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change http to https for external databases urls
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@ahmadshadab
ahmadshadab committed Dec 9, 2024
1 parent 72a1f51 commit 2750d75
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Showing 2 changed files with 38 additions and 38 deletions.
74 changes: 37 additions & 37 deletions controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json
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Original file line number Diff line number Diff line change
Expand Up @@ -48,14 +48,14 @@
"name": "DDBJ",
"displayName": "DDBJ",
"category": "SEQ",
"uriLink": "http://getentry.ddbj.nig.ac.jp/search/get_entry?accnumber=%id",
"uriLink": "https://getentry.ddbj.nig.ac.jp/search/get_entry?accnumber=%id",
"implicit": true,
"linkedReason": "DR:EMBL",
"attributes": [
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://getentry.ddbj.nig.ac.jp/getentry/na/%ProteinId"
"uriLink":"https://getentry.ddbj.nig.ac.jp/getentry/na/%ProteinId"
},
{
"name": "Status",
Expand Down Expand Up @@ -227,7 +227,7 @@
"name": "CORUM",
"displayName": "CORUM",
"category": "PPI",
"uriLink": "http://mips.helmholtz-muenchen.de/corum/#?uniprotID=%id"
"uriLink": "https://mips.helmholtz-muenchen.de/corum/#?uniprotID=%id"
},
{
"name": "DIP",
Expand Down Expand Up @@ -314,7 +314,7 @@
"name": "Allergome",
"displayName": "Allergome",
"category": "PFAM",
"uriLink": "http://www.allergome.org/script/dettaglio.php?id_molecule=%id",
"uriLink": "https://www.allergome.org/script/dettaglio.php?id_molecule=%id",
"idMappingName": "ALLERGOME_ID",
"attributes": [
{
Expand All @@ -327,7 +327,7 @@
"name": "CAZy",
"displayName": "CAZy",
"category": "PFAM",
"uriLink": "http://www.cazy.org/%id.html",
"uriLink": "https://www.cazy.org/%id.html",
"attributes": [
{
"name": "FamilyName",
Expand Down Expand Up @@ -383,7 +383,7 @@
"name": "PeroxiBase",
"displayName": "PeroxiBase",
"category": "PFAM",
"uriLink": "http://peroxibase.toulouse.inra.fr/display_perox/view_perox/%id",
"uriLink": "https://peroxibase.toulouse.inra.fr/display_perox/view_perox/%id",
"idMappingName": "PEROXIBASE_ID",
"attributes": [
{
Expand All @@ -396,7 +396,7 @@
"name": "REBASE",
"displayName": "REBASE",
"category": "PFAM",
"uriLink": "http://rebase.neb.com/rebase/enz/%id.html",
"uriLink": "https://rebase.neb.com/rebase/enz/%id.html",
"idMappingName": "REBASE_ID",
"attributes": [
{
Expand All @@ -409,7 +409,7 @@
"name": "TCDB",
"displayName": "TCDB",
"category": "PFAM",
"uriLink": "http://www.tcdb.org/search/result.php?tc=%id",
"uriLink": "https://www.tcdb.org/search/result.php?tc=%id",
"idMappingName": "TCDB_ID",
"attributes": [
{
Expand Down Expand Up @@ -437,13 +437,13 @@
"name": "CarbonylDB",
"displayName": "CarbonylDB",
"category": "PTM",
"uriLink": "http://carbonyldb.missouri.edu/CarbonylDB/index.php/detail/protein/%id"
"uriLink": "https://carbonyldb.missouri.edu/CarbonylDB/index.php/detail/protein/%id"
},
{
"name": "DEPOD",
"displayName": "DEPOD",
"category": "PTM",
"uriLink": "http://depod.bioss.uni-freiburg.de/showp.php?name=%id"
"uriLink": "https://depod.bioss.uni-freiburg.de/showp.php?name=%id"
},
{
"name": "GlyConnect",
Expand Down Expand Up @@ -486,7 +486,7 @@
"name": "iPTMnet",
"displayName": "iPTMnet",
"category": "PTM",
