[Rd] Post CGI forms with built-in R function?
Mike Schaffer
mschaff at bu.edu
Thu Jul 20 17:01:17 CEST 2006
Thanks Duncan. I figured there was some limit.
Your suggestion to check out the httpRequest code has me headed in
the right direction, but I am having problems with the data returned
from the socketConnection. Some of the returned data appears to
improperly decoded. I don't know if I've stumbled on a low-level
socket bug, or I need to error check the results myself. Can anyone
figure out the problem in the code below?
This was run using R version 2.3.1 (2006-06-01) on both Linux and OS
X with the same results.
# First, the correctly formatted data for comparison is returned by
the code below. As we've established, this works fine, but I can't
use it with long URIs:
full.url<-"http://genomics11.bu.edu/cgi-bin/Tractor_dev/external/
get_msa.cgi?
user_id=0&table=seqs_ucsc_hg18&len=350&gene_set_ids=NM_000029,NM_000064,
NM_000066&orgs=Hs,mm8,canFam2"
read<-readLines(full.url)
# This returns three tab-delimited lines with a header row.
> read
[1] "NA\tHs\tmm8\tcanFam2"
[2] "NM_000029\tTAAGCA--AGACTC-TCCCCTGCCCTCTGCCCTCTGCACCTCCGG---
CCTGCATGTC----------CCTGTGGCCTCTTGGGGGTACATCTCCCGGGG---
CTGGGTCAGAAG---------GCCTGGGTGGTTGGCCTCAGG------------------------
CTGTCACACACCTAGGGAGATGCTC------------------
CCGTTTCTGGGAACCTTGGCCCCGACTCCTGCA----
AACTTCGGTAAATGTGTAACTCGACCCTGCACCGGCTC----------------
ACTCTGTTCAGCA----GTGAAACTCTGCATCGATCACTAAGACTTCCTGG-
AAGAGGTCCCAGCGT----GAGTGTCGCT---
TCTGGCATCTGTCCTTCTGG---------------------CCAGCCTGTGGTC--------------
TGG-CCAAGTGATGTAACCCTCCTCT---CCAGCCT\tTGCAAGTGAGCCCC-
CTTCCTG-----------------------------GCATGCC----------CAGAGAGGCTTACG--
AGTGCATCACGAGGGGG-CTTTCATCCCAAG---------
GTCTGCATGGCTGGCTTCAGG------------------------TTGTCACAACCC-----
ACTCAATC------------------CTGTGACTG-------TGGTCCTGGCTCCAGGG----
AACTGGGGTAAATGTGTAACCCAAGGCCAGCC----------------------
TATTTTTGCATGA----GGCT-------CATCTGCCAGTAGGGCTTCCTGG-AAGGGG-
CCCAGAG-----GAACATCAC----CCTGGCCCTGATCCATCTTGGT-------------------
CAAGCCTGGATTCTCA-----------TGG-TTCCCTGATCTGGGTCCTCCC----CCAGCCT
\tCCGG----GGCTCC-TTCCCTG--------------CGCCCTGGGGCCTCAGCACATT----------
CTTGGGGACTCTCAGAAGCACACCTCGAGAGG--GCTCTGTCAGAAG---------GCTTG-
GTGGCTGGCCTCGGC------------------------
TTGTCACAGCTCAGGGCAGAGACGCGACACACACACCTACACACAGGTACGGGGCGCTCCGGACCCGGCCCG
GGCAGGGGAGCTGCGGTCAATGTGTAACTCGGCGGCCCAGCGGCTC----------------
GTTCTGCTCAGCA----CAGAAAGTGTGCATCGATCTCCCTGACTTCCTGG-
AAGGCGTCCCAGCCT----GAGAGTAGCT----CTGGCGCCTGTACCCCCCACC------
CCCGTGGGGCCCCCACCCCCATGGTC--------------GGG-
CCAAGTGATGTCACCTCCCGCCTCCCCAGCCT"
[3] "NM_000064\tC-------------------------------------
CAAAAGTGAACTGGGG-ATGAG-GTCCAAGACATCTGCGGTGGGGGGTT-
CTCCAGACCTTAGTGTTCTTC--CACTACAAAGTGGGTCCAACAGAGAAAGG------------
TCTGTG----------------TTCACCAGGTGG---CCCTGACCC---
TGGGAGAGTCCAGGGCAGGGTGCAGCTGCATTCATGCTGCTGGG----GAACATGC-
CCTCAGGTTACTCACCCCATGGA----CATGTTGGCC-CCAGGGACTGAAAA-GCTTAG----
GAAATGGTATTGAGAAATCTGGGGCAGC-CCCAAAAGGG-GAGAGG--CCATGGGGAGAAGGGG--
