ambit2.pubchem

Class PUGProcessor

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<List<IStructureRecord>,List<IStructureRecord>>

ambit2.pubchem.PUGProcessor

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<List<IStructureRecord>,List<IStructureRecord>>

public class PUGProcessor
extends net.idea.modbcum.p.DefaultAmbitProcessor<List<IStructureRecord>,List<IStructureRecord>>

Queries Pubchem Power User Gateway. All communication to PUG is via XML sent to the CGI at the URL: http://pubchem.ncbi.nlm.nih.gov/pug/pug.cgi

Author:

Nina Jeliazkova nina@acad.bg Modified Apr 20, 2008

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Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	PCT_attribute_value
protected static String[]	PCT_download_compression
protected static int	PCT_download_compression_bzip2
protected static int	PCT_download_compression_gzip
protected static int	PCT_download_compression_none
protected static String[]	PCT_download_format
protected static int	PCT_download_format_binary_asn
protected static int	PCT_download_format_sdf
protected static int	PCT_download_format_text_asn
protected static int	PCT_download_format_xml
protected static String[]	PCT_status
static String	PUBCHEM_CID
protected static String	pugURL
protected boolean	retrieveConformers
protected QuerySupport<List<IStructureRecord>,List<IStructureRecord>>	support
protected static String	tag_PCT_Data
protected static String	tag_PCT_Data_input
protected static String	tag_PCT_Data_output
protected static String	tag_PCT_Download
protected static String	tag_PCT_download_3D
protected static String	tag_PCT_Download_compression
protected static String	tag_PCT_Download_format
protected static String	tag_PCT_Download_uids
protected static String	tag_PCT_Download_URL
protected static String	tag_PCT_Download_URL_url
protected static String	tag_PCT_ID_List
protected static String	tag_PCT_ID_List_db
protected static String	tag_PCT_ID_List_uids
protected static String	tag_PCT_ID_List_uids_E
protected static String	tag_PCT_InputData
protected static String	tag_PCT_InputData_download
protected static String	tag_PCT_OutputData
protected static String	tag_PCT_OutputData_output
protected static String	tag_PCT_OutputData_output_download_url
protected static String	tag_PCT_OutputData_output_waiting
protected static String	tag_PCT_OutputData_status
protected static String	tag_PCT_QueryUids
protected static String	tag_PCT_QueryUids_ids
protected static String	tag_PCT_Waiting
protected static String	tag_PCT_Waiting_reqid

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
PUGProcessor()

Method Summary

Modifier and Type	Method and Description
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	createDownloadHTTPRequest(List<IStructureRecord> record)
void	createDownloadRequest(List<IStructureRecord> sids, Writer out)
static void	createPollRequest(IStructureRecord regid, Writer out)
protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>>	createPollRequest(List<IStructureRecord> waitingregids)
protected static Element	getNodes(Document doc, Element parent, String tag)
boolean	isRetrieveConformers()
static List<IStructureRecord>	parseOutput(Document doc)
List<IStructureRecord>	process(List<IStructureRecord> target) Example: You want to download CID 1 and CID 99 being uids 1 and 99 in the 'pccompound' Entrez database in SDF format with gzip compression.
protected static List<IStructureRecord>	processDownloadURL(Document doc, Element download)
protected static List<IStructureRecord>	processWaiting(Document doc, Element waiting)
void	setRetrieveConformers(boolean retrieveConformers)

