> I have installed cpath ver0.7 and loaded Reactome data. I am able to
> get webservice worked to retrieve html content. However when I try
> following cmd
> Can you provide me with URL you are constructing to make web service
> request ? Also, what response are you getting from server ?
> Thx
> -Benjamin
> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>> I have installed cpath ver0.7 and loaded Reactome data. I am able to
>> get webservice worked to retrieve html content. However when I try
>> following cmd
> An Error Has Occurred
> Command: 'get_neighbors' is not recognized. Please try again.
> I am trying to get result in some xml format so that I can parse and
> use for some other purpose.
> Thank you very much.
> Sincerely,
> --Pradeep
> On Wed, Oct 21, 2009 at 11:33 PM, Benjamin Gross
> <benjamin.gr...@gmail.com> wrote:
>> Pradeep,
>> Can you provide me with URL you are constructing to make web service
>> request ? Also, what response are you getting from server ?
>> Thx
>> -Benjamin
>> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>>> I have installed cpath ver0.7 and loaded Reactome data. I am able to
>>> get webservice worked to retrieve html content. However when I try
>>> following cmd
I downloaded the source from the link that is given on cPath download page.
Do I have to download latest build from SVN to avail all the
webservice functionality?
>> An Error Has Occurred
>> Command: 'get_neighbors' is not recognized. Please try again.
>> I am trying to get result in some xml format so that I can parse and
>> use for some other purpose.
>> Thank you very much.
>> Sincerely,
>> --Pradeep
>> On Wed, Oct 21, 2009 at 11:33 PM, Benjamin Gross
>> <benjamin.gr...@gmail.com> wrote:
>>> Pradeep,
>>> Can you provide me with URL you are constructing to make web service
>>> request ? Also, what response are you getting from server ?
>>> Thx
>>> -Benjamin
>>> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>>>> I have installed cpath ver0.7 and loaded Reactome data. I am able to
>>>> get webservice worked to retrieve html content. However when I try
>>>> following cmd
You shouldn't have to grab the latest build for web service
functionality, but I would grab it (we just released a new version of
cpath with enhanced searching capabilities). Would you mind
downloading the latest source and creating a new war file ?
On Oct 21, 2009, at 9:10 PM, pradeep kumar s wrote:
> I downloaded the source from the link that is given on cPath
> download page.
> Do I have to download latest build from SVN to avail all the
> webservice functionality?
> --Pradeep
> On Thu, Oct 22, 2009 at 1:30 AM, Benjamin Gross
> <benjamin.gr...@gmail.com> wrote:
>> Hi Pradeep,
>> You want to use version 2.0 for all webservice calls except
>> get_neighbors (which is version 3.0). Where did you grab the source
>> code ?
>> -B
>> On Oct 21, 2009, at 11:12 AM, pradeep kumar s wrote:
>>> An Error Has Occurred
>>> Command: 'get_neighbors' is not recognized. Please try again.
>>> I am trying to get result in some xml format so that I can parse and
>>> use for some other purpose.
>>> Thank you very much.
>>> Sincerely,
>>> --Pradeep
>>> On Wed, Oct 21, 2009 at 11:33 PM, Benjamin Gross
>>> <benjamin.gr...@gmail.com> wrote:
>>>> Pradeep,
>>>> Can you provide me with URL you are constructing to make web
>>>> service
>>>> request ? Also, what response are you getting from server ?
>>>> Thx
>>>> -Benjamin
>>>> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>>>>> I have installed cpath ver0.7 and loaded Reactome data. I am
>>>>> able to
>>>>> get webservice worked to retrieve html content. However when I try
>>>>> following cmd
As suggested by you, I tried to check out the latest CVS build. I am
unsuccessful to do so with anonymous credentials. I have been trying
it for past 2 to 3 days thinking that the server may be down. But this
appears to be persistent. Could you please check if, I am wrong on
this or some problem with server.
This is what I used:
For anonoymous CVS access:
export CVS_RSH=ssh
cvs -d :ext:anonym...@cbiocvs2.nci.nih.gov:/share/content/gforge/cpath
checkout cpath
When prompted, enter password: anonymous.
Attached is the pic of tortoiseCVS:
I faced similar problems from command line.
Thank you for the attention and help.
Regards,
--Pradeep
P.S: I have also applied for an account, yet to receive email from the admin.
> You shouldn't have to grab the latest build for web service
> functionality, but I would grab it (we just released a new version of
> cpath with enhanced searching capabilities). Would you mind
> downloading the latest source and creating a new war file ?
