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@lszeremeta
lszeremeta committed Apr 5, 2021
1 parent 505d424 commit bd879ea
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80 changes: 40 additions & 40 deletions src/main/java/pl/edu/uwb/ii/sdfeater/File.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -84,30 +84,30 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
" \"@graph\" : [\n" +
" {\n" +
" \"@id\": \"https://github.com/lszeremeta/SDFEater\",\n" +
" \"@type\": \"http://schema.org/Organization\",\n" +
" \"http://schema.org/name\": \"SDFEater\"\n" +
" \"@type\": \"https://schema.org/Organization\",\n" +
" \"https://schema.org/name\": \"SDFEater\"\n" +
" },\n" +
" {\n" +
" \"@id\": \"#\",\n" +
" \"@type\": \"http://schema.org/Dataset\",\n" +
" \"http://schema.org/about\": {\n" +
" \"@type\": \"https://schema.org/Dataset\",\n" +
" \"https://schema.org/about\": {\n" +
" \"@id\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" },\n" +
" \"http://schema.org/description\": \"This is a dataset of molecules generated by SDFEater.\",\n" +
" \"http://schema.org/keywords\": [\n" +
" \"https://schema.org/description\": \"This is a dataset of molecules generated by SDFEater.\",\n" +
" \"https://schema.org/keywords\": [\n" +
" \"molecules\",\n" +
" \"cheminformatics\",\n" +
" \"chemical compounds\"\n" +
" ],\n" +
" \"http://schema.org/license\": {\n" +
" \"@id\": \"http://opendatacommons.org/licenses/pddl/1.0/\"\n" +
" \"https://schema.org/license\": {\n" +
" \"@id\": \"https://opendatacommons.org/licenses/pddl/1.0/\"\n" +
" },\n" +
" \"http://schema.org/name\": \"Molecules\",\n" +
" \"http://schema.org/creator\": {\n" +
" \"https://schema.org/name\": \"Molecules\",\n" +
" \"https://schema.org/creator\": {\n" +
" \"@id\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" },\n" +
" \"http://schema.org/temporal\": " + Year.now().toString() + ",\n" +
" \"http://schema.org/url\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" \"https://schema.org/temporal\": " + Year.now().toString() + ",\n" +
" \"https://schema.org/url\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" },");
break;
case jsonld:
Expand All @@ -116,30 +116,30 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
" \"@graph\" : [\n" +
" {\n" +
" \"@id\": \"https://github.com/lszeremeta/SDFEater\",\n" +
" \"@type\": \"http://schema.org/Organization\",\n" +
" \"http://schema.org/name\": \"SDFEater\"\n" +
" \"@type\": \"https://schema.org/Organization\",\n" +
" \"https://schema.org/name\": \"SDFEater\"\n" +
" },\n" +
" {\n" +
" \"@id\": \"#\",\n" +
" \"@type\": \"http://schema.org/Dataset\",\n" +
" \"http://schema.org/about\": {\n" +
" \"@type\": \"https://schema.org/Dataset\",\n" +
" \"https://schema.org/about\": {\n" +
" \"@id\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" },\n" +
" \"http://schema.org/description\": \"This is a dataset of molecules generated by SDFEater.\",\n" +
" \"http://schema.org/keywords\": [\n" +
" \"https://schema.org/description\": \"This is a dataset of molecules generated by SDFEater.\",\n" +
" \"https://schema.org/keywords\": [\n" +
" \"molecules\",\n" +
" \"cheminformatics\",\n" +
" \"chemical compounds\"\n" +
" ],\n" +
" \"http://schema.org/license\": {\n" +
" \"@id\": \"http://opendatacommons.org/licenses/pddl/1.0/\"\n" +
" \"https://schema.org/license\": {\n" +
" \"@id\": \"https://opendatacommons.org/licenses/pddl/1.0/\"\n" +
" },\n" +
" \"http://schema.org/name\": \"Molecules\",\n" +
" \"http://schema.org/creator\": {\n" +
" \"https://schema.org/name\": \"Molecules\",\n" +
" \"https://schema.org/creator\": {\n" +
" \"@id\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" },\n" +
" \"http://schema.org/temporal\": " + Year.now().toString() + ",\n" +
" \"http://schema.org/url\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" \"https://schema.org/temporal\": " + Year.now().toString() + ",\n" +
" \"https://schema.org/url\": \"https://github.com/lszeremeta/SDFEater\"\n" +
" },");
break;
// RDFa
Expand All @@ -149,7 +149,7 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
System.out.println(" <head>");
System.out.println(" <title>Example Document</title>");
System.out.println(" </head>");
System.out.println(" <body vocab='http://schema.org/'>");
System.out.println(" <body vocab='https://schema.org/'>");
