obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 179)

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Revision: 180
          http://svn.sourceforge.net/obo/?rev=180&view=rev
Author:   mgibson
Date:     2006-11-02 13:41:54 -0800 (Thu, 02 Nov 2006)

Log Message:
-----------
took out ctrl-Ms

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/servlet/PhenoteBean.java
    phenote/trunk/src/java/phenote/servlet/PhenoteController.java
    phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteBean.java
===================================================================

--- phenote/trunk/src/java/phenote/servlet/PhenoteBean.java	2006-11-02 18:29:54 UTC (rev 179)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteBean.java	2006-11-02 21:41:54 UTC (rev 180)
@@ -1,101 +1,102 @@
-package phenote.servlet;
-
-import org.apache.commons.lang.StringUtils;
-
-/**
- * This is the main form bean that contains all request parameters.
- * Spring populates these attributes automatically and make them available
- * in the controller class.
- */
-public class PhenoteBean {
-
-  private String userInput;
-  private String qualityInput;
-  private String entityInput;
-  private String ontologyName;
-  private String termId;
-  private String field;
-
-  private String ajaxList;
-
-  public boolean isTermCompletionRequest() {
-    if (!StringUtils.isEmpty(userInput))
-      return true;
-    if (!StringUtils.isEmpty(qualityInput))
-      return true;
-    return !StringUtils.isEmpty(entityInput);
-
-  }
-
-  public String getTermCompletionTerm() {
-    if (!StringUtils.isEmpty(userInput))
-      return userInput;
-    if (!StringUtils.isEmpty(qualityInput))
-      return qualityInput;
-    if (!StringUtils.isEmpty(entityInput))
-      return entityInput;
-
-    return null;
-  }
-
-  public boolean isTermInfoRequest() {
-    return !StringUtils.isEmpty(termId);
-  }
-
-  public String getUserInput() {
-    return userInput;
-  }
-
-  public void setUserInput(String userInput) {
-    this.userInput = userInput;
-  }
-
-  public String getQualityInput() {
-    return qualityInput;
-  }
-
-  public void setQualityInput(String qualityInput) {
-    this.qualityInput = qualityInput;
-  }
-
-  public String getEntityInput() {
-    return entityInput;
-  }
-
-  public void setEntityInput(String entityInput) {
-    this.entityInput = entityInput;
-  }
-
-  public String getOntologyName() {
-    return ontologyName;
-  }
-
-  public void setOntologyName(String ontologyName) {
-    this.ontologyName = ontologyName;
-  }
-
-  public String getField() {
-    return field;
-  }
-
-  public void setField(String field) {
-    this.field = field;
-  }
-
-  public String getAjaxList() {
-    return ajaxList;
-  }
-
-  public void setAjaxList(String ajaxList) {
-    this.ajaxList = ajaxList;
-  }
-
-  public String getTermId() {
-    return termId;
-  }
-
-  public void setTermId(String termId) {
-    this.termId = termId;
-  }
-
-}
+package phenote.servlet;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * This is the main form bean that contains all request parameters.
+ * Spring populates these attributes automatically and make them available
+ * in the controller class.
+ */
+public class PhenoteBean {
+
+  private String userInput;
+  private String qualityInput;
+  private String entityInput;
+  private String ontologyName;
+  private String termId;
+  private String field;
+
+  private String ajaxList;
+
+  public boolean isTermCompletionRequest() {
+    if (!StringUtils.isEmpty(userInput))
+      return true;
+    if (!StringUtils.isEmpty(qualityInput))
+      return true;
+    return !StringUtils.isEmpty(entityInput);
+
+  }
+
+  public String getTermCompletionTerm() {
+    if (!StringUtils.isEmpty(userInput))
+      return userInput;
+    if (!StringUtils.isEmpty(qualityInput))
+      return qualityInput;
+    if (!StringUtils.isEmpty(entityInput))
+      return entityInput;
+
+    return null;
+  }
+
+  public boolean isTermInfoRequest() {
+    return !StringUtils.isEmpty(termId);
+  }
+
+  public String getUserInput() {
+    return userInput;
+  }
+
+  public void setUserInput(String userInput) {
+    this.userInput = userInput;
+  }
+
+  public String getQualityInput() {
+    return qualityInput;
+  }
+
+  public void setQualityInput(String qualityInput) {
+    this.qualityInput = qualityInput;
+  }
+
+  public String getEntityInput() {
+    return entityInput;
+  }
+
+  public void setEntityInput(String entityInput) {
+    this.entityInput = entityInput;
+  }
+
+  public String getOntologyName() {
+    return ontologyName;
+  }
+
+  public void setOntologyName(String ontologyName) {
+    this.ontologyName = ontologyName;
+  }
+
+  public String getField() {
+    return field;
+  }
+
+  public void setField(String field) {
+    this.field = field;
+  }
+
+  public String getAjaxList() {
+    return ajaxList;
+  }
+
+  public void setAjaxList(String ajaxList) {
+    this.ajaxList = ajaxList;
+  }
+
+  public String getTermId() {
+    return termId;
+  }
+
+  public void setTermId(String termId) {
+    this.termId = termId;
+  }
+
+}
+

