import jalview.datamodel.SequenceI;
import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.StringUtils;
+import jalview.ws.api.UIinfo;
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
*/
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.details = new UIinfo(action, action, name, description, postUrl);
this.postUrl = postUrl == null ? "" : postUrl;
this.urlSuffix = urlSuffix == null ? "" : urlSuffix;
if (inputParams != null)
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);
- diff |= !details.Name.equals(other.details.Name);
- diff |= !details.Action.equals(other.details.Action);
- diff |= !details.description.equals(other.details.description);
+ diff |= !details.equals(other.details);
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 UIinfo details;
public String getAction()
{
/**
* input info given as key/value pairs - mapped to post arguments
*/
- Map<String, InputType> inputParams = new HashMap<String, InputType>();
+ Map<String, InputType> inputParams = new HashMap<>();
/**
* assigns the given inputType it to its corresponding input parameter token
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;
}
StringTokenizer st = new StringTokenizer(outstring, ";");
String tok = "";
- resultData = new ArrayList<JvDataType>();
+ resultData = new ArrayList<>();
while (st.hasMoreTokens())
{
try
resultData.add(JvDataType.valueOf(tok = st.nextToken()));
} catch (NoSuchElementException x)
{
- warnings.append("Invalid result type: '" + tok
- + "' (must be one of: ");
+ warnings.append(
+ "Invalid result type: '" + tok + "' (must be one of: ");
String sep = "";
for (JvDataType vl : JvDataType.values())
{
private String getServiceIOProperties()
{
- ArrayList<String> vls = new ArrayList<String>();
+ ArrayList<String> vls = new ArrayList<>();
if (isHseparable())
{
vls.add("hseparable");
;
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]),
+ ",");
}
+ @Override
public String toString()
{
StringBuffer result = new StringBuffer();
result.append("|");
- result.append(details.Name);
+ result.append(details.getName());
result.append('|');
- result.append(details.Action);
+ result.append(details.getAction());
result.append('|');
- if (details.description != null)
+ if (details.getDescription() != null)
{
- result.append(details.description);
+ result.append(details.getDescription());
}
;
// list job input flags
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)
* @param p
* @return
*/
- protected int parseServiceList(String[] list, StringBuffer warnings, int p)
+ 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
{
p++;
}
- details.Name = list[p];
- details.Action = list[p + 1];
- details.description = list[p + 2];
+ details = new UIinfo(list[p + 1], list[p + 1], list[p], list[p + 2],
+ postUrl);
invalid |= !configureFromServiceInputProperties(list[p + 3], warnings);
if (list.length - p > 5 && list[p + 5] != null
&& list[p + 5].trim().length() > 5)
&& list[p + 4].trim().length() > 5)
{
urlSuffix = null;
- invalid |= !configureFromInputParamEncodedUrl(list[p + 4], warnings);
+ invalid |= !configureFromInputParamEncodedUrl(list[p + 4],
+ warnings);
p += 5;
}
}
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);
- Map<String, InputType> iparams = new Hashtable<String, InputType>();
+ Matcher prms = PARAM_ENCODED_URL_PATTERN.matcher(ipurl);
+ Map<String, InputType> iparams = new Hashtable<>();
InputType jinput;
while (prms.find())
{
iprmparams = iprm.substring(colon + 1);
iprm = iprm.substring(0, colon);
}
- valid = parseTypeString(prms.group(0), tok, iprm, iprmparams,
- iparams, warnings);
+ valid = parseTypeString(prms.group(0), tok, iprm, iprmparams, iparams,
+ warnings);
}
if (valid)
{
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,
+ 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));
+ jinput = (InputType) (type.getConstructor().newInstance());
if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
{
- ArrayList<String> al = new ArrayList<String>();
- for (String prprm : separatorListToArray(iprmparams, ","))
+ ArrayList<String> al = new ArrayList<>();
+ for (String prprm : StringUtils.separatorListToArray(iprmparams,
+ ","))
{
// hack to ensure that strings like "sep=','" containing unescaped
// commas as values are concatenated
/**
* search the input types for an instance of the given class
*
- * @param <validInput.inputType> class1
+ * @param <validInput.inputType>
+ * class1
* @return
*/
public boolean inputInvolves(Class<?> class1)
return jobId + urlSuffix;
}
- private List<JvDataType> resultData = new ArrayList<JvDataType>();
+ private List<JvDataType> resultData = new ArrayList<>();
/**
*
{
if (resultData == null)
{
- resultData = new ArrayList<JvDataType>();
+ resultData = new ArrayList<>();
}
resultData.add(dt);
}
public static List<RestServiceDescription> parseDescriptions(
String services) throws Exception
{
- String[] list = separatorListToArray(services, "|");
- List<RestServiceDescription> svcparsed = new ArrayList<RestServiceDescription>();
+ String[] list = StringUtils.separatorListToArray(services, "|");
+ List<RestServiceDescription> svcparsed = new ArrayList<>();
int p = 0, lastp = 0;
StringBuffer warnings = new StringBuffer();
do
git://source.jalview.org / jalview.git / blobdiff