> On Oct 21, 2009, at 9:10 PM, pradeep kumar s wrote:
>> HI Benjamin,
>> I downloaded the source from the link that is given on cPath
>> download page.
>> Do I have to download latest build from SVN to avail all the
>> webservice functionality?
>> --Pradeep
>> On Thu, Oct 22, 2009 at 1:30 AM, Benjamin Gross
>> <benjamin.gr...@gmail.com> wrote:
>>> Hi Pradeep,
>>> You want to use version 2.0 for all webservice calls except
>>> get_neighbors (which is version 3.0). Where did you grab the source
>>> code ?
>>> -B
>>> On Oct 21, 2009, at 11:12 AM, pradeep kumar s wrote:
>>>> An Error Has Occurred
>>>> Command: 'get_neighbors' is not recognized. Please try again.
>>>> I am trying to get result in some xml format so that I can parse and
>>>> use for some other purpose.
>>>> Thank you very much.
>>>> Sincerely,
>>>> --Pradeep
>>>> On Wed, Oct 21, 2009 at 11:33 PM, Benjamin Gross
>>>> <benjamin.gr...@gmail.com> wrote:
>>>>> Pradeep,
>>>>> Can you provide me with URL you are constructing to make web
>>>>> service
>>>>> request ? Also, what response are you getting from server ?
>>>>> Thx
>>>>> -Benjamin
>>>>> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>>>>>> I have installed cpath ver0.7 and loaded Reactome data. I am
>>>>>> able to
>>>>>> get webservice worked to retrieve html content. However when I try
>>>>>> following cmd
> As suggested by you, I tried to check out the latest CVS build. I am
> unsuccessful to do so with anonymous credentials. I have been trying
> it for past 2 to 3 days thinking that the server may be down. But this
> appears to be persistent. Could you please check if, I am wrong on
> this or some problem with server.
> This is what I used:
> For anonoymous CVS access:
> export CVS_RSH=ssh
> cvs -d :ext:anonym...@cbiocvs2.nci.nih.gov:/share/content/gforge/cpath
> checkout cpath
> When prompted, enter password: anonymous.
> Attached is the pic of tortoiseCVS:
> I faced similar problems from command line.
> Thank you for the attention and help.
> Regards,
> --Pradeep
> P.S: I have also applied for an account, yet to receive email from
> the admin.
> On Thu, Oct 22, 2009 at 11:58 AM, Benjamin Gross
> <benjamin.gr...@gmail.com> wrote:
>> You shouldn't have to grab the latest build for web service
>> functionality, but I would grab it (we just released a new version of
>> cpath with enhanced searching capabilities). Would you mind
>> downloading the latest source and creating a new war file ?
>> On Oct 21, 2009, at 9:10 PM, pradeep kumar s wrote:
>>> HI Benjamin,
>>> I downloaded the source from the link that is given on cPath
>>> download page.
>>> Do I have to download latest build from SVN to avail all the
>>> webservice functionality?
>>> --Pradeep
>>> On Thu, Oct 22, 2009 at 1:30 AM, Benjamin Gross
>>> <benjamin.gr...@gmail.com> wrote:
>>>> Hi Pradeep,
>>>> You want to use version 2.0 for all webservice calls except
>>>> get_neighbors (which is version 3.0). Where did you grab the
>>>> source
>>>> code ?
>>>> -B
>>>> On Oct 21, 2009, at 11:12 AM, pradeep kumar s wrote:
>>>>> An Error Has Occurred
>>>>> Command: 'get_neighbors' is not recognized. Please try again.
>>>>> I am trying to get result in some xml format so that I can parse
>>>>> and
>>>>> use for some other purpose.
>>>>> Thank you very much.
>>>>> Sincerely,
>>>>> --Pradeep
>>>>> On Wed, Oct 21, 2009 at 11:33 PM, Benjamin Gross
>>>>> <benjamin.gr...@gmail.com> wrote:
>>>>>> Pradeep,
>>>>>> Can you provide me with URL you are constructing to make web
>>>>>> service
>>>>>> request ? Also, what response are you getting from server ?
>>>>>> Thx
>>>>>> -Benjamin
>>>>>> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>>>>>>> I have installed cpath ver0.7 and loaded Reactome data. I am
>>>>>>> able to
>>>>>>> get webservice worked to retrieve html content. However when I
>>>>>>> try
>>>>>>> following cmd
Thanks for uploading the latest build. But I get errors when I try to
build the source.
It complains of missing classes:
1)In org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteGetParentsXmlResponse
class, org.mskcc.pathdb.schemas.summary_response package does not
exist.
