2014-02-23T17:05:14
1393193114353
0
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Java version: 1.7.0_51
2014-02-23T17:05:14
1393193114361
1
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
amd64 Windows 7 6.1
2014-02-23T17:05:14
1393193114462
2
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Jalview Version: 2.8.0b1
2014-02-23T17:05:14
1393193114482
3
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
# INFO: Setting default net timeout to 30 seconds.
2014-02-23T17:05:15
1393193115697
4
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
WARN : jalview.bin.Jalview - Exception when discovering One Way services:
java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.URL.openStream(Unknown Source)
at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244)
at java.lang.Thread.run(Unknown Source)
2014-02-23T17:05:15
1393193115719
5
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
WARN - Exception when discovering One Way services:
java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.URL.openStream(Unknown Source)
at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244)
at java.lang.Thread.run(Unknown Source)
2014-02-23T17:05:15
1393193115885
6
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
WARN : jalview.bin.Jalview - Exception when discovering One Way services:
java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.URL.openStream(Unknown Source)
at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244)
at java.lang.Thread.run(Unknown Source)
2014-02-23T17:05:16
1393193116009
7
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
WARN - Exception when discovering One Way services:
java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.URL.openStream(Unknown Source)
at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244)
at java.lang.Thread.run(Unknown Source)
2014-02-23T17:05:16
1393193116150
9
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Feb 23, 2014 5:05:16 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
2014-02-23T17:05:17
1393193117095
10
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Connecting to JABAWS version 2 service
2014-02-23T17:05:17
1393193117623
12
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Feb 23, 2014 5:05:17 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
2014-02-23T17:05:17
1393193117883
13
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5dbd5a2c
2014-02-23T17:05:19
1393193119013
14
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Connecting to JABAWS version 2 service
2014-02-23T17:05:19
1393193119404
16
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Feb 23, 2014 5:05:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
2014-02-23T17:05:21
1393193121130
17
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO : jalview.bin.Jalview - Not enabling Google Tracking.
2014-02-23T17:05:21
1393193121131
18
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO - Not enabling Google Tracking.
2014-02-23T17:05:21
1393193121195
19
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO : jalview.bin.Jalview - Constructing news reader.
2014-02-23T17:05:21
1393193121198
20
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO - Constructing news reader.
2014-02-23T17:05:21
1393193121505
21
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
CacheEntry[http://www.jalview.org/feeds/desktop/rss]: updateAvailable=true,lastModified=Sun Feb 23 16:29:41 EST 2014,length=12728
2014-02-23T17:05:21
1393193121921
22
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO : jalview.bin.Jalview - Completed construction of reader.
2014-02-23T17:05:21
1393193121934
23
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO - Completed construction of reader.
2014-02-23T17:05:26
1393193126242
24
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO : jalview.bin.Jalview - Saved last read date as Jan 31, 2014 7:45:46 AM
2014-02-23T17:05:26
1393193126248
25
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO - Saved last read date as Jan 31, 2014 7:45:46 AM
2014-02-23T17:05:26
1393193126258
26
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO : jalview.bin.Jalview - Saved last read date as Jan 31, 2014 7:45:46 AM
2014-02-23T17:05:26
1393193126261
27
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO - Saved last read date as Jan 31, 2014 7:45:46 AM
2014-02-23T17:05:26
1393193126265
28
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO : jalview.bin.Jalview - Saved last read date as Jan 31, 2014 7:45:46 AM
2014-02-23T17:05:26
1393193126269
29
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
INFO - Saved last read date as Jan 31, 2014 7:45:46 AM
2014-02-23T17:05:27
1393193127774
30
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Building ws menu again Thread[Thread-37,6,javawsApplicationThreadGroup]
2014-02-23T17:05:29
1393193129777
31
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
header key X-DAS-Server=[regrest/1.5]
2014-02-23T17:05:29
1393193129777
32
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
header key Content-Type=[application/xml]
2014-02-23T17:05:29
1393193129897
33
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