System.out.println(" <div typeof='schema:Dataset'>\n" +
" <div rel='schema:creator'>\n" +
" <div typeof='schema:Organization' about='https://github.com/lszeremeta/SDFEater'>\n" +
Expand All @@ -161,7 +161,7 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
" <div property='schema:keywords' content='chemical compounds'></div>\n" +
" <div property='schema:temporal' content='" + Year.now().toString() + "'></div>\n" +
" <div property='schema:name' content='Molecules'></div>\n" +
" <div rel='schema:license' resource='http://opendatacommons.org/licenses/pddl/1.0/'></div>\n" +
" <div rel='schema:license' resource='https://opendatacommons.org/licenses/pddl/1.0/'></div>\n" +
" <div property='schema:description' content='This is a dataset of molecules generated by SDFEater.'></div>\n" +
" <div rel='schema:about' resource='https://github.com/lszeremeta/SDFEater'></div>\n" +
" <div property='schema:url' content='https://github.com/lszeremeta/SDFEater'></div>\n" +
Expand All @@ -186,7 +186,7 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
" <div itemprop='creator' itemscope itemtype='https://schema.org/Organization'>\n" +
" <div itemprop='name' content='SDFEater'></div>\n" +
" </div>\n" +
" <div itemprop='license' content='http://opendatacommons.org/licenses/pddl/1.0/'></div>\n" +
" <div itemprop='license' content='https://opendatacommons.org/licenses/pddl/1.0/'></div>\n" +
" </div>");
break;
default:
Expand Down Expand Up @@ -284,33 +284,33 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
molecule.addPropertyByName(pName, "https://www.drugbank.ca/drugs/" + strLine);
break;
case "ECMDB Database Links":
molecule.addPropertyByName(pName, "http://ecmdb.ca/compounds/" + strLine);
molecule.addPropertyByName(pName, "https://ecmdb.ca/compounds/" + strLine);
break;
case "HMDB Database Links":
// metabolites
molecule.addPropertyByName(pName, "http://www.hmdb.ca/metabolites/" + strLine);
molecule.addPropertyByName(pName, "https://www.hmdb.ca/metabolites/" + strLine);
break;
case "IntAct Database Links":
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/intact/interaction/" + strLine);
break;
case "IntEnz Database Links":
strLine = strLine.replaceAll(" ", "+");
molecule.addPropertyByName(pName, "http://www.ebi.ac.uk/intenz/query?q=" + strLine);
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/intenz/query?q=" + strLine);
break;
case "KEGG COMPOUND Database Links":
molecule.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?cpd:" + strLine);
molecule.addPropertyByName(pName, "https://www.genome.jp/dbget-bin/www_bget?cpd:" + strLine);
break;
case "KEGG DRUG Database Links":
molecule.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?dr:" + strLine);
molecule.addPropertyByName(pName, "https://www.genome.jp/dbget-bin/www_bget?dr:" + strLine);
break;
case "KEGG GLYCAN Database Links":
molecule.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?gl:" + strLine);
molecule.addPropertyByName(pName, "https://www.genome.jp/dbget-bin/www_bget?gl:" + strLine);
break;
case "KNApSAcK Database Links":
molecule.addPropertyByName(pName, "http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=" + strLine);
molecule.addPropertyByName(pName, "https://kanaya.naist.jp/knapsack_jsp/information.jsp?word=" + strLine);
break;
case "LIPID MAPS instance Database Links":
molecule.addPropertyByName(pName, "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=" + strLine);
molecule.addPropertyByName(pName, "https://www.lipidmaps.org/data/LMSDRecord.php?LMID=" + strLine);
break;
case "MetaCyc Database Links":
molecule.addPropertyByName(pName, "https://metacyc.org/compound?orgid=META&id=" + strLine);
Expand All @@ -319,7 +319,7 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
molecule.addPropertyByName(pName, "https://worldwide.espacenet.com/searchResults?query=" + strLine);
break;
case "PDBeChem Database Links":
molecule.addPropertyByName(pName, "http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/" + strLine);
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/" + strLine);
break;
case "PubChem Database Links":
// custom key value for compound and substance links
Expand All @@ -342,16 +342,16 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
molecule.addPropertyByName(pName, "https://reactome.org/content/detail/" + strLine);
