X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestServiceDescription.java;h=aae225502206da4478f88768553c633322865cff;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=e0c56daf0bdd444c0d8da5d1866e7b2fd59c6efd;hpb=6bd9630607bd38aaf9b42738a0ae90de8fe5c6e8;p=jalview.git
diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java
index e0c56da..aae2255 100644
--- a/src/jalview/ws/rest/RestServiceDescription.java
+++ b/src/jalview/ws/rest/RestServiceDescription.java
@@ -1,31 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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;
-import jalview.io.packed.SimpleDataProvider;
import jalview.io.packed.DataProvider.JvDataType;
-import jalview.util.GroupUrlLink.UrlStringTooLongException;
-import jalview.util.Platform;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.AnnotationFile;
-import jalview.ws.rest.params.JobConstant;
import jalview.ws.rest.params.SeqGroupIndexVector;
import java.net.URL;
@@ -36,15 +32,9 @@ import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.StringTokenizer;
-import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import javax.swing.JViewport;
-
-import com.stevesoft.pat.Regex;
-import com.sun.org.apache.xml.internal.serialize.OutputFormat.DTD;
-
public class RestServiceDescription
{
/**
@@ -52,8 +42,9 @@ public class RestServiceDescription
*/
public RestServiceDescription()
{
-
+
}
+
/**
* @param details
* @param postUrl
@@ -379,11 +370,11 @@ public class RestServiceDescription
return null;
java.util.ArrayList jv = new ArrayList();
int cp = 0, pos, escape;
- boolean wasescaped = false,wasquoted=false;
+ boolean wasescaped = false, wasquoted = false;
String lstitem = null;
while ((pos = list.indexOf(separator, cp)) >= cp)
{
-
+
escape = (pos > 0 && list.charAt(pos - 1) == '\\') ? -1 : 0;
if (wasescaped || wasquoted)
{
@@ -402,12 +393,12 @@ public class RestServiceDescription
if (!wasescaped)
{
// last separator may be in an unmatched quote
- if (java.util.regex.Pattern.matches("('[^']*')*[^']*'",lstitem))
+ if (java.util.regex.Pattern.matches("('[^']*')*[^']*'", lstitem))
{
- wasquoted=true;
+ wasquoted = true;
}
}
-
+
}
if (cp < list.length())
{
@@ -605,8 +596,16 @@ public class RestServiceDescription
private String getServiceIOProperties()
{
ArrayList vls = new ArrayList();
- if (isHseparable()) { vls.add("hseparable");};
- if (isVseparable()) { vls.add("vseparable");};
+ if (isHseparable())
+ {
+ vls.add("hseparable");
+ }
+ ;
+ if (isVseparable())
+ {
+ vls.add("vseparable");
+ }
+ ;
vls.add(new String("gapCharacter='" + gapCharacter + "'"));
vls.add(new String("returns='" + _genOutputFormatString() + "'"));
return arrayToSeparatorList(vls.toArray(new String[0]), ",");
@@ -640,27 +639,35 @@ public class RestServiceDescription
}
/**
- * processes a service encoded as a string (as generated by RestServiceDescription.toString())
- * Note - this will only use the first service definition encountered in the string to configure the service.
+ * processes a service encoded as a string (as generated by
+ * RestServiceDescription.toString()) Note - this will only use the first
+ * service definition encountered in the string to configure the service.
+ *
* @param encoding
- * @param warnings - where warning messages are reported.
- * @return true if configuration was parsed successfully.
+ * @param warnings
+ * - where warning messages are reported.
+ * @return true if configuration was parsed successfully.
*/
public boolean configureFromEncodedString(String encoding,
StringBuffer warnings)
{
String[] list = separatorListToArray(encoding, "|");
-
- int nextpos=parseServiceList(list,warnings, 0);
- if (nextpos>0)
+
+ int nextpos = parseServiceList(list, warnings, 0);
+ if (nextpos > 0)
{
return true;
}
return false;
}
+
/**
- * processes the given list from position p, attempting to configure the service from it.
- * Service lists are formed by concatenating individual stringified services. The first character of a stringified service is '|', enabling this, and the parser will ignore empty fields in a '|' separated list when they fall outside a service definition.
+ * processes the given list from position p, attempting to configure the
+ * service from it. Service lists are formed by concatenating individual
+ * stringified services. The first character of a stringified service is '|',
+ * enabling this, and the parser will ignore empty fields in a '|' separated
+ * list when they fall outside a service definition.
