JSON tcl parser error

[Luc Moulinier]

Hello !

I try to parse a JSON string receieved from a web server used quite a lot by the bioinformatics community (EBI web services).
Parsing the string using tcllib jason package failed, as well as the json-procs.tcl from OpenFACS. Both parsers give the same error message :

unexpected token "[" at position 2; expecting STRING
while executing
"unexpected $tokenCursor $token "STRING""
(procedure "parseObjectMember" line 26)

Is there a bug in JSON Tcl parser, or is it really a mal-formed JSON string ?
(As far as I can unserstand, it seems it doesn't like the first element to be a JSON array ...)

Many thanks for your help !!
Luc

The JSON text is :

{[{"model_length":"76","align":["#HMM tvaGrvtsisdrsggkvifidlrDgt.griqvvlfreeatklaenlkeGdvvrvtGrvkrr....pgg...elelkveeiell","#MATCH ++ G++ ++ +r g+++if lrD ++iq+v ++ +l++ ++ +dvv++ G ++ + + e+e++ e+i++l","#PP 579***********************6677887777....*********************66651.15779********986","#SEQ VLNGWIEQKPKRVGKNLIFGLLRDSNgDIIQLVDNK----SLLKGFTLEDVVQAVGILSLKrklsN-EdadEYEVQLEDITVL"],"env":{"to":"128","from":"50"},"name":"tRNA_anti-codon","acc":"PF01336.22","sig":1,"evalue":"1.6e-06","hmm":{"to":"76","from":"2"},"desc":"OB-fold nucleic acid binding domain","act_site":null,"type":"Domain","bits":"27.9","clan":"CL0021","seq":{"to":"128","from":"51","name":"SYDM_YEAST"}},{"model_length":"314","align":["#HMM knryldlrtekvsavlrlrstvtkavrkyleengfieietPiLvksdteegarlFkvksrekek....effaLtqspqlylellivagldrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeeeimqvleelikslvkevlessakeiefvirrns.....kdlkkpfkrltykeaieklneigkdldkaderalvk......................................................................................................................................keknepvfvtdfP............................aelkpFyakkeedd........kkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPk","#MATCH ++ryl+lr++k+++ l+ rs++ k +r+ +++ +f+e+etP+L+k+ t+egar+F+v++r+k++ +f+aL qspq+y++ll+++g+++++q+ar+FR+Ed+r+dr++ EFtq+++em+f++ e++m+++e+ ++ +++++ +++++ ++ + + + ++ + ++ r+ty++a++ +++dk+d+ra +k + +++dfP ++++pF++ k +d+ k+l ++yDl++ngvEl+gGs+Ri+dp+++ ++++ + ++a e f+++l+a+++G+pph+G+++G+dR++++++++esIrdviaFPk","#PP 79********************************************.***************444567******************************************.********************************.6666888888777778887444444599**********.....**********98789**********************************************************************************************************************************999999**********************************************************************************************99999***********************************************9","#SEQ EFRYLQLRNPKYQDFLKKRSSISKEIRNSFNNFDFTEVETPMLFKA-TPEGAREFLVPTRTKRSdgkpSFYALDQSPQQYKQLLMASGVNKYYQMARCFRDEDLRADRQP-EFTQVDMEMAFANSEDVMKIIEKTVSGVWSKF-SKKRGLLTLDSKGTLvpakkENGTVSIFRMTYEQAMTS-----YGIDKPDLRAPDLkiinlgefnafshlnkkfpvfeviilrsafsnmeeykerwsfltnnsnynyrvpivlpiendeqansnwfenfhaiatfenphlitkflklkkgdivcgctrepnhsifenptplgrlrqlvlqsehgkniyhaVNKDVASWIVDFPlfspviiedksgkkeklaypeyekdrlcSTHHPFTMVKLKDYeklektpeKCLGRHYDLVVNGVELGGGSTRIHDPRLQDYIFEDILKIDNAYELFGHLLNAFDMGTPPHAGFAIGFDRMCAMICETESIRDVIAFPK"],"env":{"to":"628","from":"145"},"name":"tRNA-synt_2","acc":"PF00152.17","sig":1,"evalue":"4.7e-101","hmm":{"to":"312","from":"7"},"desc":"tRNA synthetases class II (D, K and N) ","act_site":null,"type":"Domain","bits":"337.8","clan":"CL0040","seq":{"to":"626","from":"150","name":"SYDM_YEAST"}}]}

[Rich]

Luc Moulinier <luc.mo...@igbmc.fr> wrote:
> Hello !
>
> I try to parse a JSON string receieved from a web server used quite a
> lot by the bioinformatics community (EBI web services). Parsing the
> string using tcllib jason package failed, as well as the
> json-procs.tcl from OpenFACS. Both parsers give the same error
> message :
>
> unexpected token "[" at position 2; expecting STRING
> while executing
> "unexpected $tokenCursor $token "STRING""
> (procedure "parseObjectMember" line 26)
>
> Is there a bug in JSON Tcl parser, or is it really a mal-formed JSON string ?
>

> {[...]}

How did you download this string from the server (i.e., what's the
download code look like?).

I ask because it is common to get curly brackets around a string when
interpreting something that is a list as if it were a string:

$ rlwrap tclsh
% set list [list "hello goodbye"]
{hello goodbye}
% puts $list
{hello goodbye}
%

The curlies above are added by the Tcl list->string formatting
procedure when you try to display the list as if it were a string.

Is it possible you have a Tcl list, and you are not doing [lindex $list
0] to get the string content of the first (or whichever) element?

[Rich]

Luc Moulinier <luc.mo...@igbmc.fr> wrote:
> Hello !
>
> I try to parse a JSON string receieved from a web server used quite a
> lot by the bioinformatics community (EBI web services). Parsing the
> string using tcllib jason package failed, as well as the
> json-procs.tcl from OpenFACS. Both parsers give the same error
> message :

Pasting your sample string here
https://jsonformatter.curiousconcept.com/ results in the same error but
a different message text. So this string is invalid.

Now you just need to figure out how it is becoming invalid.

[Luc Moulinier]

Many thanks !
You analysis is right ! Getting the real string solves the problem !

Thanks again !
Luc