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2006-11-02 18:29:54 UTC (rev 179)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2006-11-02 21:41:54 UTC (rev 180)
@@ -1,155 +1,156 @@
 package phenote.servlet;
 
-import org.apache.log4j.Logger;
-import org.springframework.validation.BindException;
-import org.springframework.web.servlet.ModelAndView;
-import org.springframework.web.servlet.mvc.AbstractCommandController;
-import org.geneontology.oboedit.datamodel.OBOClass;
-
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import phenote.gui.field.CompletionTerm;
-import phenote.gui.field.CompListSearcher;
-import phenote.gui.field.SearchParamsI;
-import phenote.datamodel.OntologyException;
-import phenote.datamodel.Ontology;
-import phenote.datamodel.OntologyManager;
-import phenote.util.HtmlUtil;
-
-import java.util.Vector;
-
-/**
- * The main controller that receives Ajax ontology requests.
- */
-public class PhenoteController extends AbstractCommandController {
-
-  private static final Logger LOG = Logger.getLogger(PhenoteController.class);
-
-  public PhenoteController() {
-    setCommandClass(PhenoteBean.class);
-  }
-
-  protected ModelAndView handle(HttpServletRequest request, HttpServletResponse response, Object command,
-                                BindException errors) throws Exception {
-    PhenoteBean form = (PhenoteBean) command;
-    String ontologyName = form.getOntologyName();
-    String field = form.getField();
-    if (form.isTermCompletionRequest()) {
-      String userInput = form.getTermCompletionTerm();
-      LOG.info("ontology: " + ontologyName);
-      LOG.info("param entityInput: " + userInput);
-      LOG.info("Field entity: " + field);
-
-      form.setAjaxList(getCompletionList(userInput, ontologyName, field));
-      LOG.debug(form.getAjaxList());
-    } else if (form.isTermInfoRequest()) {
-      String termId = form.getTermId();
-      LOG.debug("doGet term info param: " + termId + " ont " + ontologyName);
-      try {
-        Ontology ont = getOntology(ontologyName);
-        OBOClass oboClass = ont.getOboClass(termId);
-        String termInfo = HtmlUtil.termInfo(oboClass);
-        LOG.debug("term info " + termInfo.substring(0,60));
-        String termInfoObo = HtmlUtil.termInfo(oboClass, ontologyName, field);
-        form.setAjaxList(termInfoObo);
-      }
-      catch (OntologyException e) {
-        LOG.error(e.getMessage(), e);
-      }
-    }
-    return new ModelAndView("ajax", "formBean", form);
-  }
-
-
-  /**
-   * ToDo: Need to cleanup this comment.
-   * List<String>? String[]? or String htmlLiString?
-   * for now just return html ul-li list w onmouseover
-   * userInput is what user has typed which terms will be queried for
-   * ontol is the name of the ontology that user is querying
-   * field is the gui field user is querying (which may have multiple ontols)
-   * if ontologyy not found actually returns error string saying as much - why not
-   *
-   * @param userInput
-   * @param ontologyName
-   * @param field
-   */
-  private String getCompletionList(String userInput, String ontologyName, String field) {
-    StringBuffer sb = new StringBuffer("<ul>");
-    try {
-      Vector<CompletionTerm> v = getCompListSearcher(ontologyName).getStringMatchTerms(userInput);
-      //Vector<OBOClass> v = ontology.getStringMatchTerms(userInput, getSearchParams());
-      for (CompletionTerm ct : v)
-        sb.append(makeCompListHtmlItem(ct, ontologyName, field));
-    }
-    catch (OntologyException e) {
-      sb.append(e.getMessage());
-    }
-    sb.append("</ul>");
-    return sb.toString();
-  }
-
-  private Object makeCompListHtmlItem(CompletionTerm term, String ontol, String field) {
-    String id = term.getID(), name = term.getName();
-    // pass in id, name & ontology - name for setting field on UseTerm
-    StringBuffer info = dq(fn("getTermInfo", new String[]{id, name, ontol, field}));
-    //String info = "\"getTermInfo("+id +","+q(name)+","+ q(ontol) + ")\"";
-    return "<li onmouseover=" + info + " id=" + q(id) + " " +
-            "onclick=" + info + ">" + name + "</li>\n";
-  }
-
-  private CompListSearcher getCompListSearcher(String ontologyName) throws OntologyException {
-    return new CompListSearcher(getOntology(ontologyName), getSearchParams());
-  }
-
-  /**
-   * throws ex if ontolName not found
-   */
-  private Ontology getOntology(String ontolName) throws OntologyException {
-    return OntologyManager.inst().getOntologyForName(ontolName);
-  }
-
-  private static String q(String s) {
-    return "'" + s + "'";
-  }
-
-  /**
-   * for now search params hard wired - eventually from buttons on web page
-   */
-  private SearchParamsI getSearchParams() {
-    return new HardWiredSearchParams();
-  }
-
-  private static StringBuffer dq(StringBuffer sb) {
-    return new StringBuffer("\"" + sb + "\"");
-  }
-
-  private static StringBuffer fn(String fnName, String[] params) {
-    return HtmlUtil.fn(fnName, params);
-  }
-
-  private class HardWiredSearchParams implements SearchParamsI {
-    public boolean searchTerms() {
-      return true;
-    }
-
-    public boolean searchSynonyms() {
-      return false; // --> true
-    }
-
-    public boolean searchDefinitions() {
-      return false; // ?? w [def]??
-    }
-
-    /**
-     * Whether to include obsoletes in searching terms, syns, & definitions
-     * This should be in conjunction with the other 3