header key Date=[Sun, 23 Feb 2014 22:05:28 GMT]
2014-02-23T17:05:29
1393193129930
34
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
header key Transfer-Encoding=[chunked]
2014-02-23T17:05:29
1393193129932
35
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
header key Access-Control-Allow-Origin=[*]
2014-02-23T17:05:29
1393193129935
36
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
header key X-DAS-Status=[200]
2014-02-23T17:05:29
1393193129938
37
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Contig 2.0) (DAS))
2014-02-23T17:05:29
1393193129941
38
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Scaffold 2.0) (DAS))
2014-02-23T17:05:29
1393193129944
39
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Bos_taurus.UMD3.1.reference (Bos_taurus.UMD3.1.reference (UMD Scaffold 3.1) (DAS))
2014-02-23T17:05:29
1393193129947
40
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Callithrix_jacchus.C_jacchus3.2.1.reference (Callithrix_jacchus.C_jacchus3.2.1.reference (C_jacchus Chromosome 3.2.1) (DAS))
2014-02-23T17:05:29
1393193129975
41
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Choloepus_hoffmanni.choHof1.reference (Choloepus_hoffmanni.choHof1.reference (choHof Gene Scaffold 1) (DAS))
2014-02-23T17:05:29
1393193129978
42
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Danio_rerio.Zv9.reference (Danio_rerio.Zv9.reference (Zv Scaffold 9) (DAS))
2014-02-23T17:05:29
1393193129980
43
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Dasypus_novemcinctus.dasNov2.reference (Dasypus_novemcinctus.dasNov2.reference (dasNov Scaffold 2) (DAS))
2014-02-23T17:05:29
1393193129984
44
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Dipodomys_ordii.dipOrd1.reference (Dipodomys_ordii.dipOrd1.reference (dipOrd Scaffold 1) (DAS))
2014-02-23T17:05:29
1393193129987
45
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Echinops_telfairi.TENREC.reference (Echinops_telfairi.TENREC.reference (TENREC Scaffold) (DAS))
2014-02-23T17:05:29
1393193129990
46
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Erinaceus_europaeus.HEDGEHOG.reference (Erinaceus_europaeus.HEDGEHOG.reference (HEDGEHOG Scaffold) (DAS))
2014-02-23T17:05:29
1393193129993
47
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Felis_catus.CAT.reference (Felis_catus.CAT.reference (CAT Gene Scaffold) (DAS))
2014-02-23T17:05:29
1393193129996
48
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130003
49
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130031
50
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Gasterosteus_aculeatus.BROADS1.reference (Gasterosteus_aculeatus.BROADS1.reference (BROADS Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130041
51
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Homo_sapiens.GRCh37.reference (Homo_sapiens.GRCh37.reference (GRCh Chromosome 37) (DAS))
2014-02-23T17:05:30
1393193130043
52
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Macaca_mulatta.MMUL_1.reference (Macaca_mulatta.MMUL_1.reference (MMUL Chromosome 1) (DAS))
2014-02-23T17:05:30
1393193130056
53
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Macropus_eugenii.Meug_1.0.reference (Macropus_eugenii.Meug_1.0.reference (Meug Scaffold 1.0) (DAS))
2014-02-23T17:05:30
1393193130058
54
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Scaffold 2) (DAS))
2014-02-23T17:05:30
1393193130065
55
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Contig 2) (DAS))
2014-02-23T17:05:30
1393193130068
56
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Microcebus_murinus.micMur1.reference (Microcebus_murinus.micMur1.reference (micMur Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130075
57
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Mus_musculus.NCBIM37.reference (Mus_musculus.NCBIM37.reference (NCBIM Supercontig 37) (DAS))
2014-02-23T17:05:30
1393193130078
58
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Nomascus_leucogenys.Nleu1.0.reference (Nomascus_leucogenys.Nleu1.0.reference (Nleu Contig 1.0) (DAS))
2014-02-23T17:05:30
1393193130090
59
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Ochotona_princeps.pika.reference (Ochotona_princeps.pika.reference (pika Gene Scaffold) (DAS))
2014-02-23T17:05:30
1393193130092
60
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Ultracontig 5) (DAS))
2014-02-23T17:05:30
1393193130095
61
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Supercontig 5) (DAS))
2014-02-23T17:05:30
1393193130097
62
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Oryctolagus_cuniculus.oryCun2.reference (Oryctolagus_cuniculus.oryCun2.reference (oryCun Chromosome 2) (DAS))
2014-02-23T17:05:30
1393193130101
63
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (Oryzias_latipes.MEDAKA1.reference (MEDAKA Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130104
64
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (Oryzias_latipes.MEDAKA1.reference (MEDAKA Chromosome 1) (DAS))
2014-02-23T17:05:30
1393193130107
65
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Pan_troglodytes.CHIMP2.1.4.reference (Pan_troglodytes.CHIMP2.1.4.reference (CHIMP Chromosome 2.1.4) (DAS))
