/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.util.StringUtils;
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;
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;
-import com.sun.tools.doclets.internal.toolkit.util.DocFinder.Output;
-
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
this.gapCharacter = gapCharacter;
}
+ @Override
public boolean equals(Object o)
{
if (o == null || !(o instanceof RestServiceDescription))
boolean diff = (gapCharacter != other.gapCharacter);
diff |= vseparable != other.vseparable;
diff |= hseparable != other.hseparable;
- diff |= !(urlSuffix.equals(other.urlSuffix));
+ 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);
return invalidMessage == null;
}
- private static boolean debug = false;
-
- /**
- * parse the string into a list
- *
- * @param list
- * @param separator
- * @return elements separated by separator
- */
- public static String[] separatorListToArray(String list, String separator)
- {
- int seplen = separator.length();
- if (list == null || list.equals("") || list.equals(separator))
- return null;
- java.util.ArrayList<String> jv = new ArrayList<String>();
- int cp = 0, pos, escape;
- 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)
- {
- // append to previous pos
- jv.set(jv.size() - 1,
- lstitem = lstitem + separator
- + list.substring(cp, pos + escape));
-
- }
- else
- {
- jv.add(lstitem = list.substring(cp, pos + escape));
- }
- cp = pos + seplen;
- wasescaped = escape == -1;
- if (!wasescaped)
- {
- // last separator may be in an unmatched quote
- if (java.util.regex.Pattern.matches("('[^']*')*[^']*'",lstitem))
- {
- wasquoted=true;
- }
- }
-
- }
- if (cp < list.length())
- {
- String c = list.substring(cp);
- if (wasescaped || wasquoted)
- {
- // append final separator
- jv.set(jv.size() - 1, lstitem + separator + c);
- }
- else
- {
- if (!c.equals(separator))
- {
- jv.add(c);
- }
- }
- }
- if (jv.size() > 0)
- {
- String[] v = jv.toArray(new String[jv.size()]);
- jv.clear();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println("Empty Array from '" + separator
- + "' separated List");
- }
- return null;
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public static String arrayToSeparatorList(String[] list, String separator)
- {
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (v.length() > 0)
- {
- v.append(separator);
- }
- // TODO - escape any separator values in list[i]
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err.println("Returning '" + separator
- + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
- }
- return "" + separator;
- }
-
/**
* parse a string containing a list of service properties and configure the
* service description
private boolean configureFromServiceInputProperties(String propList,
StringBuffer warnings)
{
- String[] props = separatorListToArray(propList, ",");
+ String[] props = StringUtils.separatorListToArray(propList, ",");
if (props == null)
{
return true;
private String getServiceIOProperties()
{
ArrayList<String> vls = new ArrayList<String>();
- 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]), ",");
+ return StringUtils
+ .arrayToSeparatorList(vls.toArray(new String[0]), ",");
}
public String toString()
}
/**
- * 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)
+ String[] list = StringUtils.separatorListToArray(encoding, "|");
+
+ 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
{
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
url.append("$");
url.append(param.getValue().getURLtokenPrefix());
url.append(":");
- url.append(arrayToSeparatorList(vals.toArray(new String[0]),
- ","));
+ url.append(StringUtils.arrayToSeparatorList(
+ vals.toArray(new String[0]), ","));
url.append("$");
}
}
boolean valid = true;
int lastp = 0;
String url = new String();
- Matcher prms = Pattern.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$")
- .matcher(ipurl);
+ Matcher prms = PARAM_ENCODED_URL_PATTERN.matcher(ipurl);
Map<String, InputType> iparams = new Hashtable<String, InputType>();
InputType jinput;
while (prms.find())
public static Class[] getInputTypes()
{
// TODO - find a better way of maintaining this classlist
- return new Class[]
- { jalview.ws.rest.params.Alignment.class,
+ return new Class[] { jalview.ws.rest.params.Alignment.class,
jalview.ws.rest.params.AnnotationFile.class,
SeqGroupIndexVector.class,
jalview.ws.rest.params.SeqIdVector.class,
{
try
{
- jinput = (InputType) (type.getConstructor().newInstance(null));
+ jinput = (InputType) (type.getConstructor().newInstance());
if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
{
ArrayList<String> al = new ArrayList<String>();
- for (String prprm : separatorListToArray(iprmparams, ","))
+ for (String prprm : StringUtils.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))
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()
/**
* 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<RestServiceDescription> parseDescriptions(String services) throws Exception
+ public static List<RestServiceDescription> parseDescriptions(
+ String services) throws Exception
{
- String[] list = separatorListToArray(services, "|");
+ String[] list = StringUtils.separatorListToArray(services, "|");
List<RestServiceDescription> svcparsed = new ArrayList<RestServiceDescription>();
- 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<lastp && p<list.length-1);
+ 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 < lastp && p < list.length - 1);
return svcparsed;
}
git://source.jalview.org / jalview.git / blobdiff