GGGCTGAG----TGGGGGAAAGGCAGGAGCCAG--ATAAAA----AGCCAGCTCCAGCAGGCGCTGCTCA
\tATTTAGCAAGACCTTGGGGGTAGGGAGAACCAGCCATCCAGAAGTG--CTGGGTTACTGG-
GACCCAGCTAAGTGTGGGAGGAGGTCACTCTAGACTTCAATGGTCTCTGGTGTAACCAAGTA----
CAACAGGGACCAG------------CCCAGG----------------TTCAGCATCTGG---
CCTTGACCC---CAAGAAAAGCCTGAGCCAAG--
CAGGTACTTTCAAGCTCCAGGGTAATGGAAATGTGCCTAGGGTTACTCACCCCA-AGG----
CTTGTTGCCC-CAGGTTTGTGAAAAAGCTTAG----GAAACTATGTTGCGAAATTTTGGGCAGT-
CCCTGGTG--------------CAGGAACAGGGAG--GGACCAGA------GAGGA-------
GAGCCAT--ATAAAG----AGCCAGCGGCTACAGCCCCAGCTCG
\t----------------------------------------------------------------------
---------------------------------------------------------
CCACGGGGAAAGG------------T----------------------TCACCAGCTGG---
CCTTGACCC---TGAGGGAGGCCATGGCAAGGGGAAGGTGTGTTCATGTTGCAGGA----GGACATGC-
CCTTGGGTTAGTTACCCCC--GA----CACACTGGCC-CCGGGGATTGAAAA-ACTTAG----
GAAATGGTATTGAGTAATCTGGGGCAGC-TGCAGGGAGG-GGGAGG--
CTACAGGAGCTGTGGGCTGGGCTGAA---GGTGGGGGGAGGCTGGGGCCAG--ATAAAA----
GGCAATCCCCAACAGCCTCTGCTCA"
[4] "NM_000066
\tAGCTGTTAGGTTGGTGCAAAAGTAATTGTGGTTTTTGCCATTAAAAGCAATGACAA--------------
--AAACTG-------------
CAATTACTTTTGCACCAACCTAGTCAGTGGCAGAGAATGTACTTGAACCCAGGCTGTCTAGACCTAGATCCC
ACAGTCCTTGCCACCTCA--CTAATAGCCTGTCCAC---TTGGCAGCTTACCCTAAAGTTA-----
CAGAGGAATAAACACCATGCTGCTACA-
GATTTTTCATTAT-----------------------------------
TCTGGTTGGTTTCCAGAGTGACAGG---TAAGTTT-TTGGTC-TGTGCAAAGTCTG-----
TTTCCAGTCACTAGTGGCTTTCTGTTTACTTTGCAGAGCTATTTGCTCT-TGGGGACAGAAGCTGACAGT
\t----------------------------------------------------------------------
------------------------------------------------------------------------
--------------------------------------------------------------
GGCTGCTT-CCATGGAATCA---------------------------------
CAGTTCTCACTGT-----------------------------------CCTAG---
GTGTGCGGTATCACAAG---TGAGTACATTCGTGCTGTGCAAAGCTGA----
GGTTCCAGGTACAAGCG----CCTGTTTGCTTTGCTGACCTGTTTGCTCTATGTCAACAGAA-
CTGAGAGC
\t----------------------------------------------------------------------
-------------------------------------------
GCAAGTGGCAGAGAAAGGATTTGAACCCAGGCAGTCTGGACCTCGAGCC--------------
CCTCATCCTAACAGCTTGTCCTT---TTGGCTGCCT--------CTTT-----
CTTGTGTAGAA-------------------
CTTTCCATTGT-----------------------------------
TCTCCCTGGTGTCCAGAGTCATAGG---TAAGT-T-TCTGTC-
TGTACAAAGTCTAAGGGGTTTCCGGTCACTGTTGATTTTTTGTTTACTTTGCTGACCTGTTTGCTCTATGGG
GACAGAAGCTGACAGC"
# Now, if I try to use sockets with a POST request, I get some of
the correct data, but some of it is incorrect or improperly decoded:
host<-"genomics11.bu.edu"
path<-"/cgi-bin/Tractor_dev/external/get_msa.cgi"
dat<-"user_id=0&table=seqs_ucsc_hg18&len=350&gene_set_ids=NM_000029,NM_0
00064,NM_000066&orgs=Hs,mm8,canFam2"
len <- length( strsplit(dat,"")[[1]])
request<-paste("POST ",path," HTTP/1.1\nHost: ",host,"\nReferer:
\nContent-type: application/x-www-form-urlencoded\nContent-length:
",len,"\nConnection: Keep-Alive\n\n",dat,sep="")
fp <- socketConnection(host=host,port=80,server=FALSE,blocking=TRUE)
