Menu
▾
▴
treebase-guts — Commit and tracker messages
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
(1) |
Apr
(14) |
May
(36) |
Jun
(148) |
Jul
(33) |
Aug
(2) |
Sep
(17) |
Oct
(42) |
Nov
(137) |
Dec
(88) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2010 |
Jan
(89) |
Feb
(80) |
Mar
(217) |
Apr
(76) |
May
(5) |
Jun
(39) |
Jul
(35) |
Aug
(4) |
Sep
(7) |
Oct
(14) |
Nov
(12) |
Dec
(9) |
| 2011 |
Jan
(6) |
Feb
(4) |
Mar
(11) |
Apr
(55) |
May
(90) |
Jun
(39) |
Jul
(15) |
Aug
(15) |
Sep
(23) |
Oct
(12) |
Nov
(17) |
Dec
(20) |
| 2012 |
Jan
(22) |
Feb
(63) |
Mar
|
Apr
(1) |
May
(6) |
Jun
(3) |
Jul
(1) |
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
(3) |
Feb
(6) |
Mar
|
Apr
|
May
|
Jun
(4) |
Jul
(1) |
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
| 2014 |
Jan
|
Feb
|
Mar
|
Apr
(7) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <rv...@us...> - 2010-01-15 17:08:04
|
Revision: 460
http://treebase.svn.sourceforge.net/treebase/?rev=460&view=rev
Author: rvos
Date: 2010-01-15 17:07:52 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Cancel redirects with extra parameter "agreement=cancel"
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:56:16 UTC (rev 459)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 17:07:52 UTC (rev 460)
@@ -241,7 +241,7 @@
</div>
<div style="width:100%;text-align:center;padding-top:10px">
<input type="submit" id="agreementOk" value="OK" onclick="$('agreement').style.display = 'none'"/>
- <input type="submit" id="agreementCancel" value="Cancel" onclick="document.href='/treebase-web/accessviolation.html'"/>
+ <input type="submit" id="agreementCancel" value="Cancel" onclick="window.location=location.href+'&agreement=cancel'"/>
</div>
</div>
</c:if>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 16:56:22
|
Revision: 459
http://treebase.svn.sourceforge.net/treebase/?rev=459&view=rev
Author: rvos
Date: 2010-01-15 16:56:16 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Set agreement cancellation to re-direct to access violation page
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:48:09 UTC (rev 458)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:56:16 UTC (rev 459)
@@ -241,7 +241,7 @@
</div>
<div style="width:100%;text-align:center;padding-top:10px">
<input type="submit" id="agreementOk" value="OK" onclick="$('agreement').style.display = 'none'"/>
- <input type="submit" id="agreementCancel" value="Cancel" onclick="history.back(1)"/>
+ <input type="submit" id="agreementCancel" value="Cancel" onclick="document.href='/treebase-web/accessviolation.html'"/>
</div>
</div>
</c:if>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 16:48:17
|
Revision: 458
http://treebase.svn.sourceforge.net/treebase/?rev=458&view=rev
Author: rvos
Date: 2010-01-15 16:48:09 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Changed agreement to floating div instead of javascript confirm dialog.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:04:17 UTC (rev 457)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:48:09 UTC (rev 458)
@@ -186,59 +186,64 @@
<span style="color: red; ">You are in reviewer mode.</span>
</div>
<c:if test="${displayAgreement}">
- <script type="text/javascript">
- TreeBASE.register(
- function() {
- var msg = "Reviewer/Referee Access Agreement\n"
- + "\n"
- + "You have reached this page using a special URL that is intended to be used\n"
- + "by journal editors and reviewers or referees of a paper that is under\n"
- + "consideration for publication. This URL gives you access to the submitted\n"
- + "data and metadata associated with analyses and results presented in the\n"
- + "paper under review. Please carefully examine the data paying special\n"
- + "attention to the following:\n"
- + "\n"
- + "* The citation data (authors, year, citation, abstract) should be\n"
- + " complete, except for information that is not yet known (e.g. volume or\n"
- + " page numbers).\n"
- + "* Verify that nexus files are error-free and executable by software\n"
- + " programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the\n"
- + " taxon labels for trees are identical, or a subset of, the taxon labels in\n"
