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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