Add a new java class/to convert all the sparql-examples into one turt…

…le file, or one per project. Also closes #13
sib-swiss · Jun 12, 2024 · 2f6315c · 2f6315c
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diff --git 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
@@ -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
diff --git a/bgee/1.ttl → examples/bgee/1.ttl b/bgee/1.ttl → examples/bgee/1.ttl
diff --git a/bgee/10.ttl → examples/bgee/10.ttl b/bgee/10.ttl → examples/bgee/10.ttl
diff --git a/bgee/11-a.ttl → examples/bgee/11-a.ttl b/bgee/11-a.ttl → examples/bgee/11-a.ttl
diff --git a/bgee/11.ttl → examples/bgee/11.ttl b/bgee/11.ttl → examples/bgee/11.ttl
diff --git a/bgee/12-a.ttl → examples/bgee/12-a.ttl b/bgee/12-a.ttl → examples/bgee/12-a.ttl
diff --git a/bgee/12.ttl → examples/bgee/12.ttl b/bgee/12.ttl → examples/bgee/12.ttl
diff --git a/bgee/13.ttl → examples/bgee/13.ttl b/bgee/13.ttl → examples/bgee/13.ttl
diff --git a/bgee/14.ttl → examples/bgee/14.ttl b/bgee/14.ttl → examples/bgee/14.ttl
diff --git a/bgee/15.ttl → examples/bgee/15.ttl b/bgee/15.ttl → examples/bgee/15.ttl
diff --git a/bgee/2.ttl → examples/bgee/2.ttl b/bgee/2.ttl → examples/bgee/2.ttl
diff --git a/bgee/3.ttl → examples/bgee/3.ttl b/bgee/3.ttl → examples/bgee/3.ttl
diff --git a/bgee/4.ttl → examples/bgee/4.ttl b/bgee/4.ttl → examples/bgee/4.ttl
diff --git a/bgee/5.ttl → examples/bgee/5.ttl b/bgee/5.ttl → examples/bgee/5.ttl
diff --git a/bgee/6.ttl → examples/bgee/6.ttl b/bgee/6.ttl → examples/bgee/6.ttl
diff --git a/bgee/7.ttl → examples/bgee/7.ttl b/bgee/7.ttl → examples/bgee/7.ttl
diff --git a/bgee/8-a.ttl → examples/bgee/8-a.ttl b/bgee/8-a.ttl → examples/bgee/8-a.ttl
diff --git a/bgee/8-b.ttl → examples/bgee/8-b.ttl b/bgee/8-b.ttl → examples/bgee/8-b.ttl
diff --git a/bgee/8.ttl → examples/bgee/8.ttl b/bgee/8.ttl → examples/bgee/8.ttl
diff --git a/bgee/9.ttl → examples/bgee/9.ttl b/bgee/9.ttl → examples/bgee/9.ttl
diff --git a/bgee/prefixes.ttl → examples/bgee/prefixes.ttl b/bgee/prefixes.ttl → examples/bgee/prefixes.ttl
diff --git a/glyconnect/.gitkeep → examples/glyconnect/.gitkeep b/glyconnect/.gitkeep → examples/glyconnect/.gitkeep
diff --git a/glyconnect/1.ttl → examples/glyconnect/1.ttl b/glyconnect/1.ttl → examples/glyconnect/1.ttl
diff --git a/glyconnect/2.ttl → examples/glyconnect/2.ttl b/glyconnect/2.ttl → examples/glyconnect/2.ttl
diff --git a/glyconnect/3.ttl → examples/glyconnect/3.ttl b/glyconnect/3.ttl → examples/glyconnect/3.ttl
diff --git a/glyconnect/4.ttl → examples/glyconnect/4.ttl b/glyconnect/4.ttl → examples/glyconnect/4.ttl
diff --git a/glyconnect/5.ttl → examples/glyconnect/5.ttl b/glyconnect/5.ttl → examples/glyconnect/5.ttl
diff --git a/hamap/1.ttl → examples/hamap/1.ttl b/hamap/1.ttl → examples/hamap/1.ttl
diff --git a/hamap/2.ttl → examples/hamap/2.ttl b/hamap/2.ttl → examples/hamap/2.ttl
diff --git a/hamap/3.ttl → examples/hamap/3.ttl b/hamap/3.ttl → examples/hamap/3.ttl
