/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.JvDataType;
+import jalview.util.StringUtils;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.AnnotationFile;
import jalview.ws.rest.params.SeqGroupIndexVector;
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
*/
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;
;
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()
public boolean configureFromEncodedString(String encoding,
StringBuffer warnings)
{
- String[] list = separatorListToArray(encoding, "|");
+ String[] list = StringUtils.separatorListToArray(encoding, "|");
int nextpos = parseServiceList(list, warnings, 0);
if (nextpos > 0)
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
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();
git://source.jalview.org / jalview.git / blobdiff