/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
import jalview.datamodel.SequenceI;
import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.StringUtils;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.AnnotationFile;
import jalview.ws.rest.params.SeqGroupIndexVector;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.StringTokenizer;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class RestServiceDescription
{
private static final Pattern PARAM_ENCODED_URL_PATTERN = Pattern
.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$");
/**
* create a new rest service description ready to be configured
*/
public RestServiceDescription()
{
}
/**
* @param details
* @param postUrl
* @param urlSuffix
* @param inputParams
* @param hseparable
* @param vseparable
* @param gapCharacter
*/
public RestServiceDescription(String action, String description,
String name, String postUrl, String urlSuffix,
Map inputParams, boolean hseparable,
boolean vseparable, char gapCharacter)
{
super();
this.details = new UIinfo();
details.Action = action == null ? "" : action;
details.description = description == null ? "" : description;
details.Name = name == null ? "" : name;
this.postUrl = postUrl == null ? "" : postUrl;
this.urlSuffix = urlSuffix == null ? "" : urlSuffix;
if (inputParams != null)
{
this.inputParams = inputParams;
}
this.hseparable = hseparable;
this.vseparable = vseparable;
this.gapCharacter = gapCharacter;
}
@Override
public boolean equals(Object o)
{
if (o == null || !(o instanceof RestServiceDescription))
{
return false;
}
RestServiceDescription other = (RestServiceDescription) o;
boolean diff = (gapCharacter != other.gapCharacter);
diff |= vseparable != other.vseparable;
diff |= hseparable != other.hseparable;
diff |= !(urlSuffix == null && other.urlSuffix == null
|| (urlSuffix != null && other.urlSuffix != null
&& urlSuffix.equals(other.urlSuffix)));
// TODO - robust diff that includes constants and reordering of URL
// diff |= !(postUrl.equals(other.postUrl));
// diff |= !inputParams.equals(other.inputParams);
diff |= !details.Name.equals(other.details.Name);
diff |= !details.Action.equals(other.details.Action);
diff |= !details.description.equals(other.details.description);
return !diff;
}
/**
* Service UI Info { Action, Specific Name of Service, Brief Description }
*/
public class UIinfo
{
public String getAction()
{
return Action;
}
public void setAction(String action)
{
Action = action;
}
public String getName()
{
return Name;
}
public void setName(String name)
{
Name = name;
}
public String getDescription()
{
return description;
}
public void setDescription(String description)
{
this.description = description;
}
String Action;
String Name;
String description;
}
public UIinfo details = new UIinfo();
public String getAction()
{
return details.getAction();
}
public void setAction(String action)
{
details.setAction(action);
}
public String getName()
{
return details.getName();
}
public void setName(String name)
{
details.setName(name);
}
public String getDescription()
{
return details.getDescription();
}
public void setDescription(String description)
{
details.setDescription(description);
}
/**
* Service base URL
*/
String postUrl;
public String getPostUrl()
{
return postUrl;
}
public void setPostUrl(String postUrl)
{
this.postUrl = postUrl;
}
public String getUrlSuffix()
{
return urlSuffix;
}
public void setUrlSuffix(String urlSuffix)
{
this.urlSuffix = urlSuffix;
}
public Map getInputParams()
{
return inputParams;
}
public void setInputParams(Map inputParams)
{
this.inputParams = inputParams;
}
public void setHseparable(boolean hseparable)
{
this.hseparable = hseparable;
}
public void setVseparable(boolean vseparable)
{
this.vseparable = vseparable;
}
public void setGapCharacter(char gapCharacter)
{
this.gapCharacter = gapCharacter;
}
/**
* suffix that should be added to any url used if it does not already end in
* the suffix.
*/
String urlSuffix;
/**
* input info given as key/value pairs - mapped to post arguments
*/
Map inputParams = new HashMap();
/**
* assigns the given inputType it to its corresponding input parameter token
* it.token
*
* @param it
*/
public void setInputParam(InputType it)
{
inputParams.put(it.token, it);
}
/**
* remove the given input type it from the set of service input parameters.
*
* @param it
*/
public void removeInputParam(InputType it)
{
inputParams.remove(it.token);
}
/**
* service requests alignment data
*/
boolean aligndata;
/**
* service requests alignment and/or seuqence annotationo data
*/
boolean annotdata;
/**
* service requests partitions defined over input (alignment) data
*/
boolean partitiondata;
/**
* process ths input data and set the appropriate shorthand flags describing
* the input the service wants
*/
public void setInvolvesFlags()
{
aligndata = inputInvolves(Alignment.class);
annotdata = inputInvolves(AnnotationFile.class);
partitiondata = inputInvolves(SeqGroupIndexVector.class);
}
/**
* Service return info { alignment, annotation file (loaded back on to
* alignment), tree (loaded back on to alignment), sequence annotation -
* loaded back on to alignment), text report, pdb structures with sequence
* mapping )
*
*/
/**
* Start with bare minimum: input is alignment + groups on alignment
*
* @author JimP
*
*/
private String invalidMessage = null;
/**
* parse the given linkString of the form '