- + " data matrices connected by way of an analysis. If taxon labels in trees do\n"
- + " not match with taxon labels in associated data matrices, the data will not\n"
- + " be useful to the scientific community.\n"
- + "* Verify that data are not missing and that opportunities to supply\n"
- + " valuable metadata are not overlooked. For example, TreeBASE can store\n"
- + " Genbank accession numbers, museum voucher IDs, latitude and longitudes for\n"
- + " specimen localities, character names and character state names for\n"
- + " morphological data, etc. Including these metadata are sometimes overlooked\n"
- + " by submitting authors, yet sharing this metadata is extremely valuable to\n"
- + " the scientific community. Please use your power as a reviewer to encourage\n"
- + " the sharing of richly-annotated metadata.\n"
- + "* Verify that analyses are not missing and that, where possible, analysis\n"
- + " entries include software commands (e.g. the contents of a PAUP block or\n"
- + " MrBayes block) so that analyses can be replicated easily (e.g. commands\n"
- + " that describe substitution models, data partitions, and heuristic search\n"
- + " parameters).\n"
- + "* Verify that taxon labels are mapped against TreeBASE's taxonomic\n"
- + " dictionary. Data in TreeBASE can only be found using a taxon name search if\n"
- + " the taxon labels are properly mapped.\n"
- + "\n"
- + "By clicking the 'OK' button below, you agree to keep these data\n"
- + "confidential; you agree not to retain these data after completing your report\n"
- + "to the journal editor; you agree not to use these data or knowledge of these\n"
- + "data for the purposes of your research until and unless the paper under\n"
- + "review has been published and the data have been made available to the\n"
- + "general public; you agree to keep the URL confidential.\n";
- if ( confirm(msg) ) {
- // do things if OK
- }
- else {
- history.back(1);
- }
- }
- );
- </script>
+ <div id="agreement" style="position:fixed;left:10%;top:5%;width:80%;height:80%;background-color:white;padding:10px;border:5px solid orange">
+ <h2>Reviewer/Referee Access Agreement</h2>
+ <div style="width:100%;overflow:auto">
+ You have reached this page using a special URL that is intended to be used
+ by journal editors and reviewers or referees of a paper that is under
+ consideration for publication. This URL gives you access to the submitted
+ data and metadata associated with analyses and results presented in the
+ paper under review. Please carefully examine the data paying special
+ attention to the following:
+ <ul>
+ <li>
+ The citation data (authors, year, citation, abstract) should be
+ complete, except for information that is not yet known (e.g. volume or
+ page numbers).
+ </li>
+ <li>
+ Verify that nexus files are error-free and executable by software
+ programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the
+ taxon labels for trees are identical, or a subset of, the taxon labels in
+ data matrices connected by way of an analysis. If taxon labels in trees do
+ not match with taxon labels in associated data matrices, the data will not
+ be useful to the scientific community.
+ </li>
+ <li>
+ Verify that data are not missing and that opportunities to supply
+ valuable metadata are not overlooked. For example, TreeBASE can store
+ Genbank accession numbers, museum voucher IDs, latitude and longitudes for
+ specimen localities, character names and character state names for
+ morphological data, etc. Including these metadata are sometimes overlooked
+ by submitting authors, yet sharing this metadata is extremely valuable to
+ the scientific community. Please use your power as a reviewer to encourage
+ the sharing of richly-annotated metadata.
+ </li>
+ <li>
+ Verify that analyses are not missing and that, where possible, analysis
+ entries include software commands (e.g. the contents of a PAUP block or
+ MrBayes block) so that analyses can be replicated easily (e.g. commands
+ that describe substitution models, data partitions, and heuristic search
+ parameters).
