From 11bbccaab947ba4465c27c5d0619ef202fc4e75e Mon Sep 17 00:00:00 2001 From: James Procter Date: Mon, 17 Jul 2023 11:15:07 +0100 Subject: [PATCH] =?utf8?q?JAL-4119=20TRACE=20level=20console=20message=20rep?= =?utf8?q?orting=20download=20URL=20for=20sifts.=20Also=20more=20informative?= =?utf8?q?=20message=20when=20=E2=80=98Sifts=20Mapping=20Failed=E2=80=99=20i?= =?utf8?q?s=20reported=20as=20an=20exception=20-=20since=20this=20message=20?= =?utf8?q?can=20be=20reported=20when=20some=20chains=20in=20the=20PDB=20file?= =?utf8?q?=20do=20not=20match=20sequences=20being=20associated=20(but=20othe?= =?utf8?q?rs=20do!!).?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/ws/sifts/SiftsClient.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 037854b..24526cf 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -57,6 +57,7 @@ import jalview.analysis.scoremodels.ScoreMatrix; import jalview.analysis.scoremodels.ScoreModels; import jalview.api.DBRefEntryI; import jalview.api.SiftsClientI; +import jalview.bin.Console; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; @@ -350,7 +351,10 @@ public class SiftsClient implements SiftsClientI public static String getDownloadUrlFor(String siftFile) { - return SIFTS_SPLIT_FTP_BASE_URL +siftFile.substring(1, 3)+"/"+siftFile; + String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile; + Console.trace("SIFTS URL for "+siftFile+" is "+durl); + return durl; + } /** @@ -540,7 +544,7 @@ public class SiftsClient implements SiftsClientI if (mapping.isEmpty()) { - throw new SiftsException("SIFTS mapping failed"); + throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName()); } // also construct a mapping object between the seq-coord sys and the PDB // seq's coord sys -- 1.7.10.2