2014-02-23T17:05:30
1393193130111
66
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Procavia_capensis.proCap1.reference (Procavia_capensis.proCap1.reference (proCap Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130114
67
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Pteropus_vampyrus.pteVam1.reference (Pteropus_vampyrus.pteVam1.reference (pteVam Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130120
68
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Sorex_araneus.COMMON_SHREW1.reference (Sorex_araneus.COMMON_SHREW1.reference (COMMON_SHREW Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130126
69
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Spermophilus_tridecemlineatus.SQUIRREL.reference (Spermophilus_tridecemlineatus.SQUIRREL.reference (SQUIRREL Gene Scaffold) (DAS))
2014-02-23T17:05:30
1393193130129
70
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Tarsius_syrichta.tarSyr1.reference (Tarsius_syrichta.tarSyr1.reference (tarSyr Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130131
71
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Tupaia_belangeri.TREESHREW.reference (Tupaia_belangeri.TREESHREW.reference (TREESHREW Scaffold) (DAS))
2014-02-23T17:05:30
1393193130134
72
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Tursiops_truncatus.turTru1.reference (Tursiops_truncatus.turTru1.reference (turTru Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130136
73
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Vicugna_pacos.vicPac1.reference (Vicugna_pacos.vicPac1.reference (vicPac Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130138
74
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Ciona_intestinalis.JGI2.reference (Ciona_intestinalis.JGI2.reference (JGI Chromosome 2) (DAS))
2014-02-23T17:05:30
1393193130140
75
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Bos_taurus.Btau_4.0.reference (Bos_taurus.Btau_4.0.reference (Btau Contig 4.0) (DAS))
2014-02-23T17:05:30
1393193130143
76
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Otolemur_garnettii.BUSHBABY1.reference (Otolemur_garnettii.BUSHBABY1.reference (BUSHBABY Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130145
77
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Myotis_lucifugus.MICROBAT1.reference (Myotis_lucifugus.MICROBAT1.reference (MICROBAT Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130147
78
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Danio_rerio.Zv8.reference (Danio_rerio.Zv8.reference (Zv Scaffold 8) (DAS))
2014-02-23T17:05:30
1393193130150
79
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Gorilla_gorilla.gorGor1.reference (Gorilla_gorilla.gorGor1.reference (gorGor Gene Scaffold 1) (DAS))
2014-02-23T17:05:30
1393193130152
80
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Loxodonta_africana.loxAfr2.reference (Loxodonta_africana.loxAfr2.reference (loxAfr Scaffold 2) (DAS))
2014-02-23T17:05:30
1393193130154
81
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Oryctolagus_cuniculus.RABBIT.reference (Oryctolagus_cuniculus.RABBIT.reference (RABBIT Scaffold) (DAS))
2014-02-23T17:05:30
1393193130156
82
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Homo_sapiens.NCBI36.reference (Homo_sapiens.NCBI36.reference (NCBI Supercontig 36) (DAS))
2014-02-23T17:05:30
1393193130159
83
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Added another sequence DB source for Danio_rerio.ZFISH7.reference (Danio_rerio.ZFISH7.reference (ZFISH Scaffold 7) (DAS))
2014-02-23T17:05:41
1393193141150
84
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
javax.xml.ws.WebServiceException: java.net.SocketTimeoutException: Read timed out
2014-02-23T17:05:41
1393193141200
85
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.readResponseCodeAndMessage(Unknown Source)
2014-02-23T17:05:41
1393193141203
86
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.createResponsePacket(Unknown Source)
2014-02-23T17:05:41
1393193141207
87
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(Unknown Source)
2014-02-23T17:05:41
1393193141211
88
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(Unknown Source)
2014-02-23T17:05:41
1393193141214
89
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(Unknown Source)
2014-02-23T17:05:41
1393193141217
90
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Unknown Source)
2014-02-23T17:05:41
1393193141220
91
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Unknown Source)
2014-02-23T17:05:41
1393193141223
92
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Unknown Source)
2014-02-23T17:05:41
1393193141227
93
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Unknown Source)
2014-02-23T17:05:41
1393193141230
94
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.client.Stub.process(Unknown Source)
2014-02-23T17:05:41
1393193141233
95
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(Unknown Source)
2014-02-23T17:05:41
1393193141236
96
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
2014-02-23T17:05:41
1393193141239
97
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
2014-02-23T17:05:41
1393193141243
98
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source)