-     */
-    public boolean searchObsoletes() {
-      return false; // --> true w [obs], disallow selection
-    }
-  }
-
-
-}
+import org.apache.log4j.Logger;
+import org.springframework.validation.BindException;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.AbstractCommandController;
+import org.geneontology.oboedit.datamodel.OBOClass;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import phenote.gui.field.CompletionTerm;
+import phenote.gui.field.CompListSearcher;
+import phenote.gui.field.SearchParamsI;
+import phenote.datamodel.OntologyException;
+import phenote.datamodel.Ontology;
+import phenote.datamodel.OntologyManager;
+import phenote.util.HtmlUtil;
+
+import java.util.Vector;
+
+/**
+ * The main controller that receives Ajax ontology requests.
+ */
+public class PhenoteController extends AbstractCommandController {
+
+  private static final Logger LOG = Logger.getLogger(PhenoteController.class);
+
+  public PhenoteController() {
+    setCommandClass(PhenoteBean.class);
+  }
+
+  protected ModelAndView handle(HttpServletRequest request, HttpServletResponse response, Object command,
+                                BindException errors) throws Exception {
+    PhenoteBean form = (PhenoteBean) command;
+    String ontologyName = form.getOntologyName();
+    String field = form.getField();
+    if (form.isTermCompletionRequest()) {
+      String userInput = form.getTermCompletionTerm();
+      LOG.info("ontology: " + ontologyName);
+      LOG.info("param entityInput: " + userInput);
+      LOG.info("Field entity: " + field);
+
+      form.setAjaxList(getCompletionList(userInput, ontologyName, field));
+      LOG.debug(form.getAjaxList());
+    } else if (form.isTermInfoRequest()) {
+      String termId = form.getTermId();
+      LOG.debug("doGet term info param: " + termId + " ont " + ontologyName);
+      try {
+        Ontology ont = getOntology(ontologyName);
+        OBOClass oboClass = ont.getOboClass(termId);
+        String termInfo = HtmlUtil.termInfo(oboClass);
+        LOG.debug("term info " + termInfo.substring(0,60));
+        String termInfoObo = HtmlUtil.termInfo(oboClass, ontologyName, field);
+        form.setAjaxList(termInfoObo);
+      }
+      catch (OntologyException e) {
+        LOG.error(e.getMessage(), e);
+      }
+    }
+    return new ModelAndView("ajax", "formBean", form);
+  }
+
+
+  /**
+   * ToDo: Need to cleanup this comment.
+   * List<String>? String[]? or String htmlLiString?
+   * for now just return html ul-li list w onmouseover
+   * userInput is what user has typed which terms will be queried for
+   * ontol is the name of the ontology that user is querying
+   * field is the gui field user is querying (which may have multiple ontols)
+   * if ontologyy not found actually returns error string saying as much - why not
+   *
+   * @param userInput
+   * @param ontologyName
+   * @param field
+   */
+  private String getCompletionList(String userInput, String ontologyName, String field) {
+    StringBuffer sb = new StringBuffer("<ul>");
+    try {
+      Vector<CompletionTerm> v = getCompListSearcher(ontologyName).getStringMatchTerms(userInput);
+      //Vector<OBOClass> v = ontology.getStringMatchTerms(userInput, getSearchParams());
+      for (CompletionTerm ct : v)
+        sb.append(makeCompListHtmlItem(ct, ontologyName, field));
+    }
+    catch (OntologyException e) {
+      sb.append(e.getMessage());
+    }
+    sb.append("</ul>");
+    return sb.toString();
+  }
+
+  private Object makeCompListHtmlItem(CompletionTerm term, String ontol, String field) {
+    String id = term.getID(), name = term.getName();
+    // pass in id, name & ontology - name for setting field on UseTerm
+    StringBuffer info = dq(fn("getTermInfo", new String[]{id, name, ontol, field}));
+    //String info = "\"getTermInfo("+id +","+q(name)+","+ q(ontol) + ")\"";
+    return "<li onmouseover=" + info + " id=" + q(id) + " " +
+            "onclick=" + info + ">" + name + "</li>\n";
+  }
+
+  private CompListSearcher getCompListSearcher(String ontologyName) throws OntologyException {
+    return new CompListSearcher(getOntology(ontologyName), getSearchParams());
+  }
+
+  /**
+   * throws ex if ontolName not found
+   */
+  private Ontology getOntology(String ontolName) throws OntologyException {
+    return OntologyManager.inst().getOntologyForName(ontolName);
+  }
+
+  private static String q(String s) {
+    return "'" + s + "'";
+  }
+
+  /**
+   * for now search params hard wired - eventually from buttons on web page
+   */
+  private SearchParamsI getSearchParams() {
+    return new HardWiredSearchParams();
+  }
+
+  private static StringBuffer dq(StringBuffer sb) {
+    return new StringBuffer("\"" + sb + "\"");
+  }
+
+  private static StringBuffer fn(String fnName, String[] params) {
+    return HtmlUtil.fn(fnName, params);
+  }
+
+  private class HardWiredSearchParams implements SearchParamsI {
+    public boolean searchTerms() {
+      return true;
+    }
+
+    public boolean searchSynonyms() {
+      return false; // --> true
+    }
+
+    public boolean searchDefinitions() {
+      return false; // ?? w [def]??
+    }
+
+    /**
+     * Whether to include obsoletes in searching terms, syns, & definitions
+     * This should be in conjunction with the other 3
+     */
+    public boolean searchObsoletes() {
+      return false; // --> true w [obs], disallow selection
+    }
+  }
+
+
+}
+

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java	2006-11-02 18:29:54 UTC (rev 179)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java	2006-11-02 21:41:54 UTC (rev 180)
@@ -1,30 +1,31 @@
-package phenote.servlet;
-
-/**
- * This contains configuration parameters pertaining to the web application only.
- */
-public class PhenoteWebConfiguration {
-
-  private String webRoot;
-  private static PhenoteWebConfiguration instance;
-
-  private PhenoteWebConfiguration(){
-
-  }
-
-  public static PhenoteWebConfiguration getInstance(){
-    if(instance == null){
-      instance = new PhenoteWebConfiguration();
-    }
-    return instance;
-  }
-
-
-  public String getWebRoot() {
-    return webRoot;
-  }
-
-  public void setWebRoot(String webRoot) {
-    this.webRoot = webRoot;
-  }
-}
+package phenote.servlet;
+
+/**
+ * This contains configuration parameters pertaining to the web application only.
+ */
+public class PhenoteWebConfiguration {
+
+  private String webRoot;
+  private static PhenoteWebConfiguration instance;
+
+  private PhenoteWebConfiguration(){
+
+  }
+
+  public static PhenoteWebConfiguration getInstance(){
+    if(instance == null){
+      instance = new PhenoteWebConfiguration();
+    }
+    return instance;
+  }
+
+
+  public String getWebRoot() {
+    return webRoot;
+  }
+
+  public void setWebRoot(String webRoot) {
+    this.webRoot = webRoot;
+  }
+}
+


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.




2006	Jan	Feb	Mar	Apr	May	Jun	Jul (18)	Aug (33)	Sep (30)	Oct (27)	Nov (59)	Dec (30)
2007	Jan (67)	Feb (44)	Mar (70)	Apr (73)	May (119)	Jun (31)	Jul (92)	Aug (86)	Sep (76)	Oct (152)	Nov (156)	Dec (85)
2008	Jan (111)	Feb (121)	Mar (107)	Apr (102)	May (45)	Jun (65)	Jul (62)	Aug (133)	Sep (56)	Oct (56)	Nov (17)	Dec (15)
2009	Jan (10)	Feb (5)	Mar (10)	Apr (14)	May (49)	Jun (94)	Jul (67)	Aug (23)	Sep (9)	Oct (92)	Nov (26)	Dec (51)
2010	Jan (105)	Feb (83)	Mar (52)	Apr (59)	May (68)	Jun (71)	Jul (127)	Aug (49)	Sep (91)	Oct (27)	Nov (33)	Dec (26)
2011	Jan (26)	Feb (45)	Mar (26)	Apr (28)	May (17)	Jun (15)	Jul (45)	Aug (33)	Sep (50)	Oct (22)	Nov (10)	Dec (21)
2012	Jan (33)	Feb (24)	Mar (36)	Apr (60)	May (60)	Jun (43)	Jul (114)	Aug (19)	Sep (35)	Oct (24)	Nov (64)	Dec (12)
2013	Jan (54)	Feb (58)	Mar (51)	Apr (46)	May (21)	Jun (29)	Jul (25)	Aug (25)	Sep (13)	Oct (7)	Nov (14)	Dec (27)
2014	Jan (10)	Feb (7)	Mar (16)	Apr (14)	May (19)	Jun (8)	Jul (15)	Aug (11)	Sep (5)	Oct (11)	Nov (11)	Dec (4)
2015	Jan (52)	Feb (27)	Mar (22)	Apr (17)	May (2)	Jun (2)	Jul (2)	Aug (2)	Sep (2)	Oct	Nov (2)	Dec
2016	Jan (2)	Feb	Mar	Apr (2)	May (1)	Jun (1)	Jul (3)	Aug (2)	Sep (2)	Oct (2)	Nov (2)	Dec
2017	Jan	Feb	Mar (1)	Apr (1)	May (4)	Jun	Jul	Aug (1)	Sep (1)	Oct (2)	Nov	Dec (1)
2018	Jan	Feb	Mar (4)	Apr	May (2)	Jun (2)	Jul (2)	Aug (2)	Sep (1)	Oct (2)	Nov (1)	Dec
2019	Jan	Feb	Mar	Apr	May	Jun	Jul (2)	Aug	Sep	Oct	Nov	Dec (3)
2020	Jan	Feb	Mar	Apr	May (2)	Jun (3)	Jul	Aug	Sep (2)	Oct	Nov	Dec

obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 179)

obo-svn-commit — sends mail for all commits to svn repository