+ </li>
+ <li>
+ Verify that taxon labels are mapped against TreeBASE's taxonomic
+ dictionary. Data in TreeBASE can only be found using a taxon name search if
+ the taxon labels are properly mapped.
+ </li>
+ </ul>
+ By clicking the 'OK' button below, you agree to keep these data
+ confidential; you agree not to retain these data after completing your report
+ to the journal editor; you agree not to use these data or knowledge of these
+ data for the purposes of your research until and unless the paper under
+ review has been published and the data have been made available to the
+ general public; you agree to keep the URL confidential.
+ </div>
+ <div style="width:100%;text-align:center;padding-top:10px">
+ <input type="submit" id="agreementOk" value="OK" onclick="$('agreement').style.display = 'none'"/>
+ <input type="submit" id="agreementCancel" value="Cancel" onclick="history.back(1)"/>
+ </div>
+ </div>
</c:if>
</c:if>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 16:04:23
|
Revision: 457
http://treebase.svn.sourceforge.net/treebase/?rev=457&view=rev
Author: rvos
Date: 2010-01-15 16:04:17 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Added missing closing parenthesis.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:01:45 UTC (rev 456)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:04:17 UTC (rev 457)
@@ -230,7 +230,7 @@
+ "data for the purposes of your research until and unless the paper under\n"
+ "review has been published and the data have been made available to the\n"
+ "general public; you agree to keep the URL confidential.\n";
- if (confirm(msg) {
+ if ( confirm(msg) ) {
// do things if OK
}
else {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 16:01:51
|
Revision: 456
http://treebase.svn.sourceforge.net/treebase/?rev=456&view=rev
Author: rvos
Date: 2010-01-15 16:01:45 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Added reviewer agreement confirmation dialog as onLoad() callback
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 15:55:17 UTC (rev 455)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 16:01:45 UTC (rev 456)
@@ -187,53 +187,57 @@
</div>
<c:if test="${displayAgreement}">
<script type="text/javascript">
-var msg = "Reviewer/Referee Access Agreement\n"
-+ "\n"
-+ "You have reached this page using a special URL that is intended to be used\n"
-+ "by journal editors and reviewers or referees of a paper that is under\n"
-+ "consideration for publication. This URL gives you access to the submitted\n"
-+ "data and metadata associated with analyses and results presented in the\n"
-+ "paper under review. Please carefully examine the data paying special\n"
-+ "attention to the following:\n"
-+ "\n"
-+ "* The citation data (authors, year, citation, abstract) should be\n"
-+ " complete, except for information that is not yet known (e.g. volume or\n"
-+ " page numbers).\n"
-+ "* Verify that nexus files are error-free and executable by software\n"
-+ " programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the\n"
-+ " taxon labels for trees are identical, or a subset of, the taxon labels in\n"
-+ " data matrices connected by way of an analysis. If taxon labels in trees do\n"
-+ " not match with taxon labels in associated data matrices, the data will not\n"
-+ " be useful to the scientific community.\n"
-+ "* Verify that data are not missing and that opportunities to supply\n"
-+ " valuable metadata are not overlooked. For example, TreeBASE can store\n"
-+ " Genbank accession numbers, museum voucher IDs, latitude and longitudes for\n"
-+ " specimen localities, character names and character state names for\n"
-+ " morphological data, etc. Including these metadata are sometimes overlooked\n"
-+ " by submitting authors, yet sharing this metadata is extremely valuable to\n"
-+ " the scientific community. Please use your power as a reviewer to encourage\n"
-+ " the sharing of richly-annotated metadata.\n"
-+ "* Verify that analyses are not missing and that, where possible, analysis\n"
-+ " entries include software commands (e.g. the contents of a PAUP block or\n"
-+ " MrBayes block) so that analyses can be replicated easily (e.g. commands\n"