diff --git a/hamap/4.ttl → examples/hamap/4.ttl b/hamap/4.ttl → examples/hamap/4.ttl
diff --git a/nextprot/NXQ_00001.ttl → examples/nextprot/NXQ_00001.ttl b/nextprot/NXQ_00001.ttl → examples/nextprot/NXQ_00001.ttl
diff --git a/nextprot/NXQ_00002.ttl → examples/nextprot/NXQ_00002.ttl b/nextprot/NXQ_00002.ttl → examples/nextprot/NXQ_00002.ttl
diff --git a/nextprot/NXQ_00003.ttl → examples/nextprot/NXQ_00003.ttl b/nextprot/NXQ_00003.ttl → examples/nextprot/NXQ_00003.ttl
diff --git a/nextprot/NXQ_00004.ttl → examples/nextprot/NXQ_00004.ttl b/nextprot/NXQ_00004.ttl → examples/nextprot/NXQ_00004.ttl
diff --git a/nextprot/NXQ_00005.ttl → examples/nextprot/NXQ_00005.ttl b/nextprot/NXQ_00005.ttl → examples/nextprot/NXQ_00005.ttl
diff --git a/nextprot/NXQ_00006.ttl → examples/nextprot/NXQ_00006.ttl b/nextprot/NXQ_00006.ttl → examples/nextprot/NXQ_00006.ttl
diff --git a/nextprot/NXQ_00007.ttl → examples/nextprot/NXQ_00007.ttl b/nextprot/NXQ_00007.ttl → examples/nextprot/NXQ_00007.ttl
diff --git a/nextprot/NXQ_00008.ttl → examples/nextprot/NXQ_00008.ttl b/nextprot/NXQ_00008.ttl → examples/nextprot/NXQ_00008.ttl
diff --git a/nextprot/NXQ_00009.ttl → examples/nextprot/NXQ_00009.ttl b/nextprot/NXQ_00009.ttl → examples/nextprot/NXQ_00009.ttl
diff --git a/nextprot/NXQ_00010.ttl → examples/nextprot/NXQ_00010.ttl b/nextprot/NXQ_00010.ttl → examples/nextprot/NXQ_00010.ttl
diff --git a/nextprot/NXQ_00011.ttl → examples/nextprot/NXQ_00011.ttl b/nextprot/NXQ_00011.ttl → examples/nextprot/NXQ_00011.ttl
diff --git a/nextprot/NXQ_00012.ttl → examples/nextprot/NXQ_00012.ttl b/nextprot/NXQ_00012.ttl → examples/nextprot/NXQ_00012.ttl
diff --git a/nextprot/NXQ_00013.ttl → examples/nextprot/NXQ_00013.ttl b/nextprot/NXQ_00013.ttl → examples/nextprot/NXQ_00013.ttl
diff --git a/nextprot/NXQ_00014.ttl → examples/nextprot/NXQ_00014.ttl b/nextprot/NXQ_00014.ttl → examples/nextprot/NXQ_00014.ttl
diff --git a/nextprot/NXQ_00015.ttl → examples/nextprot/NXQ_00015.ttl b/nextprot/NXQ_00015.ttl → examples/nextprot/NXQ_00015.ttl
diff --git a/nextprot/NXQ_00016.ttl → examples/nextprot/NXQ_00016.ttl b/nextprot/NXQ_00016.ttl → examples/nextprot/NXQ_00016.ttl
diff --git a/nextprot/NXQ_00017.ttl → examples/nextprot/NXQ_00017.ttl b/nextprot/NXQ_00017.ttl → examples/nextprot/NXQ_00017.ttl
diff --git a/nextprot/NXQ_00018.ttl → examples/nextprot/NXQ_00018.ttl b/nextprot/NXQ_00018.ttl → examples/nextprot/NXQ_00018.ttl
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diff --git a/nextprot/NXQ_00026.ttl → examples/nextprot/NXQ_00026.ttl b/nextprot/NXQ_00026.ttl → examples/nextprot/NXQ_00026.ttl
diff --git a/nextprot/NXQ_00027.ttl → examples/nextprot/NXQ_00027.ttl b/nextprot/NXQ_00027.ttl → examples/nextprot/NXQ_00027.ttl
diff --git a/nextprot/NXQ_00028.ttl → examples/nextprot/NXQ_00028.ttl b/nextprot/NXQ_00028.ttl → examples/nextprot/NXQ_00028.ttl
diff --git a/nextprot/NXQ_00029.ttl → examples/nextprot/NXQ_00029.ttl b/nextprot/NXQ_00029.ttl → examples/nextprot/NXQ_00029.ttl