write(request,fp)
socketSelect(list(fp)) # Wait until results are ready
sock<-readLines(fp)
close(fp)
# Returns:
> sock
[1] "HTTP/1.1 200 OK"
[2] "Date: Thu, 20 Jul 2006 14:27:37 GMT"
[3] "Server: Apache/2.0.53 (Fedora)"
[4] "Connection: close"
[5] "Transfer-Encoding: chunked"
[6] "Content-Type: text/plain; charset=ISO-8859-1"
[7] ""
[8] "fd0"
[9] "NA\tHs\tmm8\tcanFam2"
[10] "NM_000029\tTAAGCA--AGACTC-TCCCCTGCCCTCTGCCCTCTGCACCTCCGG---
CCTGCATGTC----------CCTGTGGCCTCTTGGGGGTACATCTCCCGGGG---
CTGGGTCAGAAG---------GCCTGGGTGGTTGGCCTCAGG------------------------
CTGTCACACACCTAGGGAGATGCTC------------------
CCGTTTCTGGGAACCTTGGCCCCGACTCCTGCA----
AACTTCGGTAAATGTGTAACTCGACCCTGCACCGGCTC----------------
ACTCTGTTCAGCA----GTGAAACTCTGCATCGATCACTAAGACTTCCTGG-
AAGAGGTCCCAGCGT----GAGTGTCGCT---
TCTGGCATCTGTCCTTCTGG---------------------CCAGCCTGTGGTC--------------
TGG-CCAAGTGATGTAACCCTCCTCT---CCAGCCT\tTGCAAGTGAGCCCC-
CTTCCTG-----------------------------GCATGCC----------CAGAGAGGCTTACG--
AGTGCATCACGAGGGGG-CTTTCATCCCAAG---------
GTCTGCATGGCTGGCTTCAGG------------------------TTGTCACAACCC-----
ACTCAATC------------------CTGTGACTG-------TGGTCCTGGCTCCAGGG----
AACTGGGGTAAATGTGTAACCCAAGGCCAGCC----------------------
TATTTTTGCATGA----GGCT-------CATCTGCCAGTAGGGCTTCCTGG-AAGGGG-
CCCAGAG-----GAACATCAC----CCTGGCCCTGATCCATCTTGGT-------------------
CAAGCCTGGATTCTCA-----------TGG-TTCCCTGATCTGGGTCCTCCC----CCAGCCT
\tCCGG----GGCTCC-TTCCCTG--------------CGCCCTGGGGCCTCAGCACATT----------
CTTGGGGACTCTCAGAAGCACACCTCGAGAGG--GCTCTGTCAGAAG---------GCTTG-
GTGGCTGGCCTCGGC------------------------
TTGTCACAGCTCAGGGCAGAGACGCGACACACACACCTACACACAGGTACGGGGCGCTCCGGACCCGGCCCG
GGCAGGGGAGCTGCGGTCAATGTGTAACTCGGCGGCCCAGCGGCTC----------------
GTTCTGCTCAGCA----CAGAAAGTGTGCATCGATCTCCCTGACTTCCTGG-
AAGGCGTCCCAGCCT----GAGAGTAGCT----CTGGCGCCTGTACCCCCCACC------
CCCGTGGGGCCCCCACCCCCATGGTC--------------GGG-
CCAAGTGATGTCACCTCCCGCCTCCCCAGCCT"
[11] "NM_000064\tC-------------------------------------
CAAAAGTGAACTGGGG-ATGAG-GTCCAAGACATCTGCGGTGGGGGGTT-
CTCCAGACCTTAGTGTTCTTC--CACTACAAAGTGGGTCCAACAGAGAAAGG------------
TCTGTG----------------TTCACCAGGTGG---CCCTGACCC---
TGGGAGAGTCCAGGGCAGGGTGCAGCTGCATTCATGCTGCTGGG----GAACATGC-
CCTCAGGTTACTCACCCCATGGA----CATGTTGGCC-CCAGGGACTGAAAA-GCTTAG----
GAAATGGTATTGAGAAATCTGGGGCAGC-CCCAAAAGGG-GAGAGG--CCATGGGGAGAAGGGG--
GGGCTGAG----TGGGGGAAAGGCAGGAGCCAG--ATAAAA----AGCCAGCTCCAGCAGGCGCTGCTCA
\tATTTAGCAAGACCTTGGGGGTAGGGAGAACCAGCCATCCAGAAGTG--CTGGGTTACTGG-
GACCCAGCTAAGTGTGGGAGGAGGTCACTCTAGACTTCAATGGTCTCTGGTGTAACCAAGTA----
CAACAGGGACCAG------------CCCAGG----------------TTCAGCATCTGG---
CCTTGACCC---CAAGAAAAGCCTGAGCCAAG--
CAGGTACTTTCAAGCTCCAGGGTAATGGAAATGTGCCTAGGGTTACTCACCCCA-AGG----
CTTGTTGCCC-CAGGTTTGTGAAAAAGCTTAG----GAAACTATGTTGCGAAATTTTGGGCAGT-
CCCTGGTG--------------CAGGAACAGGGAG--GGACCAGA------GAGGA-------
GAGCCAT--ATAAAG----AGCCAGCGGCTACAGCCCCAGCTCG
\t----------------------------------------------------------------------
---------------------------------------------------------