-+ " that describe substitution models, data partitions, and heuristic search\n"
-+ " parameters).\n"
-+ "* Verify that taxon labels are mapped against TreeBASE's taxonomic\n"
-+ " dictionary. Data in TreeBASE can only be found using a taxon name search if\n"
-+ " the taxon labels are properly mapped.\n"
-+ "\n"
-+ "By clicking the 'OK' button below, you agree to keep these data\n"
-+ "confidential; you agree not to retain these data after completing your report\n"
-+ "to the journal editor; you agree not to use these data or knowledge of these\n"
-+ "data for the purposes of your research until and unless the paper under\n"
-+ "review has been published and the data have been made available to the\n"
-+ "general public; you agree to keep the URL confidential.\n";
- if (confirm(msg) {
- // do things if OK
+ TreeBASE.register(
+ function() {
+ var msg = "Reviewer/Referee Access Agreement\n"
+ + "\n"
+ + "You have reached this page using a special URL that is intended to be used\n"
+ + "by journal editors and reviewers or referees of a paper that is under\n"
+ + "consideration for publication. This URL gives you access to the submitted\n"
+ + "data and metadata associated with analyses and results presented in the\n"
+ + "paper under review. Please carefully examine the data paying special\n"
+ + "attention to the following:\n"
+ + "\n"
+ + "* The citation data (authors, year, citation, abstract) should be\n"
+ + " complete, except for information that is not yet known (e.g. volume or\n"
+ + " page numbers).\n"
+ + "* Verify that nexus files are error-free and executable by software\n"
+ + " programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the\n"
+ + " taxon labels for trees are identical, or a subset of, the taxon labels in\n"
+ + " data matrices connected by way of an analysis. If taxon labels in trees do\n"
+ + " not match with taxon labels in associated data matrices, the data will not\n"
+ + " be useful to the scientific community.\n"
+ + "* Verify that data are not missing and that opportunities to supply\n"
+ + " valuable metadata are not overlooked. For example, TreeBASE can store\n"
+ + " Genbank accession numbers, museum voucher IDs, latitude and longitudes for\n"
+ + " specimen localities, character names and character state names for\n"
+ + " morphological data, etc. Including these metadata are sometimes overlooked\n"
+ + " by submitting authors, yet sharing this metadata is extremely valuable to\n"
+ + " the scientific community. Please use your power as a reviewer to encourage\n"
+ + " the sharing of richly-annotated metadata.\n"
+ + "* Verify that analyses are not missing and that, where possible, analysis\n"
+ + " entries include software commands (e.g. the contents of a PAUP block or\n"
+ + " MrBayes block) so that analyses can be replicated easily (e.g. commands\n"
+ + " that describe substitution models, data partitions, and heuristic search\n"
+ + " parameters).\n"
+ + "* Verify that taxon labels are mapped against TreeBASE's taxonomic\n"
+ + " dictionary. Data in TreeBASE can only be found using a taxon name search if\n"
+ + " the taxon labels are properly mapped.\n"
+ + "\n"
+ + "By clicking the 'OK' button below, you agree to keep these data\n"
+ + "confidential; you agree not to retain these data after completing your report\n"
+ + "to the journal editor; you agree not to use these data or knowledge of these\n"
+ + "data for the purposes of your research until and unless the paper under\n"
+ + "review has been published and the data have been made available to the\n"
+ + "general public; you agree to keep the URL confidential.\n";
+ if (confirm(msg) {
+ // do things if OK
+ }
+ else {
+ history.back(1);
+ }
}
- else {
- history.back(1);
- }
+ );
</script>
</c:if>
</c:if>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 15:55:25
|
Revision: 455
http://treebase.svn.sourceforge.net/treebase/?rev=455&view=rev
Author: rvos
Date: 2010-01-15 15:55:17 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Added reviewer agreement.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 15:23:47 UTC (rev 454)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 15:55:17 UTC (rev 455)
