprot_with_rec_protein_name_if_pref_gene_name_contains_word_DNA.ttl b/examples/uniprot/7_swissprot_with_rec_protein_name_if_pref_gene_name_contains_word_DNA.ttl similarity index 100% rename from uniprot/7_swissprot_with_rec_protein_name_if_pref_gene_name_contains_word_DNA.ttl rename to examples/uniprot/7_swissprot_with_rec_protein_name_if_pref_gene_name_contains_word_DNA.ttl diff --git a/uniprot/8_prefered_gene_name_of_human_disease_related_proteins.ttl b/examples/uniprot/8_prefered_gene_name_of_human_disease_related_proteins.ttl similarity index 100% rename from uniprot/8_prefered_gene_name_of_human_disease_related_proteins.ttl rename to examples/uniprot/8_prefered_gene_name_of_human_disease_related_proteins.ttl diff --git a/uniprot/9_human_variant_loss_of_function.ttl b/examples/uniprot/9_human_variant_loss_of_function.ttl similarity index 100% rename from uniprot/9_human_variant_loss_of_function.ttl rename to examples/uniprot/9_human_variant_loss_of_function.ttl diff --git a/uniprot/diseases_involving_enzymes.ttl b/examples/uniprot/diseases_involving_enzymes.ttl similarity index 100% rename from uniprot/diseases_involving_enzymes.ttl rename to examples/uniprot/diseases_involving_enzymes.ttl diff --git a/uniprot/diseases_involving_enzymes_located_in_mitochondrion.ttl b/examples/uniprot/diseases_involving_enzymes_located_in_mitochondrion.ttl similarity index 100% rename from uniprot/diseases_involving_enzymes_located_in_mitochondrion.ttl rename to examples/uniprot/diseases_involving_enzymes_located_in_mitochondrion.ttl diff --git a/uniprot/diseases_related_to_mutation_in_active_site.ttl b/examples/uniprot/diseases_related_to_mutation_in_active_site.ttl similarity index 100% rename from uniprot/diseases_related_to_mutation_in_active_site.ttl rename to examples/uniprot/diseases_related_to_mutation_in_active_site.ttl diff --git a/uniprot/distinct_extinct_organisms_in_uniprotkb.ttl b/examples/uniprot/distinct_extinct_organisms_in_uniprotkb.ttl similarity index 100% rename from uniprot/distinct_extinct_organisms_in_uniprotkb.ttl rename to examples/uniprot/distinct_extinct_organisms_in_uniprotkb.ttl diff --git a/uniprot/draft_human_metabolome.ttl b/examples/uniprot/draft_human_metabolome.ttl similarity index 100% rename from uniprot/draft_human_metabolome.ttl rename to examples/uniprot/draft_human_metabolome.ttl diff --git a/uniprot/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl b/examples/uniprot/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl similarity index 100% rename from uniprot/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl rename to examples/uniprot/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl diff --git a/uniprot/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl b/examples/uniprot/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl similarity index 100% rename from uniprot/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl rename to examples/uniprot/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl diff --git a/uniprot/enzymes_interacting_with_molecules_similar_to_dopamine.ttl b/examples/uniprot/enzymes_interacting_with_molecules_similar_to_dopamine.ttl similarity index 100% rename from uniprot/enzymes_interacting_with_molecules_similar_to_dopamine.ttl rename to examples/uniprot/enzymes_interacting_with_molecules_similar_to_dopamine.ttl diff --git a/uniprot/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl b/examples/uniprot/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl similarity index 100% rename from uniprot/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl rename to examples/uniprot/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl diff --git a/uniprot/enzymes_mapping_to_PDB.ttl