2)In org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteSearchXmlResponse
class, org.mskcc.pathdb.schemas.search_response package does not
exist.
Please do the needful.
Question2:
Documentation of cpath mentions about Biogrid(PSI format) to biopax
converters. where can I find the scripts to convert in cpath src
directory?
> I've put cpath.zip into the pc-dump directory of the cbio web server I
> referred you to last week. That contains the lastest code.
> Let me know if you have any problems with it.
> Regards,
> -Benjamin
> On Oct 25, 2009, at 9:14 PM, pradeep kumar s wrote:
>> Dear Benjamin,
>> As suggested by you, I tried to check out the latest CVS build. I am
>> unsuccessful to do so with anonymous credentials. I have been trying
>> it for past 2 to 3 days thinking that the server may be down. But this
>> appears to be persistent. Could you please check if, I am wrong on
>> this or some problem with server.
>> This is what I used:
>> For anonoymous CVS access:
>> export CVS_RSH=ssh
>> cvs -d :ext:anonym...@cbiocvs2.nci.nih.gov:/share/content/gforge/cpath
>> checkout cpath
>> When prompted, enter password: anonymous.
>> Attached is the pic of tortoiseCVS:
>> I faced similar problems from command line.
>> Thank you for the attention and help.
>> Regards,
>> --Pradeep
>> P.S: I have also applied for an account, yet to receive email from
>> the admin.
>> On Thu, Oct 22, 2009 at 11:58 AM, Benjamin Gross
>> <benjamin.gr...@gmail.com> wrote:
>>> You shouldn't have to grab the latest build for web service
>>> functionality, but I would grab it (we just released a new version of
>>> cpath with enhanced searching capabilities). Would you mind
>>> downloading the latest source and creating a new war file ?
>>> On Oct 21, 2009, at 9:10 PM, pradeep kumar s wrote:
>>>> HI Benjamin,
>>>> I downloaded the source from the link that is given on cPath
>>>> download page.
>>>> Do I have to download latest build from SVN to avail all the
>>>> webservice functionality?
>>>> --Pradeep
>>>> On Thu, Oct 22, 2009 at 1:30 AM, Benjamin Gross
>>>> <benjamin.gr...@gmail.com> wrote:
>>>>> Hi Pradeep,
>>>>> You want to use version 2.0 for all webservice calls except
>>>>> get_neighbors (which is version 3.0). Where did you grab the
>>>>> source
>>>>> code ?
>>>>> -B
>>>>> On Oct 21, 2009, at 11:12 AM, pradeep kumar s wrote:
>>>>>> An Error Has Occurred
>>>>>> Command: 'get_neighbors' is not recognized. Please try again.
>>>>>> I am trying to get result in some xml format so that I can parse
>>>>>> and
>>>>>> use for some other purpose.
>>>>>> Thank you very much.
>>>>>> Sincerely,
>>>>>> --Pradeep
>>>>>> On Wed, Oct 21, 2009 at 11:33 PM, Benjamin Gross
>>>>>> <benjamin.gr...@gmail.com> wrote:
>>>>>>> Pradeep,
>>>>>>> Can you provide me with URL you are constructing to make web
>>>>>>> service
>>>>>>> request ? Also, what response are you getting from server ?
>>>>>>> Thx
>>>>>>> -Benjamin
>>>>>>> On Oct 20, 4:40 am, pradeep <pradeep20...@gmail.com> wrote:
>>>>>>>> I have installed cpath ver0.7 and loaded Reactome data. I am
>>>>>>>> able to
>>>>>>>> get webservice worked to retrieve html content. However when I
>>>>>>>> try
>>>>>>>> following cmd
>> 1)In >> org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteGetParentsXmlResponse >> class, org.mskcc.pathdb.schemas.summary_response package does not >> exist. >> 2)In >> org.mskcc.pathdb.action.web_api.biopax_mode.ExecuteSearchXmlResponse >> class, org.mskcc.pathdb.schemas.search_response package does not >> exist. >> Please do the needful.
These packages get created when you run ant. How are you building the source ?
>> Question2:
>> Documentation of cpath mentions about Biogrid(PSI format) to biopax >> converters. where can I find the scripts to convert in cpath src >> directory?
I've placed psi-2-biopax.zip onto the web server (pc-dump dir) which contains the psi to biopax converter. To use the converter, you need to set an environment variable PATHWAY_TOOLS_ROOT with the paths to the jars in this zip. You can process an entire directory using psi- mi-batch-converter.py or a single file using psi-mi-converter.sh.
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