diff --git a/nextprot/NXQ_00030.ttl → examples/nextprot/NXQ_00030.ttl b/nextprot/NXQ_00030.ttl → examples/nextprot/NXQ_00030.ttl
diff --git a/nextprot/NXQ_00031.ttl → examples/nextprot/NXQ_00031.ttl b/nextprot/NXQ_00031.ttl → examples/nextprot/NXQ_00031.ttl
diff --git a/nextprot/NXQ_00032.ttl → examples/nextprot/NXQ_00032.ttl b/nextprot/NXQ_00032.ttl → examples/nextprot/NXQ_00032.ttl
diff --git a/nextprot/NXQ_00033.ttl → examples/nextprot/NXQ_00033.ttl b/nextprot/NXQ_00033.ttl → examples/nextprot/NXQ_00033.ttl
diff --git a/nextprot/NXQ_00034.ttl → examples/nextprot/NXQ_00034.ttl b/nextprot/NXQ_00034.ttl → examples/nextprot/NXQ_00034.ttl
diff --git a/nextprot/NXQ_00035.ttl → examples/nextprot/NXQ_00035.ttl b/nextprot/NXQ_00035.ttl → examples/nextprot/NXQ_00035.ttl
diff --git a/nextprot/NXQ_00036.ttl → examples/nextprot/NXQ_00036.ttl b/nextprot/NXQ_00036.ttl → examples/nextprot/NXQ_00036.ttl
diff --git a/nextprot/NXQ_00037.ttl → examples/nextprot/NXQ_00037.ttl b/nextprot/NXQ_00037.ttl → examples/nextprot/NXQ_00037.ttl
diff --git a/nextprot/NXQ_00038.ttl → examples/nextprot/NXQ_00038.ttl b/nextprot/NXQ_00038.ttl → examples/nextprot/NXQ_00038.ttl
diff --git a/nextprot/NXQ_00039.ttl → examples/nextprot/NXQ_00039.ttl b/nextprot/NXQ_00039.ttl → examples/nextprot/NXQ_00039.ttl
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diff --git a/nextprot/NXQ_00044.ttl → examples/nextprot/NXQ_00044.ttl b/nextprot/NXQ_00044.ttl → examples/nextprot/NXQ_00044.ttl
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diff --git a/nextprot/NXQ_00053.ttl → examples/nextprot/NXQ_00053.ttl b/nextprot/NXQ_00053.ttl → examples/nextprot/NXQ_00053.ttl
diff --git a/nextprot/NXQ_00054.ttl → examples/nextprot/NXQ_00054.ttl b/nextprot/NXQ_00054.ttl → examples/nextprot/NXQ_00054.ttl
diff --git a/nextprot/NXQ_00055.ttl → examples/nextprot/NXQ_00055.ttl b/nextprot/NXQ_00055.ttl → examples/nextprot/NXQ_00055.ttl
diff --git a/nextprot/NXQ_00057.ttl → examples/nextprot/NXQ_00057.ttl b/nextprot/NXQ_00057.ttl → examples/nextprot/NXQ_00057.ttl
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diff --git a/nextprot/NXQ_00065.ttl → examples/nextprot/NXQ_00065.ttl b/nextprot/NXQ_00065.ttl → examples/nextprot/NXQ_00065.ttl
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diff --git a/nextprot/NXQ_00068.ttl → examples/nextprot/NXQ_00068.ttl b/nextprot/NXQ_00068.ttl → examples/nextprot/NXQ_00068.ttl
diff --git a/nextprot/NXQ_00069.ttl → examples/nextprot/NXQ_00069.ttl b/nextprot/NXQ_00069.ttl → examples/nextprot/NXQ_00069.ttl
diff --git a/nextprot/NXQ_00070.ttl → examples/nextprot/NXQ_00070.ttl b/nextprot/NXQ_00070.ttl → examples/nextprot/NXQ_00070.ttl
diff --git a/nextprot/NXQ_00072.ttl → examples/nextprot/NXQ_00072.ttl b/nextprot/NXQ_00072.ttl → examples/nextprot/NXQ_00072.ttl
diff --git a/nextprot/NXQ_00073.ttl → examples/nextprot/NXQ_00073.ttl b/nextprot/NXQ_00073.ttl → examples/nextprot/NXQ_00073.ttl