"uriLink": "http://research.bioinformatics.udel.edu/iptmnet/entry/%id"
"uriLink": "https://research.bioinformatics.udel.edu/iptmnet/entry/%id"
},
{
"name": "PhosphoSitePlus",
Expand All @@ -504,7 +504,7 @@
"name": "UniCarbKB",
"displayName": "UniCarbKB",
"category": "PTM",
"uriLink": "http://www.unicarbkb.org/proteinsummary/%id/annotated"
"uriLink": "https://www.unicarbkb.org/proteinsummary/%id/annotated"
},
{
"name": "MetOSite",
Expand Down Expand Up @@ -542,7 +542,7 @@
"name": "REPRODUCTION-2DPAGE",
"displayName": "REPRODUCTION-2DPAGE",
"category": "2DG",
"uriLink": "http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?%id"
"uriLink": "http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?%id"
},
{
"name": "CPTAC",
Expand Down Expand Up @@ -644,12 +644,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://www.ensemblgenomes.org/id/%ProteinId"
"uriLink":"https://www.ensemblgenomes.org/id/%ProteinId"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://www.ensemblgenomes.org/id/%GeneId"
"uriLink":"https://www.ensemblgenomes.org/id/%GeneId"
}
]
},
Expand All @@ -662,12 +662,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://www.ensemblgenomes.org/id/%ProteinId"
"uriLink":"https://www.ensemblgenomes.org/id/%ProteinId"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://www.ensemblgenomes.org/id/%GeneId"
"uriLink":"https://www.ensemblgenomes.org/id/%GeneId"
}
]
},
Expand All @@ -680,12 +680,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://www.ensemblgenomes.org/id/%ProteinId"
"uriLink":"https://www.ensemblgenomes.org/id/%ProteinId"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://www.ensemblgenomes.org/id/%GeneId"
"uriLink":"https://www.ensemblgenomes.org/id/%GeneId"
}
]
},
Expand All @@ -698,12 +698,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://www.ensemblgenomes.org/id/%ProteinId"
"uriLink":"https://www.ensemblgenomes.org/id/%ProteinId"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://www.ensemblgenomes.org/id/%GeneId"
"uriLink":"https://www.ensemblgenomes.org/id/%GeneId"
}
]
},
Expand All @@ -716,12 +716,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://www.ensemblgenomes.org/id/%ProteinId"
"uriLink":"https://www.ensemblgenomes.org/id/%ProteinId"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://www.ensemblgenomes.org/id/%GeneId"
"uriLink":"https://www.ensemblgenomes.org/id/%GeneId"
}
]
},
Expand All @@ -741,12 +741,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://ensembl.gramene.org/id/%ProteinId"
"uriLink":"https://ensembl.gramene.org/id/%ProteinId"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://ensembl.gramene.org/id/%GeneId"
"uriLink":"https://ensembl.gramene.org/id/%GeneId"
}
]
},
Expand Down Expand Up @@ -847,7 +847,7 @@
"name": "ArachnoServer",
"displayName": "ArachnoServer",
"category": "ORG",
"uriLink": "http://www.arachnoserver.org/toxincard.html?id=%id",
"uriLink": "https://www.arachnoserver.org/toxincard.html?id=%id",
"idMappingName": "ARACHNOSERVER_ID",
"attributes": [
{
Expand Down Expand Up @@ -880,7 +880,7 @@
"name": "ConoServer",
"displayName": "ConoServer",
"category": "ORG",
"uriLink": "http://www.conoserver.org/?page=card&table=protein&id=%id",
"uriLink": "https://www.conoserver.org/?page=card&table=protein&id=%id",
"idMappingName": "CONOSERVER_ID",
"attributes": [
{
Expand Down Expand Up @@ -1052,7 +1052,7 @@
"name": "MGI",
"displayName": "MGI",
"category": "ORG",
"uriLink": "http://www.informatics.jax.org/marker/%id",
"uriLink": "https://www.informatics.jax.org/marker/%id",
"idMappingName": "MGI_ID",
"attributes": [
{
Expand Down Expand Up @@ -1202,12 +1202,12 @@
{
"name": "ProteinId",
"xmlTag":"protein sequence ID",
"uriLink":"http://www.wormbase.org/db/seq/protein?name=%ProteinId;class=Protein"
"uriLink":"https://www.wormbase.org/db/seq/protein?name=%ProteinId;class=Protein"
},
{
"name": "GeneId",
"xmlTag":"gene ID",
"uriLink":"http://www.wormbase.org/db/gene/gene?name=%GeneId;class=Gene"
"uriLink":"https://www.wormbase.org/db/gene/gene?name=%GeneId;class=Gene"
},
{ "name": "GeneName",
"xmlTag":"gene designation"
Expand Down Expand Up @@ -1244,15 +1244,15 @@
"category": "ORG",
"implicit": true,
"linkedReason": "GN:KIAAnnnn, Human Entries, can be multiple",
"uriLink": "http://www.kazusa.or.jp/huge/gfpage/%gene"
"uriLink": "https://www.kazusa.or.jp/huge/gfpage/%gene"
},
{
"name": "Rouge",
"displayName": "Rouge",
"category": "ORG",
"implicit": true,
"linkedReason": "GN:KIAAnnnn, Mouse Entries, can be multiple",
"uriLink": "http://www.kazusa.or.jp/rouge/gfpage/%gene"
"uriLink": "https://www.kazusa.or.jp/rouge/gfpage/%gene"
},

{
Expand Down Expand Up @@ -1310,7 +1310,7 @@
"name": "PhylomeDB",
"displayName": "PhylomeDB",
"category": "PLG",
"uriLink": "http://phylomedb.org/search_phylome/?seqid=%id"
"uriLink": "https://phylomedb.org/search_phylome/?seqid=%id"
},
{
"name": "TreeFam",
Expand Down Expand Up @@ -1354,7 +1354,7 @@
"name": "SABIO-RK",
"displayName": "SABIO-RK",
"category": "EAP",
"uriLink": "http://sabiork.h-its.org/newSearch?q=UniProtKB_AC:%id"
"uriLink": "https://sabiork.h-its.org/newSearch?q=UniProtKB_AC:%id"
},
{
"name": "SignaLink",
Expand Down Expand Up @@ -1543,7 +1543,7 @@
"name": "Gene3D",
"displayName": "Gene3D",
"category": "FMD",
"uriLink": "http://www.cathdb.info/superfamily/%id",
"uriLink": "https://www.cathdb.info/superfamily/%id",
"attributes": [
{ "name": "EntryName",
"xmlTag":"entry name"
Expand Down Expand Up @@ -1589,7 +1589,7 @@
"name": "PANTHER",
"displayName": "PANTHER",
"category": "FMD",
"uriLink": "http://www.pantherdb.org/panther/family.do?clsAccession=%id",
"uriLink": "https://www.pantherdb.org/panther/family.do?clsAccession=%id",
"attributes": [
{ "name": "EntryName",
"xmlTag":"entry name"
Expand Down Expand Up @@ -1656,7 +1656,7 @@
"name": "SMART",
"displayName": "SMART",
"category": "FMD",
"uriLink": "http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%id",
"uriLink": "https://smart.embl.de/smart/do_annotation.pl?DOMAIN=%id",
"attributes": [
{ "name": "EntryName",
"xmlTag":"entry name"
Expand Down
2 changes: 1 addition & 1 deletion controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ void testiPTMnetType() {
assertEquals("iPTMnet", opType.getDisplayName());
assertEquals(PTM_DATABASES, opType.getCategory());
assertEquals(
"http://research.bioinformatics.udel.edu/iptmnet/entry/%id", opType.getUriLink());
"https://research.bioinformatics.udel.edu/iptmnet/entry/%id", opType.getUriLink());
assertEquals(1, opType.getAttributes().size());
verifyAttribute(opType.getAttributes().get(0), "Description", "description", null);
}
Expand Down

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