b/examples/uniprot/enzymes_mapping_to_PDB.ttl similarity index 100% rename from uniprot/enzymes_mapping_to_PDB.ttl rename to examples/uniprot/enzymes_mapping_to_PDB.ttl diff --git a/uniprot/enzymes_with_at_least_two_transmembrane_domains.ttl b/examples/uniprot/enzymes_with_at_least_two_transmembrane_domains.ttl similarity index 100% rename from uniprot/enzymes_with_at_least_two_transmembrane_domains.ttl rename to examples/uniprot/enzymes_with_at_least_two_transmembrane_domains.ttl diff --git a/uniprot/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl b/examples/uniprot/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl similarity index 100% rename from uniprot/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl rename to examples/uniprot/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl diff --git a/uniprot/enzymes_with_mutagenesis_affecting_active_site.ttl b/examples/uniprot/enzymes_with_mutagenesis_affecting_active_site.ttl similarity index 100% rename from uniprot/enzymes_with_mutagenesis_affecting_active_site.ttl rename to examples/uniprot/enzymes_with_mutagenesis_affecting_active_site.ttl diff --git a/uniprot/enzymes_with_tyrosine_as_active_site.ttl b/examples/uniprot/enzymes_with_tyrosine_as_active_site.ttl similarity index 100% rename from uniprot/enzymes_with_tyrosine_as_active_site.ttl rename to examples/uniprot/enzymes_with_tyrosine_as_active_site.ttl diff --git a/uniprot/genetic_disease_related_proteins.ttl b/examples/uniprot/genetic_disease_related_proteins.ttl similarity index 100% rename from uniprot/genetic_disease_related_proteins.ttl rename to examples/uniprot/genetic_disease_related_proteins.ttl diff --git a/uniprot/mnemonic_also_known_as_id.ttl b/examples/uniprot/mnemonic_also_known_as_id.ttl similarity index 100% rename from uniprot/mnemonic_also_known_as_id.ttl rename to examples/uniprot/mnemonic_also_known_as_id.ttl diff --git a/pom.xml b/pom.xml index fc8fbf80a..77a0dbd85 100644 --- a/pom.xml +++ b/pom.xml @@ -61,22 +61,26 @@ org.eclipse.rdf4j rdf4j-rio-turtle - test + + + org.eclipse.rdf4j + rdf4j-rio-rdfxml + + + org.eclipse.rdf4j + rdf4j-rio-jsonld org.eclipse.rdf4j rdf4j-model - test org.eclipse.rdf4j rdf4j-model-api - test org.eclipse.rdf4j rdf4j-model-vocabulary - test org.eclipse.rdf4j @@ -103,6 +107,11 @@ rdf4j-shacl test + + info.picocli + picocli + 4.7.6 + scm:git:git://github.com:sib-swiss/sparql-examplesj.git @@ -120,12 +129,47 @@ maven-surefire-plugin 3.0.0-M6 + + org.apache.maven.plugins + maven-shade-plugin + 3.2.4 + + + + *:* + + META-INF/*.SF + META-INF/*.DSA + META-INF/*.RSA + + + + + + + package + + shade + + + true + uber + + + + swiss.sib.rdf.sparql.examples.Converter + + + + + + - ${basedir}/ + ${basedir}/examples/ - **/*.ttl + **/*.ttl target/**/*.ttl diff --git a/src/main/java/swiss/sib/rdf/sparql/examples/Converter.java b/src/main/java/swiss/sib/rdf/sparql/examples/Converter.java new file mode 100644 index 000000000..2a3ad8e80 --- /dev/null +++ b/src/main/java/swiss/sib/rdf/sparql/examples/Converter.java @@ -0,0 +1,121 @@ +package swiss.sib.rdf.sparql.examples; + +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Set; +import java.util.regex.Pattern; +import java.util.stream.Stream; + +import org.eclipse.rdf4j.model.Model; +import org.eclipse.rdf4j.model.impl.LinkedHashModel; +import org.eclipse.rdf4j.rio.RDFFormat; +import org.eclipse.rdf4j.rio.RDFHandlerException; +import org.eclipse.rdf4j.rio.RDFParseException; +import org.eclipse.rdf4j.rio.RDFParser; +import org.eclipse.rdf4j.rio.Rio; +import org.eclipse.rdf4j.rio.helpers.StatementCollector; + +import picocli.CommandLine; +import picocli.CommandLine.Option; + +public class Converter { + private static enum Failure { + CANT_READ_INPUT_DIRECTORY(1), CANT_PARSE_EXAMPLE(2), CANT_READ_EXAMPLE(3); + + private final int exitCode; + + Failure(int i) { + this.exitCode = i; + } + + void exit(Exception e) { + System.err.println(e.getMessage()); + System.exit(exitCode); + } + + } + + private final Set outputFormats = Set.of(RDFFormat.TURTLE, RDFFormat.RDFXML, RDFFormat.NTRIPLES, RDFFormat.JSONLD, RDFFormat.NDJSONLD); + + @Option(names = { "-f", + "--format" }, paramLabel = "output RDF format", description = "the format that the example queries with their prefixes should be concattenated into", defaultValue = "ttl") + private String outputFormat; + + @Option(names = { "-i", + "--input-directory" }, paramLabel = "directory containing example files to convert", description = "The root directory where the examples and their prefixes can be found.", required = true) + private Path inputDirectory; + + @Option(names = { "-h", "--help" }, usageHelp = true, description = "display this help message") + private boolean usageHelpRequested; + + @Option(names = { "-p", "--project" }, paramLabel = "projects to convert", defaultValue = "all") + private String projects; + + public static void main(String[] args) { + Converter converter = new Converter(); + CommandLine commandLine = new CommandLine(converter); + commandLine.parseArgs(args); + if (commandLine.isUsageHelpRequested()) { + commandLine.usage(System.out); + return; + } else if (commandLine.isVersionHelpRequested()) { + commandLine.printVersionHelp(System.out); + return; + } else { + converter.convert(); + } + } + + private static final Pattern COMMA = Pattern.compile(",", Pattern.LITERAL); + + private void convert() { +// String commonPrefixes = extractPrefixes(FindFiles.commonPrefixes()); + Model model = new LinkedHashModel(); + if ("all".equals(projects)) { + try (Stream list = Files.list(inputDirectory)) { + parse(list, model); + } catch (IOException e) { + Failure.CANT_READ_INPUT_DIRECTORY.exit(e); + } + } else { + try (Stream list = COMMA.splitAsStream(projects).map(inputDirectory::resolve)) { + parse(list, model); + } + } + print(model); + } + + private void parse(Stream paths, Model model) { + Stream.concat(FindFiles.prefixFile(inputDirectory), paths.flatMap(arg0 -> { + try { + return Stream.concat(FindFiles.prefixFile(arg0), FindFiles.sparqlExamples(arg0)); + } catch (IOException e) { + Failure.CANT_READ_EXAMPLE.exit(e); + throw new RuntimeException(e); + } + })).filter(Files::exists).forEach(p -> { + parseTurtleFileIntoModel(model, p); + }); + } + + private void parseTurtleFileIntoModel(Model model, Path p) { + RDFParser rdfParser = Rio.createParser(RDFFormat.TURTLE); + + rdfParser.setRDFHandler(new StatementCollector(model)); + try (InputStream is = Files.newInputStream(p)) { + rdfParser.parse(is); + } catch (RDFParseException | RDFHandlerException e) { + Failure.CANT_PARSE_EXAMPLE.exit(e); + } catch (IOException e) { + Failure.CANT_READ_EXAMPLE.exit(e); + } + } + + private void print(Model model) { + Rio.write(model, System.out, + RDFFormat.matchFileName("a." + outputFormat, outputFormats).orElse(RDFFormat.TURTLE)); + } + +} diff --git a/src/main/java/swiss/sib/rdf/sparql/examples/FindFiles.java b/src/main/java/swiss/sib/rdf/sparql/examples/FindFiles.java index aa6472744..22109416f 100644 --- a/src/main/java/swiss/sib/rdf/sparql/examples/FindFiles.java +++ b/src/main/java/swiss/sib/rdf/sparql/examples/FindFiles.java @@ -41,4 +41,8 @@ public static Stream allPrefixFiles() throws IOException, URISyntaxExcepti public static Path commonPrefixes() throws URISyntaxException { return Paths.get(FindFiles.class.getResource("/prefixes.ttl").toURI()); } + + public static Stream prefixFile(Path p) { + return Stream.of(p.resolve("prefixes.ttl")); + } }