@@ -183,8 +183,59 @@
<c:if test="${reviewerAccessGranted}">
<div>
<img src="<fmt:message key="icons.info"/>" alt="<fmt:message key="icon.information"/>" class="icon" />
- <span style="color: red; ">You are in reviewer mode ${displayAgreement}.</span>
+ <span style="color: red; ">You are in reviewer mode.</span>
</div>
+ <c:if test="${displayAgreement}">
+ <script type="text/javascript">
+var msg = "Reviewer/Referee Access Agreement\n"
++ "\n"
++ "You have reached this page using a special URL that is intended to be used\n"
++ "by journal editors and reviewers or referees of a paper that is under\n"
++ "consideration for publication. This URL gives you access to the submitted\n"
++ "data and metadata associated with analyses and results presented in the\n"
++ "paper under review. Please carefully examine the data paying special\n"
++ "attention to the following:\n"
++ "\n"
++ "* The citation data (authors, year, citation, abstract) should be\n"
++ " complete, except for information that is not yet known (e.g. volume or\n"
++ " page numbers).\n"
++ "* Verify that nexus files are error-free and executable by software\n"
++ " programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the\n"
++ " taxon labels for trees are identical, or a subset of, the taxon labels in\n"
++ " data matrices connected by way of an analysis. If taxon labels in trees do\n"
++ " not match with taxon labels in associated data matrices, the data will not\n"
++ " be useful to the scientific community.\n"
++ "* Verify that data are not missing and that opportunities to supply\n"
++ " valuable metadata are not overlooked. For example, TreeBASE can store\n"
++ " Genbank accession numbers, museum voucher IDs, latitude and longitudes for\n"
++ " specimen localities, character names and character state names for\n"
++ " morphological data, etc. Including these metadata are sometimes overlooked\n"
++ " by submitting authors, yet sharing this metadata is extremely valuable to\n"
++ " the scientific community. Please use your power as a reviewer to encourage\n"
++ " the sharing of richly-annotated metadata.\n"
++ "* Verify that analyses are not missing and that, where possible, analysis\n"
++ " entries include software commands (e.g. the contents of a PAUP block or\n"
++ " MrBayes block) so that analyses can be replicated easily (e.g. commands\n"
++ " that describe substitution models, data partitions, and heuristic search\n"
++ " parameters).\n"
++ "* Verify that taxon labels are mapped against TreeBASE's taxonomic\n"
++ " dictionary. Data in TreeBASE can only be found using a taxon name search if\n"
++ " the taxon labels are properly mapped.\n"
++ "\n"
++ "By clicking the 'OK' button below, you agree to keep these data\n"
++ "confidential; you agree not to retain these data after completing your report\n"
++ "to the journal editor; you agree not to use these data or knowledge of these\n"
++ "data for the purposes of your research until and unless the paper under\n"
++ "review has been published and the data have been made available to the\n"
++ "general public; you agree to keep the URL confidential.\n";
+ if (confirm(msg) {
+ // do things if OK
+ }
+ else {
+ history.back(1);
+ }
+ </script>
+ </c:if>
</c:if>
<c:if test="${! empty study.citation.title}">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 15:23:54
|
Revision: 454
http://treebase.svn.sourceforge.net/treebase/?rev=454&view=rev
Author: rvos
Date: 2010-01-15 15:23:47 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Flag needs to be turned off after initial access granting.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 15:21:14 UTC (rev 453)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 15:23:47 UTC (rev 454)
@@ -200,6 +200,9 @@
if ( pRequest.getSession().getAttribute(Constants.REVIEWER_ACCESS_GRANTED) == null ) {
pRequest.getSession().setAttribute("displayAgreement",true);
}
+ else {
+ pRequest.getSession().setAttribute("displayAgreement",false);
+ }
pRequest.getSession().setAttribute(Constants.REVIEWER_ACCESS_GRANTED, reviewerAccessGranted);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 15:21:20