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diff --git a/swisslipids/37.ttl → examples/swisslipids/37.ttl b/swisslipids/37.ttl → examples/swisslipids/37.ttl
diff --git a/swisslipids/38.ttl → examples/swisslipids/38.ttl b/swisslipids/38.ttl → examples/swisslipids/38.ttl
diff --git a/swisslipids/4.ttl → examples/swisslipids/4.ttl b/swisslipids/4.ttl → examples/swisslipids/4.ttl
diff --git a/swisslipids/5.ttl → examples/swisslipids/5.ttl b/swisslipids/5.ttl → examples/swisslipids/5.ttl
diff --git a/swisslipids/6.ttl → examples/swisslipids/6.ttl b/swisslipids/6.ttl → examples/swisslipids/6.ttl
diff --git a/swisslipids/7.ttl → examples/swisslipids/7.ttl b/swisslipids/7.ttl → examples/swisslipids/7.ttl
diff --git a/swisslipids/8.ttl → examples/swisslipids/8.ttl b/swisslipids/8.ttl → examples/swisslipids/8.ttl
diff --git a/swisslipids/9.ttl → examples/swisslipids/9.ttl b/swisslipids/9.ttl → examples/swisslipids/9.ttl
diff --git a/...position_of_tyrosine_to_phenylalanine.ttl → ...position_of_tyrosine_to_phenylalanine.ttl b/...position_of_tyrosine_to_phenylalanine.ttl → ...position_of_tyrosine_to_phenylalanine.ttl
diff --git a/..._with_transmem_on_cannonical_sequence.ttl → ..._with_transmem_on_cannonical_sequence.ttl b/..._with_transmem_on_cannonical_sequence.ttl → ..._with_transmem_on_cannonical_sequence.ttl
diff --git a/uniprot/12_entries_integrated_on_date.ttl → ...uniprot/12_entries_integrated_on_date.ttl b/uniprot/12_entries_integrated_on_date.ttl → ...uniprot/12_entries_integrated_on_date.ttl
diff --git a/uniprot/13_entries_added_on_date.ttl → ...ples/uniprot/13_entries_added_on_date.ttl b/uniprot/13_entries_added_on_date.ttl → ...ples/uniprot/13_entries_added_on_date.ttl
diff --git a/uniprot/14_make_your_own_triples.ttl → ...ples/uniprot/14_make_your_own_triples.ttl b/uniprot/14_make_your_own_triples.ttl → ...ples/uniprot/14_make_your_own_triples.ttl
diff --git a/uniprot/15_describe_an_EMBL_cds.ttl → examples/uniprot/15_describe_an_EMBL_cds.ttl b/uniprot/15_describe_an_EMBL_cds.ttl → examples/uniprot/15_describe_an_EMBL_cds.ttl
diff --git a/...about_species_human_in_taxonomy_graph.ttl → ...about_species_human_in_taxonomy_graph.ttl b/...about_species_human_in_taxonomy_graph.ttl → ...about_species_human_in_taxonomy_graph.ttl
diff --git a/uniprot/17_average_count_to_PDB.ttl → examples/uniprot/17_average_count_to_PDB.ttl b/uniprot/17_average_count_to_PDB.ttl → examples/uniprot/17_average_count_to_PDB.ttl
diff --git a/...evel_ec_classification_group_by_count.ttl → ...evel_ec_classification_group_by_count.ttl b/...evel_ec_classification_group_by_count.ttl → ...evel_ec_classification_group_by_count.ttl
diff --git a/...al_variants_associated_with_pubmed_id.ttl → ...al_variants_associated_with_pubmed_id.ttl b/...al_variants_associated_with_pubmed_id.ttl → ...al_variants_associated_with_pubmed_id.ttl
diff --git a/...rot/1_select_all_taxa_used_in_uniprot.ttl → ...rot/1_select_all_taxa_used_in_uniprot.ttl b/...rot/1_select_all_taxa_used_in_uniprot.ttl → ...rot/1_select_all_taxa_used_in_uniprot.ttl