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

PUBCHEM_CID

public static final String PUBCHEM_CID

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Constant Field Values

pugURL

protected static String pugURL

support

protected QuerySupport<List<IStructureRecord>,List<IStructureRecord>> support

PCT_attribute_value

protected static final String PCT_attribute_value

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Constant Field Values

PCT_status

protected static final String[] PCT_status

PCT_download_compression_none

protected static final int PCT_download_compression_none

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Constant Field Values

PCT_download_compression_gzip

protected static final int PCT_download_compression_gzip

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Constant Field Values

PCT_download_compression_bzip2

protected static final int PCT_download_compression_bzip2

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Constant Field Values

PCT_download_compression

protected static final String[] PCT_download_compression

PCT_download_format_text_asn

protected static final int PCT_download_format_text_asn

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Constant Field Values

PCT_download_format_binary_asn

protected static final int PCT_download_format_binary_asn

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Constant Field Values

PCT_download_format_xml

protected static final int PCT_download_format_xml

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Constant Field Values

PCT_download_format_sdf

protected static final int PCT_download_format_sdf

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Constant Field Values

PCT_download_format

protected static final String[] PCT_download_format

tag_PCT_Data

protected static final String tag_PCT_Data

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Constant Field Values

tag_PCT_Data_input

protected static final String tag_PCT_Data_input

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Constant Field Values

tag_PCT_Data_output

protected static final String tag_PCT_Data_output

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Constant Field Values

tag_PCT_InputData

protected static final String tag_PCT_InputData

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Constant Field Values

tag_PCT_OutputData

protected static final String tag_PCT_OutputData

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Constant Field Values

tag_PCT_OutputData_status

protected static final String tag_PCT_OutputData_status

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Constant Field Values

tag_PCT_OutputData_output

protected static final String tag_PCT_OutputData_output

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Constant Field Values

tag_PCT_OutputData_output_download_url

protected static final String tag_PCT_OutputData_output_download_url

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Constant Field Values

tag_PCT_Download_URL

protected static final String tag_PCT_Download_URL

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Constant Field Values

tag_PCT_Download_URL_url

protected static final String tag_PCT_Download_URL_url

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Constant Field Values

tag_PCT_OutputData_output_waiting

protected static final String tag_PCT_OutputData_output_waiting

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Constant Field Values

tag_PCT_Waiting

protected static final String tag_PCT_Waiting

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Constant Field Values

tag_PCT_Waiting_reqid

protected static final String tag_PCT_Waiting_reqid

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Constant Field Values

tag_PCT_InputData_download

protected static final String tag_PCT_InputData_download

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Constant Field Values

tag_PCT_Download

protected static final String tag_PCT_Download

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Constant Field Values

tag_PCT_Download_uids

protected static final String tag_PCT_Download_uids

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Constant Field Values

tag_PCT_QueryUids

protected static final String tag_PCT_QueryUids

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Constant Field Values

tag_PCT_QueryUids_ids

protected static final String tag_PCT_QueryUids_ids

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Constant Field Values

tag_PCT_ID_List

protected static final String tag_PCT_ID_List

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Constant Field Values

tag_PCT_ID_List_uids

protected static final String tag_PCT_ID_List_uids

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Constant Field Values

tag_PCT_ID_List_uids_E

protected static final String tag_PCT_ID_List_uids_E

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Constant Field Values

tag_PCT_ID_List_db

protected static final String tag_PCT_ID_List_db

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Constant Field Values

tag_PCT_Download_format

protected static final String tag_PCT_Download_format

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Constant Field Values

tag_PCT_Download_compression

protected static final String tag_PCT_Download_compression

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Constant Field Values

tag_PCT_download_3D

protected static final String tag_PCT_download_3D

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Constant Field Values

retrieveConformers

protected boolean retrieveConformers

Constructor Detail

PUGProcessor

public PUGProcessor()

Method Detail

isRetrieveConformers

public boolean isRetrieveConformers()

setRetrieveConformers

public void setRetrieveConformers(boolean retrieveConformers)

process

public List<IStructureRecord> process(List<IStructureRecord> target)
                               throws net.idea.modbcum.i.exceptions.AmbitException

Example:   You want to download CID 1 and CID 99  being uids 1 and 99 in the 'pccompound' Entrez database  in SDF format with gzip compression.

The typical flow of information is as follows.  First, the initial input XML is sent to PUG via HTTP POST.  Note the input data container with the download request and uid and format options:


  
    
      
        
          
            
              
                
                  pccompound
                  
                    1
                    99
                  
                
              
            
          
          
          
        
      
    
  



If the request is small and finishes very quickly, you may get a final URL right away (see further below). But usually PUG will respond initially with a waiting message and a request ID () such as:


  
    
      
        
          
            
          
        
      
      
        
          
            402936103567975582
          
        
      
    
  



You would then parse out this request id, being '402936103567975582', in this case, and use this id to 'poll' PUG on the status of the request, composing an XML message like:


  
    
      
        
          402936103567975582
          
        
      
    
  


Note that here the request type 'status' is used; there is also the request type 'cancel' that you may use to cancel a running job. 

If the request is still running, you well get back another waiting message as above, and then you would poll again after some reasonable interval. If the request is finished, you will get a final result message like:


  
    
      
        
          
            
          
        
      
      
        
          
            
          ftp://ftp-private.ncbi.nlm.nih.gov/pubchem/.fetch/1064385222466625960.sdf.gz
        
          
        
      
    
  


You would parse out the URL from the  tag, and then use a tool of your choice to connect to that URL to retrieve the actual requested data.

Throws:

net.idea.modbcum.i.exceptions.AmbitException

createDownloadHTTPRequest

protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>> createDownloadHTTPRequest(List<IStructureRecord> record)

createPollRequest

protected HTTPRequest<List<IStructureRecord>,List<IStructureRecord>> createPollRequest(List<IStructureRecord> waitingregids)

createDownloadRequest

public void createDownloadRequest(List<IStructureRecord> sids,
                                  Writer out)
                           throws ParserConfigurationException,
                                  TransformerException,
                                  IOException

Throws:

ParserConfigurationException

TransformerException

IOException

createPollRequest

public static void createPollRequest(IStructureRecord regid,
                                     Writer out)
                              throws ProcessorException

Throws:

ProcessorException

parseOutput

public static List<IStructureRecord> parseOutput(Document doc)
                                          throws ProcessorException

Parameters:

doc -

Throws:

ProcessorException

processWaiting

protected static List<IStructureRecord> processWaiting(Document doc,
                                                       Element waiting)
                                                throws ProcessorException

Throws:

ProcessorException

processDownloadURL

protected static List<IStructureRecord> processDownloadURL(Document doc,
                                                           Element download)
                                                    throws ProcessorException

Throws:

ProcessorException

getNodes

protected static Element getNodes(Document doc,
                                  Element parent,
                                  String tag)
                           throws ProcessorException

Throws:

ProcessorException