|
Revision: 453
http://treebase.svn.sourceforge.net/treebase/?rev=453&view=rev
Author: rvos
Date: 2010-01-15 15:21:14 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
NPE workaround
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 15:17:49 UTC (rev 452)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 15:21:14 UTC (rev 453)
@@ -197,7 +197,7 @@
//saveMessage(pRequest,"You are in reviewer access mode.");
LOGGER.info("x-access-code matches computed hashed study id");
LOGGER.info("Reviewer access is granted");
- if ( ! (Boolean)pRequest.getSession().getAttribute(Constants.REVIEWER_ACCESS_GRANTED) ) {
+ if ( pRequest.getSession().getAttribute(Constants.REVIEWER_ACCESS_GRANTED) == null ) {
pRequest.getSession().setAttribute("displayAgreement",true);
}
pRequest.getSession().setAttribute(Constants.REVIEWER_ACCESS_GRANTED, reviewerAccessGranted);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 15:17:55
|
Revision: 452
http://treebase.svn.sourceforge.net/treebase/?rev=452&view=rev
Author: rvos
Date: 2010-01-15 15:17:49 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Added flag and logic for displaying reviewer notice/agreement on initial access check.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java 2010-01-15 15:05:00 UTC (rev 451)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/Constants.java 2010-01-15 15:17:49 UTC (rev 452)
@@ -25,6 +25,8 @@
* objects to be stores in the session
*/
public static final String X_ACCESS_CODE = "x-access-code";
+ public static final String REVIEWER_ACCESS_GRANTED = "reviewerAccessGranted";
+
public static final String STUDY_MAP = "studyMap";
public static final String ANALYSIS_MAP = "analysisMap";
public static final String ANALYSIS_STEP_MAP = "analysisStepMap";
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 15:05:00 UTC (rev 451)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 15:17:49 UTC (rev 452)
@@ -197,6 +197,11 @@
//saveMessage(pRequest,"You are in reviewer access mode.");
LOGGER.info("x-access-code matches computed hashed study id");
LOGGER.info("Reviewer access is granted");
+ if ( ! (Boolean)pRequest.getSession().getAttribute(Constants.REVIEWER_ACCESS_GRANTED) ) {
+ pRequest.getSession().setAttribute("displayAgreement",true);
+ }
+ pRequest.getSession().setAttribute(Constants.REVIEWER_ACCESS_GRANTED, reviewerAccessGranted);
+
}
else {
LOGGER.info("x-access-code doesn't match computed hashed study id");
@@ -206,7 +211,6 @@
else {
LOGGER.info("No x-access-code parameter supplied");
}
- pRequest.setAttribute("reviewerAccessGranted", reviewerAccessGranted);
return reviewerAccessGranted;
}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 15:05:00 UTC (rev 451)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 15:17:49 UTC (rev 452)
@@ -183,7 +183,7 @@
<c:if test="${reviewerAccessGranted}">
<div>
<img src="<fmt:message key="icons.info"/>" alt="<fmt:message key="icon.information"/>" class="icon" />
- <span style="color: red; ">You are in reviewer mode ${initialReviewerRedirect}.</span>
+ <span style="color: red; ">You are in reviewer mode ${displayAgreement}.</span>
</div>
</c:if>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 15:05:06
|
Revision: 451
http://treebase.svn.sourceforge.net/treebase/?rev=451&view=rev
Author: rvos
Date: 2010-01-15 15:05:00 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Now stores and displays initialReviewerRedirect flag, to be used for displaying the reviewer notice and agreement
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-15 14:53:41 UTC (rev 450)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-01-15 15:05:00 UTC (rev 451)
@@ -37,6 +37,7 @@
throw new ObjectNotFoundException("Can't find study " + objectId);
}
if ( ! TreebaseUtil.isEmpty(request.getParameter(Constants.X_ACCESS_CODE))) {
+ request.setAttribute("initialReviewerRedirect", true);
return base
.append("/summary.html?id=")
.append(objectId)
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 14:53:41 UTC (rev 450)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 15:05:00 UTC (rev 451)
