From 2f6315c390be12273e8f98b76525f48a9d5acb5a Mon Sep 17 00:00:00 2001 From: Jerven Bolleman Date: Wed, 12 Jun 2024 21:48:19 +0200 Subject: [PATCH] Add a new java class/to convert all the sparql-examples into one turtle file, or one per project. Also closes #13 --- README.md | 6 + convertToOneTurtle.sh | 8 +- convertToRDFXml.sh | 3 - {bgee => examples/bgee}/1.ttl | 0 {bgee => examples/bgee}/10.ttl | 0 {bgee => examples/bgee}/11-a.ttl | 0 {bgee => examples/bgee}/11.ttl | 0 {bgee => examples/bgee}/12-a.ttl | 0 {bgee => examples/bgee}/12.ttl | 0 {bgee => examples/bgee}/13.ttl | 0 {bgee => examples/bgee}/14.ttl | 0 {bgee => examples/bgee}/15.ttl | 0 {bgee => examples/bgee}/2.ttl | 0 {bgee => examples/bgee}/3.ttl | 0 {bgee => examples/bgee}/4.ttl | 0 {bgee => examples/bgee}/5.ttl | 0 {bgee => examples/bgee}/6.ttl | 0 {bgee => examples/bgee}/7.ttl | 0 {bgee => examples/bgee}/8-a.ttl | 0 {bgee => examples/bgee}/8-b.ttl | 0 {bgee => examples/bgee}/8.ttl | 0 {bgee => examples/bgee}/9.ttl | 0 {bgee => examples/bgee}/prefixes.ttl | 0 {glyconnect => examples/glyconnect}/.gitkeep | 0 {glyconnect => examples/glyconnect}/1.ttl | 0 {glyconnect => examples/glyconnect}/2.ttl | 0 {glyconnect => examples/glyconnect}/3.ttl | 0 {glyconnect => examples/glyconnect}/4.ttl | 0 {glyconnect => examples/glyconnect}/5.ttl | 0 {hamap => examples/hamap}/1.ttl | 0 {hamap => examples/hamap}/2.ttl | 0 {hamap => examples/hamap}/3.ttl | 0 {hamap => examples/hamap}/4.ttl | 0 {nextprot => examples/nextprot}/NXQ_00001.ttl | 0 {nextprot => examples/nextprot}/NXQ_00002.ttl | 0 {nextprot => examples/nextprot}/NXQ_00003.ttl | 0 {nextprot => examples/nextprot}/NXQ_00004.ttl | 0 {nextprot => examples/nextprot}/NXQ_00005.ttl | 0 {nextprot => examples/nextprot}/NXQ_00006.ttl | 0 {nextprot => examples/nextprot}/NXQ_00007.ttl | 0 {nextprot => examples/nextprot}/NXQ_00008.ttl | 0 {nextprot => examples/nextprot}/NXQ_00009.ttl | 0 {nextprot => examples/nextprot}/NXQ_00010.ttl | 0 {nextprot => examples/nextprot}/NXQ_00011.ttl | 0 {nextprot => examples/nextprot}/NXQ_00012.ttl | 0 {nextprot => examples/nextprot}/NXQ_00013.ttl | 0 {nextprot => examples/nextprot}/NXQ_00014.ttl | 0 {nextprot => examples/nextprot}/NXQ_00015.ttl | 0 {nextprot => examples/nextprot}/NXQ_00016.ttl | 0 {nextprot => examples/nextprot}/NXQ_00017.ttl | 0 {nextprot => examples/nextprot}/NXQ_00018.ttl | 0 {nextprot => examples/nextprot}/NXQ_00019.ttl | 0 {nextprot => examples/nextprot}/NXQ_00020.ttl | 0 {nextprot => examples/nextprot}/NXQ_00021.ttl | 0 {nextprot => examples/nextprot}/NXQ_00022.ttl | 0 {nextprot => examples/nextprot}/NXQ_00023.ttl | 0 {nextprot => examples/nextprot}/NXQ_00024.ttl | 0 {nextprot => examples/nextprot}/NXQ_00025.ttl | 0 {nextprot => examples/nextprot}/NXQ_00026.ttl | 0 {nextprot => examples/nextprot}/NXQ_00027.ttl | 0 {nextprot => examples/nextprot}/NXQ_00028.ttl | 0 {nextprot => examples/nextprot}/NXQ_00029.ttl | 0 {nextprot => examples/nextprot}/NXQ_00030.ttl | 0 {nextprot => examples/nextprot}/NXQ_00031.ttl | 0 {nextprot => examples/nextprot}/NXQ_00032.ttl | 0 {nextprot => examples/nextprot}/NXQ_00033.ttl | 0 {nextprot => examples/nextprot}/NXQ_00034.ttl | 0 {nextprot => examples/nextprot}/NXQ_00035.ttl | 0 {nextprot => 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examples/nextprot}/NXQ_00058.ttl | 0 {nextprot => examples/nextprot}/NXQ_00059.ttl | 0 {nextprot => examples/nextprot}/NXQ_00060.ttl | 0 {nextprot => examples/nextprot}/NXQ_00061.ttl | 0 {nextprot => examples/nextprot}/NXQ_00062.ttl | 0 {nextprot => examples/nextprot}/NXQ_00063.ttl | 0 {nextprot => examples/nextprot}/NXQ_00064.ttl | 0 {nextprot => examples/nextprot}/NXQ_00065.ttl | 0 {nextprot => examples/nextprot}/NXQ_00066.ttl | 0 {nextprot => examples/nextprot}/NXQ_00067.ttl | 0 {nextprot => examples/nextprot}/NXQ_00068.ttl | 0 {nextprot => examples/nextprot}/NXQ_00069.ttl | 0 {nextprot => examples/nextprot}/NXQ_00070.ttl | 0 {nextprot => examples/nextprot}/NXQ_00072.ttl | 0 {nextprot => examples/nextprot}/NXQ_00073.ttl | 0 {nextprot => examples/nextprot}/NXQ_00074.ttl | 0 {nextprot => examples/nextprot}/NXQ_00075.ttl | 0 {nextprot => examples/nextprot}/NXQ_00076.ttl | 0 {nextprot => examples/nextprot}/NXQ_00077.ttl | 0 {nextprot => examples/nextprot}/NXQ_00078.ttl | 0 {nextprot => 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examples/nextprot}/NXQ_00108.ttl | 0 {nextprot => examples/nextprot}/NXQ_00109.ttl | 0 {nextprot => examples/nextprot}/NXQ_00111.ttl | 0 {nextprot => examples/nextprot}/NXQ_00112.ttl | 0 {nextprot => examples/nextprot}/NXQ_00113.ttl | 0 {nextprot => examples/nextprot}/NXQ_00117.ttl | 0 {nextprot => examples/nextprot}/NXQ_00118.ttl | 0 {nextprot => examples/nextprot}/NXQ_00119.ttl | 0 {nextprot => examples/nextprot}/NXQ_00124.ttl | 0 {nextprot => examples/nextprot}/NXQ_00125.ttl | 0 {nextprot => examples/nextprot}/NXQ_00126.ttl | 0 {nextprot => examples/nextprot}/NXQ_00127.ttl | 0 {nextprot => examples/nextprot}/NXQ_00128.ttl | 0 {nextprot => examples/nextprot}/NXQ_00130.ttl | 0 {nextprot => examples/nextprot}/NXQ_00131.ttl | 0 {nextprot => examples/nextprot}/NXQ_00132.ttl | 0 {nextprot => examples/nextprot}/NXQ_00135.ttl | 0 {nextprot => examples/nextprot}/NXQ_00136.ttl | 0 {nextprot => examples/nextprot}/NXQ_00137.ttl | 0 {nextprot => examples/nextprot}/NXQ_00138.ttl | 0 {nextprot => 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examples/nextprot}/NXQ_00222.ttl | 0 {nextprot => examples/nextprot}/NXQ_00223.ttl | 0 {nextprot => examples/nextprot}/NXQ_00224.ttl | 0 {nextprot => examples/nextprot}/NXQ_00225.ttl | 0 {nextprot => examples/nextprot}/NXQ_00226.ttl | 0 {nextprot => examples/nextprot}/NXQ_00230.ttl | 0 {nextprot => examples/nextprot}/NXQ_00231.ttl | 0 {nextprot => examples/nextprot}/NXQ_00232.ttl | 0 {nextprot => examples/nextprot}/NXQ_00233.ttl | 0 {nextprot => examples/nextprot}/NXQ_00234.ttl | 0 {nextprot => examples/nextprot}/NXQ_00235.ttl | 0 {nextprot => examples/nextprot}/NXQ_00236.ttl | 0 {nextprot => examples/nextprot}/NXQ_00237.ttl | 0 {nextprot => examples/nextprot}/NXQ_00238.ttl | 0 {nextprot => examples/nextprot}/NXQ_00239.ttl | 0 {nextprot => examples/nextprot}/NXQ_00240.ttl | 0 {nextprot => examples/nextprot}/NXQ_00241.ttl | 0 {nextprot => examples/nextprot}/NXQ_00242.ttl | 0 {nextprot => examples/nextprot}/NXQ_00243.ttl | 0 {nextprot => examples/nextprot}/NXQ_00244.ttl | 0 {nextprot => 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examples/nextprot}/NXQ_00301.ttl | 0 {nextprot => examples/nextprot}/NXQ_00302.ttl | 0 .../nextprot}/convertNextProt.sh | 0 {nextprot => examples/nextprot}/prefixes.ttl | 0 prefixes.ttl => examples/prefixes.ttl | 0 {rhea => examples/rhea}/1.ttl | 0 {rhea => examples/rhea}/10.ttl | 0 {rhea => examples/rhea}/11.ttl | 0 {rhea => examples/rhea}/12.ttl | 0 {rhea => examples/rhea}/13.ttl | 0 {rhea => examples/rhea}/14.ttl | 0 {rhea => examples/rhea}/15.ttl | 0 {rhea => examples/rhea}/16.ttl | 0 {rhea => examples/rhea}/17.ttl | 0 {rhea => examples/rhea}/18.ttl | 0 {rhea => examples/rhea}/2.ttl | 0 {rhea => examples/rhea}/3.ttl | 0 {rhea => examples/rhea}/4.ttl | 0 {rhea => examples/rhea}/5.ttl | 0 {rhea => examples/rhea}/6.ttl | 0 {rhea => examples/rhea}/7.ttl | 0 {rhea => examples/rhea}/8.ttl | 0 {rhea => examples/rhea}/9.ttl | 0 .../rhea}/draft_human_metabolome.ttl | 0 {swisslipids => examples/swisslipids}/1.ttl | 0 {swisslipids => examples/swisslipids}/10.ttl | 0 {swisslipids => examples/swisslipids}/11.ttl | 0 {swisslipids => examples/swisslipids}/12.ttl | 0 {swisslipids => examples/swisslipids}/13.ttl | 0 {swisslipids => examples/swisslipids}/14.ttl | 0 {swisslipids => examples/swisslipids}/15.ttl | 0 {swisslipids => examples/swisslipids}/2.ttl | 0 {swisslipids => examples/swisslipids}/26.ttl | 0 {swisslipids => examples/swisslipids}/27.ttl | 0 {swisslipids => examples/swisslipids}/3.ttl | 0 {swisslipids => examples/swisslipids}/34.ttl | 0 {swisslipids => examples/swisslipids}/35.ttl | 0 {swisslipids => examples/swisslipids}/36.ttl | 0 {swisslipids => examples/swisslipids}/37.ttl | 0 {swisslipids => examples/swisslipids}/38.ttl | 0 {swisslipids => examples/swisslipids}/4.ttl | 0 {swisslipids => examples/swisslipids}/5.ttl | 0 {swisslipids => examples/swisslipids}/6.ttl | 0 {swisslipids => examples/swisslipids}/7.ttl | 0 {swisslipids => examples/swisslipids}/8.ttl | 0 {swisslipids => examples/swisslipids}/9.ttl | 0 ...sposition_of_tyrosine_to_phenylalanine.ttl | 0 ...s_with_transmem_on_cannonical_sequence.ttl | 0 .../12_entries_integrated_on_date.ttl | 0 .../uniprot}/13_entries_added_on_date.ttl | 0 .../uniprot}/14_make_your_own_triples.ttl | 0 .../uniprot}/15_describe_an_EMBL_cds.ttl | 0 ..._about_species_human_in_taxonomy_graph.ttl | 0 .../uniprot}/17_average_count_to_PDB.ttl | 0 ...level_ec_classification_group_by_count.ttl | 0 ...ral_variants_associated_with_pubmed_id.ttl | 0 .../1_select_all_taxa_used_in_uniprot.ttl | 0 ...ow_often_citation_used_in_evidence_tag.ttl | 0 ...tic_disease_related_proteins_in_a_cell.ttl | 0 ..._per_go_category_for_multiple_proteins.ttl | 0 ...an_proteins_related_to_kinase_activity.ttl | 0 .../24_uniprot_release_in_endpoint.ttl | 0 ...25_protein_name_of_any_kind_with_value.ttl | 0 ..._HLA_class_I_histocompatibility_domain.ttl | 0 .../uniprot}/27_all_names_of_protein.ttl | 0 ...ries_encoded_on_chromosome_of_proteome.ttl | 0 ..._search_uniprot_in_japanese_with_allie.ttl | 0 ...acteria_taxa_and_their_scientific_name.ttl | 0 .../uniprot}/30_merged_loci.ttl | 0 ...31_uniparc_record_with_most_subentries.ttl | 0 .../32_uniprot_with_more_than_x_topodom.ttl | 0 .../uniprot}/33_longest_variant_comment.ttl | 0 .../34_cooccurence_count_of_topodom.ttl | 0 ...5_similar_proteins_via_uniref_clusters.ttl | 0 .../36_orthologous_proteins_via_orthodb.ttl | 0 ...Q_where_T_is_a_phosporylated_threonine.ttl | 0 ...ene_region_in_wikidata_for_known_entry.ttl | 0 ...ntal_catalytic_activities_in_swissprot.ttl | 0 .../uniprot}/3_entry_sequences_organism.ttl | 0 ..._enzymes_that_metabolize_sphingolipids.ttl | 0 .../uniprot}/41_fragmented_sequences.ttl | 0 .../uniprot}/42_connect_patents_to_epo.ttl | 0 ...iprot_granted_twenty_years_in_the_past.ttl | 0 .../44_rhea_interpro_union_in_uniprot.ttl | 0 ...geting_human_sterol_metabolism_enzymes.ttl | 0 ...46_duck_pictures_via_eepa_and_taxonomy.ttl | 0 ...smembrane_region_with_close_by_alanine.ttl | 0 .../48_glycosylation_sites_and_glycans.ttl | 0 ..._metabolizing_cholestrol_are_expressed.ttl | 0 .../uniprot}/4_uniprot_mnemonic_id.ttl | 0 ...where_genes_sphingosines_are_expressed.ttl | 0 ...51_all_proteins_linked_to_arachidonate.ttl | 0 .../52_drugs_targeting_sterol_metabolism.ttl | 0 ...ologs_of_sterol_enzymes_via_omabrowser.ttl | 0 ...tes_for_ligands_similar_to_heme_sachem.ttl | 0 ...hur_cluster_binding_sites_experimental.ttl | 0 ...es_that_have_a_known_allosteric_effect.ttl | 0 ...pdb_identifiers_plus_chains_to_uniprot.ttl | 0 .../58_uniprot_to_HGNC_and_symbols.ttl | 0 .../59_all_isoforms_for_a_given_proteome.ttl | 0 .../uniprot}/5_mapping_to_PDB.ttl | 0 ..._on_substrate_with_Cholestene_backbone.ttl | 0 .../61_Gene_Protein_Reaction_sets.ttl | 0 .../uniprot}/6_cross_ref_in_category_3D.ttl | 0 ...me_if_pref_gene_name_contains_word_DNA.ttl | 0 ...name_of_human_disease_related_proteins.ttl | 0 .../9_human_variant_loss_of_function.ttl | 0 .../uniprot}/diseases_involving_enzymes.ttl | 0 ...lving_enzymes_located_in_mitochondrion.ttl | 0 ...ses_related_to_mutation_in_active_site.ttl | 0 ...istinct_extinct_organisms_in_uniprotkb.ttl | 0 .../uniprot}/draft_human_metabolome.ttl | 0 ...nzymes_derived_from_at_least_two_mRNAs.ttl | 0 ...oteins_derived_from_at_least_two_mRNAs.ttl | 0 ...ing_with_molecules_similar_to_dopamine.ttl | 0 ...amine_with_variants_related_to_disease.ttl | 0 .../uniprot}/enzymes_mapping_to_PDB.ttl | 0 ...ith_at_least_two_transmembrane_domains.ttl | 0 ...ast_two_transmembrane_domains_PDB_xray.ttl | 0 ...with_mutagenesis_affecting_active_site.ttl | 0 .../enzymes_with_tyrosine_as_active_site.ttl | 0 .../genetic_disease_related_proteins.ttl | 0 .../uniprot}/mnemonic_also_known_as_id.ttl | 0 pom.xml | 56 +++++++- .../sib/rdf/sparql/examples/Converter.java | 121 ++++++++++++++++++ .../sib/rdf/sparql/examples/FindFiles.java | 4 + 354 files changed, 183 insertions(+), 15 deletions(-) delete mode 100755 convertToRDFXml.sh rename {bgee => examples/bgee}/1.ttl (100%) rename {bgee => examples/bgee}/10.ttl (100%) rename {bgee => examples/bgee}/11-a.ttl (100%) rename {bgee => examples/bgee}/11.ttl (100%) rename {bgee => examples/bgee}/12-a.ttl (100%) rename {bgee => examples/bgee}/12.ttl (100%) rename {bgee => examples/bgee}/13.ttl (100%) rename {bgee => examples/bgee}/14.ttl (100%) rename {bgee => examples/bgee}/15.ttl (100%) rename {bgee => examples/bgee}/2.ttl (100%) rename {bgee => examples/bgee}/3.ttl (100%) rename {bgee => examples/bgee}/4.ttl (100%) rename {bgee => examples/bgee}/5.ttl (100%) rename {bgee => examples/bgee}/6.ttl (100%) rename {bgee => examples/bgee}/7.ttl (100%) rename {bgee => examples/bgee}/8-a.ttl (100%) rename {bgee => examples/bgee}/8-b.ttl (100%) rename {bgee => examples/bgee}/8.ttl (100%) rename {bgee => examples/bgee}/9.ttl (100%) rename {bgee => examples/bgee}/prefixes.ttl (100%) rename {glyconnect => examples/glyconnect}/.gitkeep (100%) rename {glyconnect 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(100%) rename {uniprot => examples/uniprot}/43_patents_used_in_uniprot_granted_twenty_years_in_the_past.ttl (100%) rename {uniprot => examples/uniprot}/44_rhea_interpro_union_in_uniprot.ttl (100%) rename {uniprot => examples/uniprot}/45_drugs_targeting_human_sterol_metabolism_enzymes.ttl (100%) rename {uniprot => examples/uniprot}/46_duck_pictures_via_eepa_and_taxonomy.ttl (100%) rename {uniprot => examples/uniprot}/47_protein_with_transmembrane_region_with_close_by_alanine.ttl (100%) rename {uniprot => examples/uniprot}/48_glycosylation_sites_and_glycans.ttl (100%) rename {uniprot => examples/uniprot}/49_tissues_where_genes_metabolizing_cholestrol_are_expressed.ttl (100%) rename {uniprot => examples/uniprot}/4_uniprot_mnemonic_id.ttl (100%) rename {uniprot => examples/uniprot}/50_tissues_where_genes_sphingosines_are_expressed.ttl (100%) rename {uniprot => examples/uniprot}/51_all_proteins_linked_to_arachidonate.ttl (100%) rename {uniprot => examples/uniprot}/52_drugs_targeting_sterol_metabolism.ttl (100%) rename {uniprot => examples/uniprot}/53_mouse_homologs_of_sterol_enzymes_via_omabrowser.ttl (100%) rename {uniprot => examples/uniprot}/54_binding_sites_for_ligands_similar_to_heme_sachem.ttl (100%) rename {uniprot => examples/uniprot}/55_metal_or_sulphur_cluster_binding_sites_experimental.ttl (100%) rename {uniprot => examples/uniprot}/56_enzymes_that_have_a_known_allosteric_effect.ttl (100%) rename {uniprot => examples/uniprot}/57_map_pdb_identifiers_plus_chains_to_uniprot.ttl (100%) rename {uniprot => examples/uniprot}/58_uniprot_to_HGNC_and_symbols.ttl (100%) rename {uniprot => examples/uniprot}/59_all_isoforms_for_a_given_proteome.ttl (100%) rename {uniprot => examples/uniprot}/5_mapping_to_PDB.ttl (100%) rename {uniprot => examples/uniprot}/60_enzymes_working_on_substrate_with_Cholestene_backbone.ttl (100%) rename {uniprot => examples/uniprot}/61_Gene_Protein_Reaction_sets.ttl (100%) rename {uniprot => examples/uniprot}/6_cross_ref_in_category_3D.ttl (100%) rename {uniprot => examples/uniprot}/7_swissprot_with_rec_protein_name_if_pref_gene_name_contains_word_DNA.ttl (100%) rename {uniprot => examples/uniprot}/8_prefered_gene_name_of_human_disease_related_proteins.ttl (100%) rename {uniprot => examples/uniprot}/9_human_variant_loss_of_function.ttl (100%) rename {uniprot => examples/uniprot}/diseases_involving_enzymes.ttl (100%) rename {uniprot => examples/uniprot}/diseases_involving_enzymes_located_in_mitochondrion.ttl (100%) rename {uniprot => examples/uniprot}/diseases_related_to_mutation_in_active_site.ttl (100%) rename {uniprot => examples/uniprot}/distinct_extinct_organisms_in_uniprotkb.ttl (100%) rename {uniprot => examples/uniprot}/draft_human_metabolome.ttl (100%) rename {uniprot => examples/uniprot}/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl (100%) rename {uniprot => examples/uniprot}/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_interacting_with_molecules_similar_to_dopamine.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_mapping_to_PDB.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_with_at_least_two_transmembrane_domains.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_with_mutagenesis_affecting_active_site.ttl (100%) rename {uniprot => examples/uniprot}/enzymes_with_tyrosine_as_active_site.ttl (100%) rename {uniprot => examples/uniprot}/genetic_disease_related_proteins.ttl (100%) rename {uniprot => examples/uniprot}/mnemonic_also_known_as_id.ttl (100%) create mode 100644 src/main/java/swiss/sib/rdf/sparql/examples/Converter.java 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 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examples/uniprot/3_entry_sequences_organism.ttl diff --git a/uniprot/40_human_enzymes_that_metabolize_sphingolipids.ttl b/examples/uniprot/40_human_enzymes_that_metabolize_sphingolipids.ttl similarity index 100% rename from uniprot/40_human_enzymes_that_metabolize_sphingolipids.ttl rename to examples/uniprot/40_human_enzymes_that_metabolize_sphingolipids.ttl diff --git a/uniprot/41_fragmented_sequences.ttl b/examples/uniprot/41_fragmented_sequences.ttl similarity index 100% rename from uniprot/41_fragmented_sequences.ttl rename to examples/uniprot/41_fragmented_sequences.ttl diff --git a/uniprot/42_connect_patents_to_epo.ttl b/examples/uniprot/42_connect_patents_to_epo.ttl similarity index 100% rename from uniprot/42_connect_patents_to_epo.ttl rename to examples/uniprot/42_connect_patents_to_epo.ttl diff --git a/uniprot/43_patents_used_in_uniprot_granted_twenty_years_in_the_past.ttl b/examples/uniprot/43_patents_used_in_uniprot_granted_twenty_years_in_the_past.ttl similarity index 100% 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")); + } }