/*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
+ * 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
{
super();
this.details = new UIinfo();
- details.Action = action;
- details.description = description;
- details.Name = name;
- this.postUrl = postUrl;
- this.urlSuffix = urlSuffix;
- this.inputParams = inputParams;
+ 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))
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);
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;
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<String, InputType> getInputParams()
+ {
+ return inputParams;
+ }
+
+ public void setInputParams(Map<String, InputType> 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.
/**
* input info given as key/value pairs - mapped to post arguments
*/
- Map<String, InputType> inputParams = new HashMap();
+ Map<String, InputType> inputParams = new HashMap<String, InputType>();
/**
* assigns the given inputType it to its corresponding input parameter token
public RestServiceDescription(RestServiceDescription toedit)
{
- if (toedit == null)
- {
- return;
- }
- // TODO Implement copy constructor NOW
+ // Rather then do the above, we cheat and use our human readable
+ // serialization code to clone everything
+ this(toedit.toString());
+ /**
+ * if (toedit == null) { return; } /** urlSuffix = toedit.urlSuffix; postUrl
+ * = toedit.postUrl; hseparable = toedit.hseparable; vseparable =
+ * toedit.vseparable; gapCharacter = toedit.gapCharacter; details = new
+ * RestServiceDescription.UIinfo(); details.Action = toedit.details.Action;
+ * details.description = toedit.details.description; details.Name =
+ * toedit.details.Name; for (InputType itype: toedit.inputParams.values()) {
+ * inputParams.put(itype.token, itype.clone());
+ *
+ * }
+ */
+ // TODO Implement copy constructor NOW*/
}
/**
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;
- String lstitem = null;
- while ((pos = list.indexOf(separator, cp)) > cp)
- {
- escape = (list.charAt(pos - 1) == '\\') ? -1 : 0;
- if (wasescaped)
- {
- // 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 (cp < list.length())
- {
- String c = list.substring(cp);
- if (wasescaped)
- {
- // 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 (i > 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
* param warnings a StringBuffer that any warnings about invalid
* content will be appended to.
*/
- private void configureFromServiceInputProperties(String propList,
+ private boolean configureFromServiceInputProperties(String propList,
StringBuffer warnings)
{
- String[] props = separatorListToArray(propList, ",");
+ String[] props = StringUtils.separatorListToArray(propList, ",");
if (props == null)
{
- return;
+ return true;
}
;
+ boolean valid = true;
String val = null;
+ int l = warnings.length();
int i;
for (String prop : props)
{
}
if (prop.equals("gapCharacter"))
{
- if (val == null || val.length() > 1)
+ if (val == null || val.length() == 0 || val.length() > 1)
{
+ valid = false;
warnings.append((warnings.length() > 0 ? "\n" : "")
+ ("Invalid service property: gapCharacter=' ' (single character) - was given '"
+ val + "'"));
}
if (prop.equals("returns"))
{
- _configureOurputFormatFrom(val, warnings);
+ _configureOutputFormatFrom(val, warnings);
}
}
+ // return true if valid is true and warning buffer was not appended to.
+ return valid && (l == warnings.length());
}
private String _genOutputFormatString()
{
String buff = "";
- if (resultData==null)
+ if (resultData == null)
{
return "";
}
return buff;
}
- private void _configureOurputFormatFrom(String outstring,
+ private void _configureOutputFormatFrom(String outstring,
StringBuffer warnings)
{
+ if (outstring.indexOf(";") == -1)
+ {
+ // we add a token, for simplicity
+ outstring = outstring + ";";
+ }
StringTokenizer st = new StringTokenizer(outstring, ";");
String tok = "";
resultData = new ArrayList<JvDataType>();
private String getServiceIOProperties()
{
- String[] vls = new String[]
- { isHseparable() ? "hseparable" : "",
- isVseparable() ? "vseparable" : "",
- (new String("gapCharacter='" + gapCharacter + "'")),
- (new String("returns='" + _genOutputFormatString() + "'")) };
-
- return arrayToSeparatorList(vls, ",");
+ ArrayList<String> vls = new ArrayList<String>();
+ if (isHseparable())
+ {
+ vls.add("hseparable");
+ }
+ ;
+ if (isVseparable())
+ {
+ vls.add("vseparable");
+ }
+ ;
+ vls.add(new String("gapCharacter='" + gapCharacter + "'"));
+ vls.add(new String("returns='" + _genOutputFormatString() + "'"));
+ return StringUtils
+ .arrayToSeparatorList(vls.toArray(new String[0]), ",");
}
public String toString()
{
StringBuffer result = new StringBuffer();
+ result.append("|");
result.append(details.Name);
result.append('|');
result.append(details.Action);
return result.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.
+ *
+ * @param encoding
+ * @param warnings
+ * - where warning messages are reported.
+ * @return true if configuration was parsed successfully.
