[EMBOSS] EMBOSS remote server list?
Ashika Umanga Umagiliya
aumanga at biggjapan.com
Fri Oct 10 09:20:08 UTC 2008
Thank you very much peter ,
now the following queries working well:
entret em:ab000131
entret uni:opsd_human
But my query
entret genbank:AB019441
does not work well.My entry for 'genbank' database is as :
DB genbank [ type: N method: srswww format: genbank release: "NCBI"
url: "http://www.infobiogen.fr/srsbin/cgi-bin/wgetz"
comment: "GenBank from Infobiogen" ]
I checked the URL http://www.infobiogen.fr and it says the service is
down (or something like that ,cuz i dont speak french ).
Any ideas ?
Best Regards
umanga
Following is the debug log for command 'entret genbank:AB019441'
-------------------------------------------------------
Debug file entret.dbg buffered:No
ajAcdInitP pgm 'entret' package ''
ajFileNewInNameS '/usr/local/share/EMBOSS/acd/entret.acd'
EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/entret.acd
closing file '/usr/local/share/EMBOSS/acd/entret.acd'
ajFileNewInNameS '/usr/local/share/EMBOSS/acd/codes.english'
EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/codes.english
closing file '/usr/local/share/EMBOSS/acd/codes.english'
ajTableNewFunctionLen hint 25 size 251
ajTableNewFunctionLen hint 25 size 251
ajTableNewFunctionLen hint 25 size 251
ajFileNewInNameS '/usr/local/share/EMBOSS/acd/knowntypes.standard'
EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/knowntypes.standard
closing file '/usr/local/share/EMBOSS/acd/knowntypes.standard'
Set acdprotein value '$(sequence.protein)'
ajSeqinClear called
++seqUsaProcess 'genbank:AB019441' 0..0(N) '' 0
USA to test: 'genbank:AB019441'
format regexp: No list:No
no format specified in USA
...input format not set
dbname dbexp: Yes
found dbname 'genbank' level: '<null>' qry->QryString: 'AB019441'
seqQueryFieldC usa 'sv' fields '<null>'
ajSeqQueryWild id 'AB019441' acc 'AB019441' sv '' gi '' des '' org '' key ''
no wildcard in stored qry
database type: 'N' format 'genbank'
use access method 'srswww'
Matched seqAccess[9] 'srswww'
seqAccessSrswww genbank:AB019441
seqHttpUrl db: 'genbank' url:
'http://www.infobiogen.fr/srsbin/cgi-bin/wgetz'
searching with SRS url 'GET
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441]'
httpver getValueC '<null>'
httpver after qry '<null>'
host 'www.infobiogen.fr' port 80 get 'GET
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441]
HTTP/1.1
'
seqHttpGet db: 'genbank' host 'www.infobiogen.fr' get: 'GET
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441]
HTTP/1.1
'
gethostbyname host 'www.infobiogen.fr' returns 'lovelace.infobiogen.fr'
errno 1 hp_addr 194.57.183.13
creating socket
setup socket data
connecting to socket 4
sin sizeof 16
connect status 0 errno 0 msg 'Successful system call (0 - Success)'
inet_ntoa '194.57.183.13'
sending: 'GET
/srsbin/cgi-bin/wgetz?-e+-ascii+[genbank-id:AB019441]|[genbank-acc:AB019441]
HTTP/1.1
' status: 0
send for GET errno 0 msg 'Successful system call (0 - Success)'
sending: 'Host: www.infobiogen.fr:80
' status: 0
send for host errno 0 msg 'Successful system call (0 - Success)'
sending: '
' status: 0
send for blankline errno 0 msg 'Successful system call (0 - Success)'
fdopen errno 29 msg 'Something wrong with a system call (29 - Illegal seek)'
read: <HTTP/1.1 404 Not Found
>
read: <Date: Fri, 10 Oct 2008 09:11:37 GMT
>
read: <Server: Apache/1.3.29 (Unix) PHP/4.3.6 mod_ssl/2.8.16 OpenSSL/0.9.6l
>
read: <Last-Modified: Wed, 26 Jul 2006 18:30:45 GMT
>
read: <ETag: "76f3e-16b-44c7b4d5;44b62a93"
>
read: <Accept-Ranges: bytes
>
read: <Content-Length: 363
>
read: <Content-Type: text/html
>
read: <
>
read: <<html>
>
read: <<head>
>
read: <<title>Infobiogen est ferm� - Infobiogen is closed</title>
>
read: <</head>
>
read: <<body background="/ibgbg.png" >
>
read: <<center>
>
read: <<a href="https://lovelace.infobiogen.fr/"><font size=+2
style="color:red;background-color:white">==> Acc�s au webmail <==
</font></a>
>
read: <<br>
>
read: <<br>
>
read: <<img src="/ibg.png" ALT="Infobiogen est ferm� - Infobiogen is
closed">
>
read: <</center>
>
read: <</body>
>
read: <</html>
>
EOF ajFileGetsL file
End of file - data in buffer - return ajFalse
read: <>
=== File Buffer: Before ajFileBuffStripHtml ===
* 8076b98 HTTP/1.1 404 Not Found
80786a0 Date: Fri, 10 Oct 2008 09:11:37 GMT
8077038 Server: Apache/1.3.29 (Unix) PHP/4.3.6 mod_ssl/2.8.16 OpenSSL/0.9.6l
80785a0 Last-Modified: Wed, 26 Jul 2006 18:30:45 GMT
80785d0 ETag: "76f3e-16b-44c7b4d5;44b62a93"
807b910 Accept-Ranges: bytes
807c168 Content-Length: 363
807c9c0 Content-Type: text/html
807d218
807da70 <html>
807e2c8 <head>
807eb20 <title>Infobiogen est ferm� - Infobiogen is closed</title>
807f378 </head>
807fbd0 <body background="/ibgbg.png" >
8080428 <center>
8080c80 <a href="https://lovelace.infobiogen.fr/"><font size=+2
style="color:red;background-color:white">==> Acc�s au webmail <==
</font></a>
80814d8 <br>
8081d30 <br>
8082588 <img src="/ibg.png" ALT="Infobiogen est ferm� - Infobiogen is
closed">
8082de0 </center>
8083638 </body>
8083e90 </html>
=== end of file, free list 1 lines ===
First line [1] 'HTTP/1.1 404 Not Found
'
fileBuffLineDel removing line [0/22], 'HTTP/1.1 404 Not Found
' len 24
fileBuffLineDel removing line [0/21], 'Date: Fri, 10 Oct 2008 09:11:37 GMT
' len 37
fileBuffLineDel removing line [0/20], 'Server: Apache/1.3.29 (Unix)
PHP/4.3.6 mod_ssl/2.8.16 OpenSSL/0.9.6l
' len 70
fileBuffLineDel removing line [0/19], 'Last-Modified: Wed, 26 Jul 2006
18:30:45 GMT
' len 46
fileBuffLineDel removing line [0/18], 'ETag: "76f3e-16b-44c7b4d5;44b62a93"
' len 37
fileBuffLineDel removing line [0/17], 'Accept-Ranges: bytes
' len 22
fileBuffLineDel removing line [0/16], 'Content-Length: 363
' len 21
fileBuffLineDel removing line [0/15], 'Content-Type: text/html
' len 25
fileBuffLineDel removing line [0/14], '
' len 2
=== File Buffer: About to preprocess ===
* 807da70 <html>
807e2c8 <head>
807eb20 <title>Infobiogen est ferm� - Infobiogen is closed</title>
807f378 </head>
807fbd0 <body background="/ibgbg.png" >
8080428 <center>
8080c80 <a href="https://lovelace.infobiogen.fr/"><font size=+2
style="color:red;background-color:white">==> Acc�s au webmail <==
</font></a>
80814d8 <br>
8081d30 <br>
8082588 <img src="/ibg.png" ALT="Infobiogen est ferm� - Infobiogen is
closed">
8082de0 </center>
8083638 </body>
8083e90 </html>
=== end of file, free list 1 lines ===
ajFileBuffStripHtmlPre testing for <pre> line(s)
fileBuffLineDel removing line [0/13], '' len 0
fileBuffLineDel removing line [0/12], '' len 0
fileBuffLineDel removing line [0/11], '' len 0
fileBuffLineDel removing line [0/10], '' len 0
fileBuffLineDel removing line [0/9], '' len 0
fileBuffLineDel removing line [0/8], '' len 0
fileBuffLineDel removing line [0/7], '' len 0
fileBuffLineDel removing line [0/6], '' len 0
fileBuffLineDel removing line [0/5], '' len 0
fileBuffLineDel removing line [0/4], '' len 0
fileBuffLineDel removing line [0/3], '' len 0
fileBuffLineDel removing line [0/2], '' len 0
fileBuffLineDel removing line [0/1], '' len 0
=== File Buffer: After ajFileBuffStripHtml ===
=== end of file, free list 1 lines ===
seqRead: cleared
seqRead: seqin format 16 'genbank'
seqRead: one format specified
ajFileBuffNobuff buffsize: 0
++seqRead known format 16
++seqReadFmt format 16 (genbank) 'genbank:AB019441' feat No
seqReadGenbank
at EOF: File already read to end
ajFileReopenNext for non-list file
End of file - no new file to read - return ajFalse
Testing input buffer: IsBuff: No Eof: Yes
seqRead: (d2) seqReadFmt stat == EOF *try again*
seqRead failed - try again with format 16 'genbank'
ajFileBuffEmpty Size: 0 Pos: 0 End: Y Handle: 6 Fp: 80786b8 List; 0
Search:Yes Data:0 ajFileBuffEmpty:Yes
ajFileBuffEmpty Size: 0 Pos: 0 End: Y Handle: 6 Fp: 80786b8 List; 0
seqRead: *failed* to read sequence genbank:AB019441 using format genbank
Peter Rice wrote:
> Ashika Umanga Umagiliya wrote:
>> Thanks all for the responses,
>>
>> As Alan said I changed 'srs7bin' to 'srsbin' and tried executing both
>> of following queries:
>>
>> entret em:ab000131
>> entret uni:opsd_human
>>
>> And gave the following debug log.
>
>
> Many thanks. Easy to spot now.
>
> In all your definitions, like this one:
>
>>>>
>>>> DB em [ type: N method: srswww format: embl release: "EBI"
>>>> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz";
>>>> dbalias: "EMBL"
>>>> comment: "EMBL from the EBI" ]
>
> There is an extra ';' character at the end of the URL.
>
> Unfortunately this breaks the parsing of quotes. it loses the "dbalias"
> definition, and also gives an invalid URL.
>
> You should be able to retrieve from all the databases with the ';'
> removed.
>
> regards,
>
> Peter Rice
>
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