break;
case "RESID Database Links":
molecule.addPropertyByName(pName, "http://pir.georgetown.edu/cgi-bin/resid?id=" + strLine);
molecule.addPropertyByName(pName, "https://pir.georgetown.edu/cgi-bin/resid?id=" + strLine);
break;
case "Rhea Database Links":
molecule.addPropertyByName(pName, "https://www.rhea-db.org/reaction?id=" + strLine);
break;
case "SABIO-RK Database Links":
molecule.addPropertyByName(pName, "http://sabio.h-its.org/reacdetails.jsp?reactid=" + strLine);
molecule.addPropertyByName(pName, "https://sabio.h-its.org/reacdetails.jsp?reactid=" + strLine);
break;
case "UM-BBD compID Database Links":
molecule.addPropertyByName(pName, "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=" + strLine);
molecule.addPropertyByName(pName, "https://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=" + strLine);
break;
case "UniProt Database Links":
molecule.addPropertyByName(pName, "https://www.uniprot.org/uniprot/" + strLine);
Expand All @@ -360,7 +360,7 @@ void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject)
molecule.addPropertyByName(pName, "https://en.wikipedia.org/wiki/" + strLine);
break;
case "YMDB Database Links":
molecule.addPropertyByName(pName, "http://www.ymdb.ca/compounds/" + strLine);
molecule.addPropertyByName(pName, "https://www.ymdb.ca/compounds/" + strLine);
break;
default:
molecule.addPropertyByName(pName, strLine);
Expand Down
12 changes: 6 additions & 6 deletions src/main/java/pl/edu/uwb/ii/sdfeater/Molecule.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -332,7 +332,7 @@ void addToJenaModel(SDFEater.Subject subject) {
Resource me = ResourceFactory.createResource();

if (subject == SDFEater.Subject.iri) {
me = ResourceFactory.createResource("http://example.com/molecule#entity" + createID());
me = ResourceFactory.createResource("https://example.com/molecule#entity" + createID());
} else if (subject == SDFEater.Subject.uuid) {
me = ResourceFactory.createResource("urn:uuid:" + uuid);
} else if (subject == SDFEater.Subject.bnode) {
Expand Down Expand Up @@ -439,7 +439,7 @@ void printJSONLDMolecule(SDFEater.Subject subject) {
output_str.setLength(output_str.length() - 2);
System.out.println(" {");
if (subject == SDFEater.Subject.iri) {
System.out.println(" \"@id\" : \"http://example.com/molecule#entity" + createID() + "\",");
System.out.println(" \"@id\" : \"https://example.com/molecule#entity" + createID() + "\",");
} else if (subject == SDFEater.Subject.uuid) {
System.out.println(" \"@id\" : \"urn:uuid:" + uuid + "\",");
} else if (subject == SDFEater.Subject.bnode) {
Expand Down Expand Up @@ -501,7 +501,7 @@ void printRDFaMolecule(SDFEater.Subject subject) {
if (output_str.length() > 0) {
if (subject == SDFEater.Subject.iri) {
String mID = createID();
System.out.println(" <div typeof='schema:MolecularEntity' about='http://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
System.out.println(" <div typeof='schema:MolecularEntity' about='https://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
} else if (subject == SDFEater.Subject.uuid) {
System.out.println(" <div typeof='schema:MolecularEntity' about='urn:uuid:" + uuid + "'>");
} else if (subject == SDFEater.Subject.bnode) {
Expand Down Expand Up @@ -561,11 +561,11 @@ void printMicrodataMolecule(SDFEater.Subject subject) {
if (output_str.length() > 0) {
if (subject == SDFEater.Subject.iri) {
String mID = createID();
System.out.println(" <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='http://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
System.out.println(" <div itemscope itemtype='https://schema.org/MolecularEntity' itemid='https://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
} else if (subject == SDFEater.Subject.uuid) {
System.out.println(" <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='urn:uuid:" + uuid + "'>");
System.out.println(" <div itemscope itemtype='https://schema.org/MolecularEntity' itemid='urn:uuid:" + uuid + "'>");
} else if (subject == SDFEater.Subject.bnode) {
System.out.println(" <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='_:b" + createID() + "'>");
System.out.println(" <div itemscope itemtype='https://schema.org/MolecularEntity' itemid='_:b" + createID() + "'>");
}

System.out.print(output_str);
Expand Down

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