+ */
public boolean configureFromEncodedString(String encoding,
StringBuffer warnings)
{
- boolean valid = false;
- String[] list = separatorListToArray(encoding, "|");
- details.Name = list[0];
- details.Action = list[1];
- details.description = list[2];
- configureFromServiceInputProperties(list[3], warnings);
- if (list.length > 5)
+ String[] list = StringUtils.separatorListToArray(encoding, "|");
+
+ int nextpos = parseServiceList(list, warnings, 0);
+ if (nextpos > 0)
{
- urlSuffix = list[4];
- valid |= configureFromInputParamEncodedUrl(list[5], warnings);
+ 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.
+ *
+ * @param list
+ * @param warnings
+ * @param p
+ * @return
+ */
+ protected int parseServiceList(String[] list, StringBuffer warnings, int 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)
+ {
+ 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)
+ {
+ urlSuffix = list[p + 4];
+ invalid |= !configureFromInputParamEncodedUrl(list[p + 5], warnings);
+ p += 6;
}
else
{
- urlSuffix = null;
- valid |= configureFromInputParamEncodedUrl(list[4], warnings);
+ 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;
+ }
}
- return valid;
+ return invalid ? -1 : p;
}
/**
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())
iprmparams = iprm.substring(colon + 1);
iprm = iprm.substring(0, colon);
}
- // TODO - find a better way of maintaining this classlist
- for (Class type : new Class[]
- { jalview.ws.rest.params.Alignment.class,
- jalview.ws.rest.params.AnnotationFile.class,
- SeqGroupIndexVector.class,
- jalview.ws.rest.params.SeqIdVector.class,
- jalview.ws.rest.params.SeqVector.class,
- jalview.ws.rest.params.Tree.class })
- {
- try
- {
- jinput = (InputType) (type.getConstructor().newInstance(null));
- if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
- {
- ArrayList<String> al = new ArrayList<String>();
- for (String prprm : separatorListToArray(iprmparams, ","))
- {
- al.add(prprm);
- }
- if (!jinput.configureFromURLtokenString(al, warnings))
- {
- valid = false;
- warnings.append("Failed to parse '" + prms.group(0)
- + "' as a " + jinput.getURLtokenPrefix()
- + " input tag.\n");
- }
- else
- {
- jinput.token = tok;
- iparams.put(tok, jinput);
- }
- break;
- }
-
- } catch (Throwable thr)
- {
- }
- ;
- }
+ valid = parseTypeString(prms.group(0), tok, iprm, iprmparams,
+ iparams, warnings);
}
if (valid)
{
return valid;
}
- public static void main(String argv[])
+ public static Class[] getInputTypes()
{
- 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;
- }
+ // TODO - find a better way of maintaining this classlist
+ return new Class[] { jalview.ws.rest.params.Alignment.class,
+ jalview.ws.rest.params.AnnotationFile.class,
+ SeqGroupIndexVector.class,
+ jalview.ws.rest.params.SeqIdVector.class,
+ jalview.ws.rest.params.SeqVector.class,
+ jalview.ws.rest.params.Tree.class };
}
- private static boolean testRsdExchange(String desc,
- RestServiceDescription service)
+ public static boolean parseTypeString(String fullstring, String tok,
+ String iprm, String iprmparams, Map<String, InputType> iparams,
+ StringBuffer warnings)
{
- try
+ boolean valid = true;
+ InputType jinput;
+ for (Class type : getInputTypes())
{
- String fromservicetostring = service.toString();
- RestServiceDescription newService = new RestServiceDescription(
- fromservicetostring);
- if (!newService.isValid())
+ try
{
- throw new Error("Failed to create service from '"
- + fromservicetostring + "'.\n"
- + newService.getInvalidMessage());
- }
+ jinput = (InputType) (type.getConstructor().newInstance());
+ if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
+ {
+ ArrayList<String> al = new ArrayList<String>();
+ for (String prprm : StringUtils.separatorListToArray(iprmparams,
+ ","))
+ {
+ // hack to ensure that strings like "sep=','" containing unescaped
+ // commas as values are concatenated
+ al.add(prprm.trim());
+ }
+ if (!jinput.configureFromURLtokenString(al, warnings))
+ {
+ valid = false;
+ warnings.append("Failed to parse '" + fullstring + "' as a "
+ + jinput.getURLtokenPrefix() + " input tag.\n");
+ }
+ else
+ {
+ jinput.token = tok;
+ iparams.put(tok, jinput);
+ valid = true;
+ }
+ break;
+ }
- if (!service.equals(newService))
+ } catch (Throwable thr)
{
- 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;
+ return valid;
}
/**
return jobId + urlSuffix;
}
- private List<JvDataType> resultData;
+ private List<JvDataType> resultData = new ArrayList<JvDataType>();
/**
*
{
return resultData;
}
+
+ /**
+ * 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.
+ */
+ public static List<RestServiceDescription> parseDescriptions(
+ String services) throws Exception
+ {
+ String[] list = StringUtils.separatorListToArray(services, "|");
+ List<RestServiceDescription> svcparsed = new ArrayList<RestServiceDescription>();
+ 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())
+ {
+ 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);
+ return svcparsed;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff