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treebase-guts
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From: <rv...@us...> - 2009-06-23 13:04:11
|
Revision: 83
http://treebase.svn.sourceforge.net/treebase/?rev=83&view=rev
Author: rvos
Date: 2009-06-23 11:10:53 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
Added download URL forwarding.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-23 11:10:17 UTC (rev 82)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-23 11:10:53 UTC (rev 83)
@@ -73,8 +73,13 @@
}
String prefix = pathComponents[1];
String fullyQualifiedId = pathComponents[2];
- String id = fullyQualifiedId.replaceAll(".*:[a-zA-Z]*","");
- url = createUrl(prefix,id);
+ String id = fullyQualifiedId.replaceAll(".*:[a-zA-Z]*","");
+ if ( TreebaseUtil.isEmpty(req.getParameter("format")) ) {
+ url = createUrl(prefix,id);
+ }
+ else {
+ url = createDownloadUrl(prefix,id,req.getParameter("format"));
+ }
} catch ( NumberFormatException e ) {
res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string: " + e.getMessage());
} catch ( ObjectNotFoundException e ) {
@@ -89,6 +94,60 @@
return null;
}
+ private String createDownloadUrl(String prefix, String objectId, String format) throws Exception {
+ String url = "";
+ StringBuffer base = new StringBuffer("/treebase-web/search");
+ if ( prefix.equalsIgnoreCase("study") ) {
+ Long studyId = Long.parseLong(objectId);
+ Study study = getStudyService().findByID(studyId);
+ if ( study == null ) {
+ throw new ObjectNotFoundException("Can't find study " + studyId);
+ }
+ //return base + "/summary.html?id=" + objectId;
+ return base
+ .append("/downloadAStudy.html?id=")
+ .append(objectId)
+ .append("&format=")
+ .append(format)
+ .toString();
+ }
+ else if ( prefix.equalsIgnoreCase("matrix") ) {
+ Long matrixId = Long.parseLong(objectId);
+ Matrix matrix = getMatrixService().findByID(matrixId);
+ if ( matrix == null ) {
+ throw new ObjectNotFoundException("Can't find matrix " + matrixId);
+ }
+ Study study = matrix.getStudy();
+ //http://localhost:8080/treebase-web/search/downloadAMatrix.html?id=830&matrixid=263
+ return base
+ .append("/downloadAMatrix.html?id=")
+ .append(study.getId())
+ .append("&matrixid=")
+ .append(objectId)
+ .append("&format=")
+ .append(format)
+ .toString();
+ }
+ else if ( prefix.equalsIgnoreCase("tree") ) {
+ Long treeId = Long.parseLong(objectId);
+ PhyloTree phyloTree = getPhyloTreeService().findByID(treeId);
+ if ( phyloTree == null ) {
+ throw new ObjectNotFoundException("Can't find tree " + treeId);
+ }
+ Study study = phyloTree.getStudy();
+ //http://localhost:8080/treebase-web/search/downloadATree.html?id=830&treeid=3983
+ return base
+ .append("/downloadATree.html?id=")
+ .append(study.getId())
+ .append("&treeid=")
+ .append(objectId)
+ .append("&format=")
+ .append(format)
+ .toString();
+ }
+ return url;
+ }
+
public MatrixService getMatrixService() {
return mMatrixService;
}
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|
From: <rv...@us...> - 2009-06-25 02:48:13
|
Revision: 111
http://treebase.svn.sourceforge.net/treebase/?rev=111&view=rev
Author: rvos
Date: 2009-06-25 02:48:12 +0000 (Thu, 25 Jun 2009)
Log Message:
-----------
Refactored to use TreebaseIDString and NamespacedGUID classes as opposed to direct ID string manipulation
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-25 02:45:59 UTC (rev 110)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-25 02:48:12 UTC (rev 111)
@@ -6,7 +6,10 @@
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
+import org.cipres.treebase.NamespacedGUID;
+import org.cipres.treebase.TreebaseIDString;
import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.TreebaseIDString.MalformedTreebaseIDString;
import org.cipres.treebase.domain.matrix.Matrix;
import org.cipres.treebase.domain.matrix.MatrixService;
import org.cipres.treebase.domain.study.Study;
@@ -20,31 +23,28 @@
private PhyloTreeService mPhyloTreeService;
private StudyService mStudyService;
- private String createUrl(String prefix, String objectId) throws Exception {
+ private String createUrl(String prefix, Long objectId) throws Exception {
String url = "";
String base = "/treebase-web/search/study";
- if ( prefix.equalsIgnoreCase("study") ) {
- Long studyId = Long.parseLong(objectId);
- Study study = getStudyService().findByID(studyId);
+ if ( prefix.equals(TreebaseIDString.getPrefixForClass(Study.class)) ) {
+ Study study = getStudyService().findByID(objectId);
if ( study == null ) {
- throw new ObjectNotFoundException("Can't find study " + studyId);
+ throw new ObjectNotFoundException("Can't find study " + objectId);
}
return base + "/summary.html?id=" + objectId;
}
- else if ( prefix.equalsIgnoreCase("matrix") ) {
- Long matrixId = Long.parseLong(objectId);
- Matrix matrix = getMatrixService().findByID(matrixId);
+ else if ( prefix.equals(TreebaseIDString.getPrefixForClass(Matrix.class)) ) {
+ Matrix matrix = getMatrixService().findByID(objectId);
if ( matrix == null ) {
- throw new ObjectNotFoundException("Can't find matrix " + matrixId);
+ throw new ObjectNotFoundException("Can't find matrix " + objectId);
}
Study study = matrix.getStudy();
return base + "/matrix.html?id=" + study.getId() + "&matrixid=" + objectId;
}
- else if ( prefix.equalsIgnoreCase("tree") ) {
- Long treeId = Long.parseLong(objectId);
- PhyloTree phyloTree = getPhyloTreeService().findByID(treeId);
+ else if ( prefix.equals(TreebaseIDString.getPrefixForClass(PhyloTree.class)) ) {
+ PhyloTree phyloTree = getPhyloTreeService().findByID(objectId);
if ( phyloTree == null ) {
- throw new ObjectNotFoundException("Can't find tree " + treeId);
+ throw new ObjectNotFoundException("Can't find tree " + objectId);
}
Study study = phyloTree.getStudy();
return base + "/tree.html?id=" + study.getId() + "&treeid=" + objectId;
@@ -62,25 +62,28 @@
throw new InvalidRequestException(
"Invalid request '"
+ pathInfo
- + "', should be /${class}/${id}");
+ + "', should be /${NamespacedGUID}");
}
String[] pathComponents = pathInfo.split("/");
- if ( pathComponents.length != 3 ) {
+ if ( pathComponents.length != 2 ) {
throw new InvalidRequestException(
"Invalid request '"
+ pathInfo
- + "', should be /${class}/${id}");
+ + "', should be /${NamespacedGUID}");
}
- String prefix = pathComponents[1];
- String fullyQualifiedId = pathComponents[2];
- String id = fullyQualifiedId.replaceAll(".*:[a-zA-Z]*","");
- if ( TreebaseUtil.isEmpty(req.getParameter("format")) ) {
- url = createUrl(prefix,id);
+ String[] idComponents = pathComponents[1].split("\\.");
+ NamespacedGUID namespacedGUID = new NamespacedGUID(idComponents[0]);
+ TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
+ if ( idComponents.length >= 2 && idComponents[1].equals("html") ) {
+ url = createUrl(tbID.getTypePrefix(),tbID.getId());
}
+ else if ( idComponents.length >= 2 ) {
+ url = createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),idComponents[1]);
+ }
else {
- url = createDownloadUrl(prefix,id,req.getParameter("format"));
+ url = "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
}
- } catch ( NumberFormatException e ) {
+ } catch ( MalformedTreebaseIDString e ) {
res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string: " + e.getMessage());
} catch ( ObjectNotFoundException e ) {
res.sendError(HttpServletResponse.SC_NOT_FOUND, e.getMessage());
@@ -93,32 +96,31 @@
}
return null;
}
-
- private String createDownloadUrl(String prefix, String objectId, String format) throws Exception {
+
+ private String createDownloadUrl(String prefix, Long objectId, String format) throws Exception {
+ if ( format.equals("xml") ) {
+ format = "nexml";
+ }
String url = "";
StringBuffer base = new StringBuffer("/treebase-web/search");
- if ( prefix.equalsIgnoreCase("study") ) {
- Long studyId = Long.parseLong(objectId);
- Study study = getStudyService().findByID(studyId);
+ if ( prefix.equals(TreebaseIDString.getPrefixForClass(Study.class)) ) {
+ Study study = getStudyService().findByID(objectId);
if ( study == null ) {
- throw new ObjectNotFoundException("Can't find study " + studyId);
+ throw new ObjectNotFoundException("Can't find study " + objectId);
}
- //return base + "/summary.html?id=" + objectId;
return base
.append("/downloadAStudy.html?id=")
.append(objectId)
.append("&format=")
.append(format)
- .toString();
+ .toString();
}
- else if ( prefix.equalsIgnoreCase("matrix") ) {
- Long matrixId = Long.parseLong(objectId);
- Matrix matrix = getMatrixService().findByID(matrixId);
+ else if ( prefix.equals(TreebaseIDString.getPrefixForClass(Matrix.class)) ) {
+ Matrix matrix = getMatrixService().findByID(objectId);
if ( matrix == null ) {
- throw new ObjectNotFoundException("Can't find matrix " + matrixId);
+ throw new ObjectNotFoundException("Can't find matrix " + objectId);
}
Study study = matrix.getStudy();
- //http://localhost:8080/treebase-web/search/downloadAMatrix.html?id=830&matrixid=263
return base
.append("/downloadAMatrix.html?id=")
.append(study.getId())
@@ -126,16 +128,14 @@
.append(objectId)
.append("&format=")
.append(format)
- .toString();
+ .toString();
}
- else if ( prefix.equalsIgnoreCase("tree") ) {
- Long treeId = Long.parseLong(objectId);
- PhyloTree phyloTree = getPhyloTreeService().findByID(treeId);
+ else if ( prefix.equals(TreebaseIDString.getPrefixForClass(PhyloTree.class)) ) {
+ PhyloTree phyloTree = getPhyloTreeService().findByID(objectId);
if ( phyloTree == null ) {
- throw new ObjectNotFoundException("Can't find tree " + treeId);
+ throw new ObjectNotFoundException("Can't find tree " + objectId);
}
Study study = phyloTree.getStudy();
- //http://localhost:8080/treebase-web/search/downloadATree.html?id=830&treeid=3983
return base
.append("/downloadATree.html?id=")
.append(study.getId())
@@ -143,7 +143,7 @@
.append(objectId)
.append("&format=")
.append(format)
- .toString();
+ .toString();
}
return url;
}
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|
From: <rv...@us...> - 2009-06-28 10:18:04
|
Revision: 142
http://treebase.svn.sourceforge.net/treebase/?rev=142&view=rev
Author: rvos
Date: 2009-06-28 10:17:15 +0000 (Sun, 28 Jun 2009)
Log Message:
-----------
Added redirect for uBio and NCBI namespaced GUIDs
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-28 10:15:53 UTC (rev 141)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-28 10:17:15 UTC (rev 142)
@@ -18,10 +18,14 @@
import org.cipres.treebase.domain.tree.PhyloTreeService;
public class PhyloWSController implements Controller {
+ private static String ncbiBaseUrl = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=";
+ private static String uBioBaseUrl = "http://www.ubio.org/browser/details.php?namebankID=";
private static final long serialVersionUID = 1L;
private MatrixService mMatrixService;
private PhyloTreeService mPhyloTreeService;
private StudyService mStudyService;
+ private static String format = "format";
+ private static String[] classesWithPages = { "tree", "study", "matrix" };
private String createUrl(String prefix, Long objectId) throws Exception {
String url = "";
@@ -62,26 +66,33 @@
throw new InvalidRequestException(
"Invalid request '"
+ pathInfo
- + "', should be /${NamespacedGUID}");
+ + "', should be /${class}/${NamespacedGUID}");
}
String[] pathComponents = pathInfo.split("/");
- if ( pathComponents.length != 2 ) {
- throw new InvalidRequestException(
- "Invalid request '"
- + pathInfo
- + "', should be /${NamespacedGUID}");
+ String rawNamespacedGUID = pathComponents[pathComponents.length-1];
+ if ( rawNamespacedGUID.startsWith("uBio:") ) {
+ url = uBioBaseUrl + rawNamespacedGUID.substring("uBio:".length());
}
- String[] idComponents = pathComponents[1].split("\\.");
- NamespacedGUID namespacedGUID = new NamespacedGUID(idComponents[0]);
- TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
- if ( idComponents.length >= 2 && idComponents[1].equals("html") ) {
- url = createUrl(tbID.getTypePrefix(),tbID.getId());
- }
- else if ( idComponents.length >= 2 ) {
- url = createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),idComponents[1]);
- }
+ else if ( rawNamespacedGUID.startsWith("NCBI:") ) {
+ url = ncbiBaseUrl + rawNamespacedGUID.substring("NCBI:".length());
+ }
else {
- url = "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+ NamespacedGUID namespacedGUID = new NamespacedGUID(rawNamespacedGUID);
+ TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
+ if ( hasWebPage(pathComponents) ) {
+ if ( TreebaseUtil.isEmpty(req.getParameter(format)) ) {
+ url = "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+ }
+ else if ( req.getParameter(format).equals("html") ) {
+ url = createUrl(tbID.getTypePrefix(),tbID.getId());
+ }
+ else {
+ url = createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),req.getParameter(format));
+ }
+ }
+ else {
+ url = "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+ }
}
} catch ( MalformedTreebaseIDString e ) {
res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string: " + e.getMessage());
@@ -91,11 +102,22 @@
res.sendError(HttpServletResponse.SC_BAD_REQUEST, e.getMessage());
}
if ( ! TreebaseUtil.isEmpty(url) ) {
- res.setStatus(HttpServletResponse.SC_MOVED_TEMPORARILY);
+ res.setStatus(HttpServletResponse.SC_FOUND);
res.setHeader("Location", url);
}
return null;
}
+
+ private boolean hasWebPage(String[] pathComponents) {
+ for ( int i = ( pathComponents.length - 1 ); i >= 0; i-- ) {
+ for ( int j = 0; j < classesWithPages.length; j++ ) {
+ if ( pathComponents[i].equals(classesWithPages[j]) ) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
private String createDownloadUrl(String prefix, Long objectId, String format) throws Exception {
if ( format.equals("xml") ) {
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|
From: <rv...@us...> - 2009-06-28 11:56:32
|
Revision: 153
http://treebase.svn.sourceforge.net/treebase/?rev=153&view=rev
Author: rvos
Date: 2009-06-28 11:56:30 +0000 (Sun, 28 Jun 2009)
Log Message:
-----------
Changed redirect response code to SEE OTHER (303)
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-28 11:49:36 UTC (rev 152)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-06-28 11:56:30 UTC (rev 153)
@@ -103,7 +103,7 @@
res.sendError(HttpServletResponse.SC_BAD_REQUEST, e.getMessage());
}
if ( ! TreebaseUtil.isEmpty(url) ) {
- res.setStatus(HttpServletResponse.SC_FOUND);
+ res.setStatus(HttpServletResponse.SC_SEE_OTHER);
res.setHeader("Location", url);
}
return null;
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|
From: <rv...@us...> - 2009-07-06 08:41:03
|
Revision: 175
http://treebase.svn.sourceforge.net/treebase/?rev=175&view=rev
Author: rvos
Date: 2009-07-06 08:41:02 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Now throws 404 instead of NPE when study not found
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-07-06 08:37:02 UTC (rev 174)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-07-06 08:41:02 UTC (rev 175)
@@ -162,6 +162,9 @@
throw new ObjectNotFoundException("Can't find matrix " + objectId);
}
Study study = matrix.getStudy();
+ if ( study == null ) {
+ throw new ObjectNotFoundException("Can't find study for matrix "+objectId);
+ }
return base
.append("/downloadAMatrix.html?id=")
.append(study.getId())
@@ -177,6 +180,9 @@
throw new ObjectNotFoundException("Can't find tree " + objectId);
}
Study study = phyloTree.getStudy();
+ if ( study == null ) {
+ throw new ObjectNotFoundException("Can't find study for tree "+objectId);
+ }
return base
.append("/downloadATree.html?id=")
.append(study.getId())
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|
From: <rv...@us...> - 2010-01-12 17:28:36
|
Revision: 418
http://treebase.svn.sourceforge.net/treebase/?rev=418&view=rev
Author: rvos
Date: 2010-01-12 17:28:29 +0000 (Tue, 12 Jan 2010)
Log Message:
-----------
The PhyloWSController now stores the x-access-granted QUERY_STRING parameter as a session variable so that it can be referred to by other pages in the same session.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-12 17:23:04 UTC (rev 417)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-12 17:28:29 UTC (rev 418)
@@ -16,6 +16,7 @@
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.PhyloTreeService;
+import org.cipres.treebase.web.Constants;
public class PhyloWSController implements Controller {
private static String ncbiBaseUrl = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=";
@@ -61,6 +62,11 @@
res.setContentType("text/plain");
String url = null;
String domain = "http://" + req.getServerName() + ":" + req.getServerPort();
+ if ( ! TreebaseUtil.isEmpty(req.getParameter(Constants.X_ACCESS_CODE)) ) {
+ req.getSession().setAttribute(
+ Constants.X_ACCESS_CODE,
+ req.getParameter(Constants.X_ACCESS_CODE));
+ }
try {
String pathInfo = req.getPathInfo();
if ( TreebaseUtil.isEmpty(pathInfo) ) {
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|
From: <rv...@us...> - 2010-01-15 12:41:39
|
Revision: 443
http://treebase.svn.sourceforge.net/treebase/?rev=443&view=rev
Author: rvos
Date: 2010-01-15 12:41:32 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Added x-access-code parameter to phylows redirect
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-15 12:18:59 UTC (rev 442)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-15 12:41:32 UTC (rev 443)
@@ -28,15 +28,30 @@
private static String format = "format";
private static String[] classesWithPages = { "tree", "study", "matrix" };
- private String createUrl(String prefix, Long objectId) throws Exception {
+ private String createUrl(String prefix, Long objectId,HttpServletRequest request) throws Exception {
String url = "";
- String base = "/treebase-web/search/study";
+ StringBuffer base = new StringBuffer("/treebase-web/search/study");
if ( prefix.equals(TreebaseIDString.getPrefixForClass(Study.class)) ) {
Study study = getStudyService().findByID(objectId);
if ( study == null ) {
throw new ObjectNotFoundException("Can't find study " + objectId);
- }
- return base + "/summary.html?id=" + objectId;
+ }
+ if ( ! TreebaseUtil.isEmpty(request.getParameter(Constants.X_ACCESS_CODE))) {
+ return base
+ .append("/summary.html?id=")
+ .append(objectId)
+ .append('&')
+ .append(Constants.X_ACCESS_CODE)
+ .append('=')
+ .append(request.getParameter(Constants.X_ACCESS_CODE))
+ .toString();
+ }
+ else {
+ return base
+ .append("/summary.html?id=")
+ .append(objectId)
+ .toString();
+ }
}
else if ( prefix.equals(TreebaseIDString.getPrefixForClass(Matrix.class)) ) {
Matrix matrix = getMatrixService().findByID(objectId);
@@ -44,7 +59,12 @@
throw new ObjectNotFoundException("Can't find matrix " + objectId);
}
Study study = matrix.getStudy();
- return base + "/matrix.html?id=" + study.getId() + "&matrixid=" + objectId;
+ return base
+ .append("/matrix.html?id=")
+ .append(study.getId())
+ .append("&matrixid=")
+ .append(objectId)
+ .toString();
}
else if ( prefix.equals(TreebaseIDString.getPrefixForClass(PhyloTree.class)) ) {
PhyloTree phyloTree = getPhyloTreeService().findByID(objectId);
@@ -52,7 +72,12 @@
throw new ObjectNotFoundException("Can't find tree " + objectId);
}
Study study = phyloTree.getStudy();
- return base + "/tree.html?id=" + study.getId() + "&treeid=" + objectId;
+ return base
+ .append("/tree.html?id=")
+ .append(study.getId())
+ .append("&treeid=")
+ .append(objectId)
+ .toString();
}
return url;
}
@@ -94,7 +119,7 @@
url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
}
else if ( req.getParameter(format).equals("html") ) {
- url = domain + createUrl(tbID.getTypePrefix(),tbID.getId());
+ url = domain + createUrl(tbID.getTypePrefix(),tbID.getId(),req);
}
else {
url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),req.getParameter(format));
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|
From: <rv...@us...> - 2010-02-12 07:22:00
|
Revision: 496
http://treebase.svn.sourceforge.net/treebase/?rev=496&view=rev
Author: rvos
Date: 2010-02-12 07:21:53 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Added placeholder method for content-negotiation
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-02-12 04:41:13 UTC (rev 495)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-02-12 07:21:53 UTC (rev 496)
@@ -106,24 +106,25 @@
url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
} else {
String rawNamespacedGUID = pathComponents[pathComponents.length-1];
- if ( rawNamespacedGUID.startsWith("uBio:") ) {
+ if ( rawNamespacedGUID.startsWith("uBio:") ) { // XXX be polite, use real URL
url = uBioBaseUrl + rawNamespacedGUID.substring("uBio:".length());
}
- else if ( rawNamespacedGUID.startsWith("NCBI:") ) {
+ else if ( rawNamespacedGUID.startsWith("NCBI:") ) { // XXX be polite, use real URL
url = ncbiBaseUrl + rawNamespacedGUID.substring("NCBI:".length());
}
else {
NamespacedGUID namespacedGUID = new NamespacedGUID(rawNamespacedGUID);
TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
if ( hasWebPage(pathComponents) ) {
- if ( TreebaseUtil.isEmpty(req.getParameter(format)) ) {
+ String serializationFormat = createSerializationFormat(req);
+ if ( TreebaseUtil.isEmpty(serializationFormat) ) {
url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
}
- else if ( req.getParameter(format).equals("html") ) {
+ else if ( serializationFormat.equals("html") ) {
url = domain + createUrl(tbID.getTypePrefix(),tbID.getId(),req);
}
else {
- url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),req.getParameter(format));
+ url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),serializationFormat);
}
}
else {
@@ -145,6 +146,16 @@
return null;
}
+ /**
+ * This is a placeholder method that might parse accept headers for content-negotiation
+ * one day
+ * @param request
+ * @return
+ */
+ private String createSerializationFormat(HttpServletRequest request) {
+ return request.getParameter(format);
+ }
+
private String createSearchUrl(String path,HttpServletRequest request) {
StringBuilder sb = new StringBuilder();
sb
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From: <rv...@us...> - 2010-03-12 23:29:59
|
Revision: 562
http://treebase.svn.sourceforge.net/treebase/?rev=562&view=rev
Author: rvos
Date: 2010-03-12 23:29:53 +0000 (Fri, 12 Mar 2010)
Log Message:
-----------
Removed runtime-computed domain name and server port, which no longer work with the new tomcat configuration (would now compute "localhost"). Using relative URLs instead.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-03-12 23:27:28 UTC (rev 561)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-03-12 23:29:53 UTC (rev 562)
@@ -26,11 +26,28 @@
private PhyloTreeService mPhyloTreeService;
private StudyService mStudyService;
private static String format = "format";
+
+ /*
+ * this array is used to identify whether a path fragment maps to an object
+ * for which web pages are available. Maybe this should be an enum or a map
+ * instead.
+ */
private static String[] classesWithPages = { "tree", "study", "matrix" };
+ /**
+ * Given an object prefix ("tree", "study" or "matrix") and an object ID, constructs
+ * a relative URL to an HTML page about that object.
+ * @param prefix identifies either studies, matrices or trees
+ * @param objectId is the primary key for the requested object
+ * @param request is the servlet request, which we need to check for reviewer access
+ * @return a relative URL to an HTML page, or an empty string
+ * @throws Exception
+ */
private String createUrl(String prefix, Long objectId,HttpServletRequest request) throws Exception {
String url = "";
StringBuffer base = new StringBuffer("/treebase-web/search/study");
+
+ // requested object is a study
if ( prefix.equals(TreebaseIDString.getPrefixForClass(Study.class)) ) {
Study study = getStudyService().findByID(objectId);
if ( study == null ) {
@@ -54,6 +71,8 @@
.toString();
}
}
+
+ // requested object is a matrix
else if ( prefix.equals(TreebaseIDString.getPrefixForClass(Matrix.class)) ) {
Matrix matrix = getMatrixService().findByID(objectId);
if ( matrix == null ) {
@@ -67,6 +86,8 @@
.append(objectId)
.toString();
}
+
+ // requested object is a tree
else if ( prefix.equals(TreebaseIDString.getPrefixForClass(PhyloTree.class)) ) {
PhyloTree phyloTree = getPhyloTreeService().findByID(objectId);
if ( phyloTree == null ) {
@@ -87,7 +108,7 @@
throws Exception {
res.setContentType("text/plain");
String url = null;
- String domain = "http://" + req.getServerName() + ":" + req.getServerPort();
+ //String domain = "http://" + req.getServerName() + ":" + req.getServerPort();
if ( ! TreebaseUtil.isEmpty(req.getParameter(Constants.X_ACCESS_CODE)) ) {
req.getSession().setAttribute(
Constants.X_ACCESS_CODE,
@@ -103,7 +124,8 @@
}
String[] pathComponents = pathInfo.split("/");
if ( pathComponents[pathComponents.length-1].equals("find") ) {
- url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
+ //url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
+ url = createSearchUrl(pathComponents[pathComponents.length-2],req);
} else {
String rawNamespacedGUID = pathComponents[pathComponents.length-1];
if ( rawNamespacedGUID.startsWith("uBio:") ) { // XXX be polite, use real URL
@@ -118,17 +140,17 @@
if ( hasWebPage(pathComponents) ) {
String serializationFormat = createSerializationFormat(req);
if ( TreebaseUtil.isEmpty(serializationFormat) ) {
- url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+ url = "/treebase-web/search/study/anyObjectAsRDF.rdf?namespacedGUID=" + namespacedGUID.toString();
}
else if ( serializationFormat.equals("html") ) {
- url = domain + createUrl(tbID.getTypePrefix(),tbID.getId(),req);
+ url = createUrl(tbID.getTypePrefix(),tbID.getId(),req);
}
else {
- url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),serializationFormat);
+ url = createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),serializationFormat);
}
}
else {
- url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+ url = "/treebase-web/search/study/anyObjectAsRDF.rdf?namespacedGUID=" + namespacedGUID.toString();
}
}
}
@@ -157,9 +179,8 @@
}
private String createSearchUrl(String path,HttpServletRequest request) {
- StringBuilder sb = new StringBuilder();
+ StringBuilder sb = new StringBuilder("/treebase-web/search/");
sb
- .append("/treebase-web/search/")
.append(path)
.append("Search.html?query=")
.append(request.getParameter("query"))
@@ -170,6 +191,12 @@
return sb.toString();
}
+ /**
+ * Given an array of path fragments, returns whether an HTML web page
+ * exists for the type of object the fragments map onto
+ * @param pathComponents
+ * @return true of web page exists, false otherwise
+ */
private boolean hasWebPage(String[] pathComponents) {
for ( int i = ( pathComponents.length - 1 ); i >= 0; i-- ) {
for ( int j = 0; j < classesWithPages.length; j++ ) {
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|
|
From: <rv...@us...> - 2011-04-25 22:15:25
|
Revision: 803
http://treebase.svn.sourceforge.net/treebase/?rev=803&view=rev
Author: rvos
Date: 2011-04-25 22:15:19 +0000 (Mon, 25 Apr 2011)
Log Message:
-----------
Added more descriptive id parsing error message; not adding null parameters to new redirect string; only pruning one character from query string.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2011-04-25 21:54:29 UTC (rev 802)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2011-04-25 22:15:19 UTC (rev 803)
@@ -75,7 +75,7 @@
url = createResourceUrl(namespacedGUID, req);
}
} catch ( MalformedTreebaseIDString e ) {
- res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string: " + e.getMessage());
+ res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string from path info '" + pathInfo + "' message: " + e.getMessage());
} catch ( ObjectNotFoundException e ) {
res.sendError(HttpServletResponse.SC_NOT_FOUND, "Object not found: " + e.getMessage());
}
@@ -127,9 +127,18 @@
StringBuffer sb = new StringBuffer(searchBase);
sb.append(getSearchPage());
Map<String,String> params = new HashMap<String,String>();
- params.put("query", request.getParameter("query"));
- params.put("format", createSerializationFormat(request));
- params.put("recordSchema", request.getParameter("recordSchema"));
+ String query = request.getParameter("query");
+ if ( ! TreebaseUtil.isEmpty(query) ) {
+ params.put("query", query);
+ }
+ String format = createSerializationFormat(request);
+ if ( ! TreebaseUtil.isEmpty(format) ) {
+ params.put("format", format);
+ }
+ String recordSchema = request.getParameter("recordSchema");
+ if ( ! TreebaseUtil.isEmpty(recordSchema) ) {
+ params.put("recordSchema", recordSchema);
+ }
return createUrl(sb,params,request);
}
@@ -168,7 +177,7 @@
base.append(key).append('=').append(params.get(key)).append('&');
}
String url = base.toString();
- return url.substring(0, url.length() - 2 );
+ return url.substring(0, url.length() - 1 );
}
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|
|
From: <rv...@us...> - 2011-04-25 22:28:05
|
Revision: 804
http://treebase.svn.sourceforge.net/treebase/?rev=804&view=rev
Author: rvos
Date: 2011-04-25 22:27:59 +0000 (Mon, 25 Apr 2011)
Log Message:
-----------
More pre-processing of the id string
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2011-04-25 22:15:19 UTC (rev 803)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2011-04-25 22:27:59 UTC (rev 804)
@@ -53,8 +53,9 @@
url = createSearchUrl(req);
}
else {
+ String substr = pathInfo.replaceAll(".*/", "");
try {
- NamespacedGUID namespacedGUID = new NamespacedGUID(pathInfo);
+ NamespacedGUID namespacedGUID = new NamespacedGUID(substr);
TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
String serializationFormat = createSerializationFormat(req);
if ( hasWebPage(tbID.getClass()) && ! TreebaseUtil.isEmpty(serializationFormat) ) {
@@ -75,7 +76,7 @@
url = createResourceUrl(namespacedGUID, req);
}
} catch ( MalformedTreebaseIDString e ) {
- res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string from path info '" + pathInfo + "' message: " + e.getMessage());
+ res.sendError(HttpServletResponse.SC_BAD_REQUEST, "Bad ID string from path info '" + substr + "' message: " + e.getMessage());
} catch ( ObjectNotFoundException e ) {
res.sendError(HttpServletResponse.SC_NOT_FOUND, "Object not found: " + e.getMessage());
}
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