CCACGGGGAAAGG------------T----------------------TCACCAGCTGG---
CCTTGACCC---TGAGGGAGGCCATGGCAAGGGGAAGGTGTGTTCATGTTGCAGGA----GGACATGC-
CCTTGGGTTAGTTACCCCC--GA----CACACTGGCC-CCGGGGATTGAAAA-ACTTAG----
GAAATGGTATTGAGTAATCTGGGGCAGC-TGCAGGGAGG-GGGAGG--
CTACAGGAGCTGTGGGCTGGGCTGAA---GGTGGGGGGAGGCTGGGGCCAG--ATAAAA----
GGCAATCCCCAACAGCCTCTGCTCA"
[12] "NM_000066
\tAGCTGTTAGGTTGGTGCAAAAGTAATTGTGGTTTTTGCCATTAAAAGCAATGACAA--------------
--AAACTG-------------
CAATTACTTTTGCACCAACCTAGTCAGTGGCAGAGAATGTACTTGAACCCAGGCTGTCTAGACCTAGATCCC
ACAGTCCTTGCCACCTCA--CTAATAGCCTGTCCAC---TTGGCAGCTTACCCTAAAGTTA-----
CAGAGGAATAAACACCATGCTGCTACA-
GATTTTTCATTAT-----------------------------------
TCTGGTTGGTTTCCAGAGTGACAGG---TAAGTTT-TTGGTC-TGTGCAAAGTCTG-----
TTTCCAGTCACTAGTGGCTTTCTGTTTACTTTGCAGAGCTATTTGCTCT-TGGGGACAGAAGCTGACAGT
\t----------------------------------------------------------------------
------------------------------------------------------------------------
--------------------------------------------------------------
GGCTGCTT-CCATGGAATCA---------------------------------
CAGTTCTCACTGT-----------------------------------CCTAG---
GTGTGCGGTATCACAAG---TGAGTACATTCGTGCTGTGCAAAGCTGA----
GGTTCCAGGTACAAGCG----CCTGTTTGCTTTGCTGACCTGTTTGCTCTATGTCAACAGAA-
CTGAGAGC
\t----------------------------------------------------------------------
-------------------------------------------
GCAAGTGGCAGAGAAAGGATTTGAACCCAGGCAGTCTGGACCTCGAGCC--------------
CCTCATCCTAACAGCTTGTCCTT---TTGGCTGCCT--------CTTT-----
CTTGTGTAGAA-------------------CTTTCCATTGT------"
[13] "a1"
[14] "-----------------------------TCTCCCTGGTGTCCAGAGTCATAGG---TAAGT-
T-TCTGTC-
TGTACAAAGTCTAAGGGGTTTCCGGTCACTGTTGATTTTTTGTTTACTTTGCTGACCTGTTTGCTCTATGGG
GACAGAAGCTGACAGC"
[15] ""
[16] "0"
[17] ""
Element 13 appears to be improperly decoded hexadecimal data. Can
anyone shed some light on why this is? Are the strings too long for
the readLines command to properly read from the socket? Thanks for
any additional help anyone can provide.
--
Mike
On Jul 20, 2006, at 9:49 AM, Duncan Temple Lang wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>
> There is a hard coded limit of 4096 characters in
> RxmlNanoHTTPScanURL and other ScanURL routines in nanohttp.c
> and nanoftp.c. And your URI is 5138 and so walks past the bounds
> of the array of length 4096.
>
> I am not yet convinced that it is worthwhile to increase this limit to
> a larger number. Using POST in this context really is a better
> solution. But we do need to add checks to the code to ensure that
> the URI string is smaller than 4096.
>
> I'll try to get an opportunity to do that tomorrow before I take off.
>
> D.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> - --
> Duncan Temple Lang duncan at wald.ucdavis.edu
> Department of Statistics work: (530) 752-4782
> 4210 Mathematical Sciences Building fax: (530) 752-7099
> One Shields Ave.
> University of California at Davis
> Davis,
> CA 95616,
> USA
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