2014-02-23T17:05:41
1393193141246
99
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at com.sun.proxy.$Proxy19.getServiceDescription(Unknown Source)
2014-02-23T17:05:41
1393193141248
100
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:172)
2014-02-23T17:05:41
1393193141298
101
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.lang.Thread.run(Unknown Source)
2014-02-23T17:05:41
1393193141301
102
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Caused by: java.net.SocketTimeoutException: Read timed out
2014-02-23T17:05:41
1393193141306
103
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.net.SocketInputStream.socketRead0(Native Method)
2014-02-23T17:05:41
1393193141309
104
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.net.SocketInputStream.read(Unknown Source)
2014-02-23T17:05:41
1393193141314
105
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.net.SocketInputStream.read(Unknown Source)
2014-02-23T17:05:41
1393193141319
106
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.io.BufferedInputStream.fill(Unknown Source)
2014-02-23T17:05:41
1393193141326
107
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.io.BufferedInputStream.read1(Unknown Source)
2014-02-23T17:05:41
1393193141334
108
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.io.BufferedInputStream.read(Unknown Source)
2014-02-23T17:05:41
1393193141336
109
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source)
2014-02-23T17:05:41
1393193141340
110
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at sun.net.www.http.HttpClient.parseHTTP(Unknown Source)
2014-02-23T17:05:41
1393193141373
111
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
2014-02-23T17:05:41
1393193141378
112
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
at java.net.HttpURLConnection.getResponseCode(Unknown Source)
2014-02-23T17:05:41
1393193141382
113
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
... 17 more
2014-02-23T17:05:41
1393193141385
114
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
WARN : jalview.bin.Jalview - Exception when discovering Jws2 services.
javax.xml.ws.WebServiceException: java.net.SocketTimeoutException: Read timed out
at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.readResponseCodeAndMessage(Unknown Source)
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.createResponsePacket(Unknown Source)
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(Unknown Source)
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(Unknown Source)
at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Unknown Source)
at com.sun.xml.internal.ws.client.Stub.process(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source)
at com.sun.proxy.$Proxy19.getServiceDescription(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:172)
at java.lang.Thread.run(Unknown Source)
Caused by: java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(Unknown Source)
at java.net.SocketInputStream.read(Unknown Source)
at java.io.BufferedInputStream.fill(Unknown Source)
at java.io.BufferedInputStream.read1(Unknown Source)
at java.io.BufferedInputStream.read(Unknown Source)
at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source)
at sun.net.www.http.HttpClient.parseHTTP(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.HttpURLConnection.getResponseCode(Unknown Source)
... 17 more
2014-02-23T17:05:41
1393193141404
115
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
WARN - Exception when discovering Jws2 services.
javax.xml.ws.WebServiceException: java.net.SocketTimeoutException: Read timed out
at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.readResponseCodeAndMessage(Unknown Source)
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.createResponsePacket(Unknown Source)
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(Unknown Source)
at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(Unknown Source)
at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Unknown Source)
at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Unknown Source)
at com.sun.xml.internal.ws.client.Stub.process(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source)
at com.sun.proxy.$Proxy19.getServiceDescription(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:172)
at java.lang.Thread.run(Unknown Source)
Caused by: java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(Unknown Source)
at java.net.SocketInputStream.read(Unknown Source)
at java.io.BufferedInputStream.fill(Unknown Source)
at java.io.BufferedInputStream.read1(Unknown Source)
at java.io.BufferedInputStream.read(Unknown Source)
at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source)
at sun.net.www.http.HttpClient.parseHTTP(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.HttpURLConnection.getResponseCode(Unknown Source)
... 17 more
2014-02-23T17:05:41
1393193141409
116
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Rebuild WS Menu for service change
2014-02-23T17:05:41
1393193141414
117
com.sun.deploy
FINE
com.sun.deploy.trace.LoggerTraceListener
print
9
Building ws menu again Thread[Thread-40,6,javawsApplicationThreadGroup]