+ *
* @param list
* @param warnings
* @param p
@@ -670,32 +677,34 @@ public class RestServiceDescription
{
boolean invalid = false;
// look for the first non-empty position - expect it to be service name
- while (list[p]!=null && list[p].trim().length()==0)
+ while (list[p] != null && list[p].trim().length() == 0)
{
p++;
}
details.Name = list[p];
- details.Action = list[p+1];
- details.description = list[p+2];
- invalid |= !configureFromServiceInputProperties(list[p+3], warnings);
- if (list.length-p > 5 && list[p+5]!=null && list[p+5].trim().length()>5)
+ details.Action = list[p + 1];
+ details.description = list[p + 2];
+ invalid |= !configureFromServiceInputProperties(list[p + 3], warnings);
+ if (list.length - p > 5 && list[p + 5] != null
+ && list[p + 5].trim().length() > 5)
{
- urlSuffix = list[p+4];
- invalid |= !configureFromInputParamEncodedUrl(list[p+5], warnings);
- p+=6;
+ urlSuffix = list[p + 4];
+ invalid |= !configureFromInputParamEncodedUrl(list[p + 5], warnings);
+ p += 6;
}
else
{
- if (list.length-p > 4 && list[p+4]!=null && list[p+4].trim().length()>5)
+ if (list.length - p > 4 && list[p + 4] != null
+ && list[p + 4].trim().length() > 5)
{
urlSuffix = null;
- invalid |= !configureFromInputParamEncodedUrl(list[p+4], warnings);
- p+=5;
+ invalid |= !configureFromInputParamEncodedUrl(list[p + 4], warnings);
+ p += 5;
}
}
return invalid ? -1 : p;
}
-
+
/**
* @return string representation of the input parameters, their type and
* constraints, appended to the service's base submission URL
@@ -838,7 +847,8 @@ public class RestServiceDescription
ArrayList al = new ArrayList();
for (String prprm : separatorListToArray(iprmparams, ","))
{
- // hack to ensure that strings like "sep=','" containing unescaped commas as values are concatenated
+ // hack to ensure that strings like "sep=','" containing unescaped
+ // commas as values are concatenated
al.add(prprm.trim());
}
if (!jinput.configureFromURLtokenString(al, warnings))
@@ -864,98 +874,6 @@ public class RestServiceDescription
return valid;
}
- public static void main(String argv[])
- {
- // test separator list
- try {
- assert(separatorListToArray("foo=',',min='foo',max='1,2,3',fa=','", ",").length==4);
- if (separatorListToArray("minsize='2', sep=','", ",").length==2)
- {
- assert(false);
- }
-
- } catch (AssertionError x)
- {
- System.err.println("separatorListToArray is faulty.");
- }
- if (argv.length == 0)
- {
- if (!testRsdExchange("Test using default Shmmr service",
- RestClient.makeShmmrRestClient().service))
- {
- System.err.println("default test failed.");
- }
- else
- {
- System.err.println("default test passed.");
- }
- }
- else
- {
- int i = 0, p = 0;
- for (String svc : argv)
- {
- p += testRsdExchange("Test " + (++i), svc) ? 1 : 0;
- }
- System.err.println("" + p + " out of " + i + " tests passed.");
-
- }
- }
-
- private static boolean testRsdExchange(String desc, String servicestring)
- {
- try
- {
- RestServiceDescription newService = new RestServiceDescription(
- servicestring);
- if (!newService.isValid())
- {
- throw new Error("Failed to create service from '" + servicestring
- + "'.\n" + newService.getInvalidMessage());
- }
- return testRsdExchange(desc, newService);
- } catch (Throwable x)
- {
- System.err.println("Failed for service (" + desc + "): "
- + servicestring);
- x.printStackTrace();
- return false;
- }
- }
-
- private static boolean testRsdExchange(String desc,
- RestServiceDescription service)
- {
- try
- {
- String fromservicetostring = service.toString();
- RestServiceDescription newService = new RestServiceDescription(
- fromservicetostring);
- if (!newService.isValid())
- {
- throw new Error("Failed to create service from '"
- + fromservicetostring + "'.\n"
- + newService.getInvalidMessage());
- }
-
- if (!service.equals(newService))
- {
- System.err.println("Failed for service (" + desc + ").");
- System.err.println("Original service and parsed service differ.");
- System.err.println("Original: " + fromservicetostring);
- System.err.println("Parsed : " + newService.toString());
- return false;
- }
- } catch (Throwable x)
- {
- System.err.println("Failed for service (" + desc + "): "
- + service.toString());
- x.printStackTrace();
- return false;
- }
- return true;
- }
-
/**
* covenience method to generate the id and sequence string vector from a set
* of seuqences using each sequence's getName() and getSequenceAsString()
@@ -1069,26 +987,37 @@ public class RestServiceDescription
/**
* parse a concatenated list of rest service descriptions into an array
+ *
* @param services
* @return zero or more services.
- * @throws exceptions if the services are improperly encoded.
+ * @throws exceptions
+ * if the services are improperly encoded.
*/
- public static List parseDescriptions(String services) throws Exception
+ public static List parseDescriptions(
+ String services) throws Exception
{
String[] list = separatorListToArray(services, "|");
List svcparsed = new ArrayList();
- int p=0,lastp=0;
- StringBuffer warnings=new StringBuffer();
- do {
+ int p = 0, lastp = 0;
+ StringBuffer warnings = new StringBuffer();
+ do
+ {
RestServiceDescription rsd = new RestServiceDescription();
- p=rsd.parseServiceList(list, warnings, lastp=p);
- if (p>lastp && rsd.isValid())
+ p = rsd.parseServiceList(list, warnings, lastp = p);
+ if (p > lastp && rsd.isValid())
{
svcparsed.add(rsd);
- } else {
- throw new Exception("Failed to parse user defined RSBS services from :"+services+"\nFirst error was encountered at token "+lastp+" starting "+list[lastp]+":\n"+rsd.getInvalidMessage());
}
- } while (p