diff --git a/...w_often_citation_used_in_evidence_tag.ttl → ...w_often_citation_used_in_evidence_tag.ttl b/...w_often_citation_used_in_evidence_tag.ttl → ...w_often_citation_used_in_evidence_tag.ttl
diff --git a/...ic_disease_related_proteins_in_a_cell.ttl → ...ic_disease_related_proteins_in_a_cell.ttl b/...ic_disease_related_proteins_in_a_cell.ttl → ...ic_disease_related_proteins_in_a_cell.ttl
diff --git a/...per_go_category_for_multiple_proteins.ttl → ...per_go_category_for_multiple_proteins.ttl b/...per_go_category_for_multiple_proteins.ttl → ...per_go_category_for_multiple_proteins.ttl
diff --git a/...n_proteins_related_to_kinase_activity.ttl → ...n_proteins_related_to_kinase_activity.ttl b/...n_proteins_related_to_kinase_activity.ttl → ...n_proteins_related_to_kinase_activity.ttl
diff --git a/uniprot/24_uniprot_release_in_endpoint.ttl → ...niprot/24_uniprot_release_in_endpoint.ttl b/uniprot/24_uniprot_release_in_endpoint.ttl → ...niprot/24_uniprot_release_in_endpoint.ttl
diff --git a/...5_protein_name_of_any_kind_with_value.ttl → ...5_protein_name_of_any_kind_with_value.ttl b/...5_protein_name_of_any_kind_with_value.ttl → ...5_protein_name_of_any_kind_with_value.ttl
diff --git a/...HLA_class_I_histocompatibility_domain.ttl → ...HLA_class_I_histocompatibility_domain.ttl b/...HLA_class_I_histocompatibility_domain.ttl → ...HLA_class_I_histocompatibility_domain.ttl
diff --git a/uniprot/27_all_names_of_protein.ttl → examples/uniprot/27_all_names_of_protein.ttl b/uniprot/27_all_names_of_protein.ttl → examples/uniprot/27_all_names_of_protein.ttl
diff --git a/...ies_encoded_on_chromosome_of_proteome.ttl → ...ies_encoded_on_chromosome_of_proteome.ttl b/...ies_encoded_on_chromosome_of_proteome.ttl → ...ies_encoded_on_chromosome_of_proteome.ttl
diff --git a/...search_uniprot_in_japanese_with_allie.ttl → ...search_uniprot_in_japanese_with_allie.ttl b/...search_uniprot_in_japanese_with_allie.ttl → ...search_uniprot_in_japanese_with_allie.ttl
diff --git a/...cteria_taxa_and_their_scientific_name.ttl → ...cteria_taxa_and_their_scientific_name.ttl b/...cteria_taxa_and_their_scientific_name.ttl → ...cteria_taxa_and_their_scientific_name.ttl
diff --git a/uniprot/30_merged_loci.ttl → examples/uniprot/30_merged_loci.ttl b/uniprot/30_merged_loci.ttl → examples/uniprot/30_merged_loci.ttl
diff --git a/...1_uniparc_record_with_most_subentries.ttl → ...1_uniparc_record_with_most_subentries.ttl b/...1_uniparc_record_with_most_subentries.ttl → ...1_uniparc_record_with_most_subentries.ttl
diff --git a/...t/32_uniprot_with_more_than_x_topodom.ttl → ...t/32_uniprot_with_more_than_x_topodom.ttl b/...t/32_uniprot_with_more_than_x_topodom.ttl → ...t/32_uniprot_with_more_than_x_topodom.ttl
diff --git a/uniprot/33_longest_variant_comment.ttl → ...es/uniprot/33_longest_variant_comment.ttl b/uniprot/33_longest_variant_comment.ttl → ...es/uniprot/33_longest_variant_comment.ttl