@@ -183,7 +183,7 @@
<c:if test="${reviewerAccessGranted}">
<div>
<img src="<fmt:message key="icons.info"/>" alt="<fmt:message key="icon.information"/>" class="icon" />
- <span style="color: red; ">You are in reviewer mode.</span>
+ <span style="color: red; ">You are in reviewer mode ${initialReviewerRedirect}.</span>
</div>
</c:if>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 14:53:55
|
Revision: 450
http://treebase.svn.sourceforge.net/treebase/?rev=450&view=rev
Author: rvos
Date: 2010-01-15 14:53:41 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Now stores reviewer mode as request attribute
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 14:52:06 UTC (rev 449)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 14:53:41 UTC (rev 450)
@@ -194,7 +194,7 @@
LOGGER.info("computedHashedStudyId="+computedHashedStudyId);
if ( storedHashedStudyId.equals(computedHashedStudyId) ) {
reviewerAccessGranted = true;
- saveMessage(pRequest,"You are in reviewer access mode.");
+ //saveMessage(pRequest,"You are in reviewer access mode.");
LOGGER.info("x-access-code matches computed hashed study id");
LOGGER.info("Reviewer access is granted");
}
@@ -206,6 +206,7 @@
else {
LOGGER.info("No x-access-code parameter supplied");
}
+ pRequest.setAttribute("reviewerAccessGranted", reviewerAccessGranted);
return reviewerAccessGranted;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 14:52:21
|
Revision: 449
http://treebase.svn.sourceforge.net/treebase/?rev=449&view=rev
Author: rvos
Date: 2010-01-15 14:52:06 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Now displays reviewer mode based on request attribute
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 14:39:53 UTC (rev 448)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 14:52:06 UTC (rev 449)
@@ -177,15 +177,14 @@
</div>
<h2><c:out value="${headerPrefix}"/> Study ${study.id}</h2>
+
<div class="message" id="searchMessages">
-<c:if test="${not empty messages}">
- <c:forEach var="msg" items="${messages}">
+<c:if test="${reviewerAccessGranted}">
<div>
<img src="<fmt:message key="icons.info"/>" alt="<fmt:message key="icon.information"/>" class="icon" />
- <span style="color: red; ">${msg}</span>
+ <span style="color: red; ">You are in reviewer mode.</span>
</div>
- </c:forEach>
</c:if>
<c:if test="${! empty study.citation.title}">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 14:40:00
|
Revision: 448
http://treebase.svn.sourceforge.net/treebase/?rev=448&view=rev
Author: rvos
Date: 2010-01-15 14:39:53 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Fixed typo.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 14:36:49 UTC (rev 447)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 14:39:53 UTC (rev 448)
@@ -106,7 +106,7 @@
messages = new ArrayList();
}
messages.add(msg);
- request.setAttribute("messsages", messages);
+ request.setAttribute("messages", messages);
}
/**
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 14:36:55
|
Revision: 447
http://treebase.svn.sourceforge.net/treebase/?rev=447&view=rev
Author: rvos
Date: 2010-01-15 14:36:49 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Added generated error/warning messages to template
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 14:19:19 UTC (rev 446)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-01-15 14:36:49 UTC (rev 447)
@@ -178,6 +178,16 @@
<h2><c:out value="${headerPrefix}"/> Study ${study.id}</h2>
<div class="message" id="searchMessages">
+
+<c:if test="${not empty messages}">
+ <c:forEach var="msg" items="${messages}">
+ <div>
+ <img src="<fmt:message key="icons.info"/>" alt="<fmt:message key="icon.information"/>" class="icon" />
+ <span style="color: red; ">${msg}</span>
+ </div>
+ </c:forEach>
+</c:if>
+
<c:if test="${! empty study.citation.title}">
<div>
<img src="<fmt:message key="icons.info"/>" alt="<fmt:message key="icon.information"/>" class="icon" />
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-01-15 14:24:35
|
Bugs item #2931595, was opened at 2010-01-13 20:37 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931595&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: phylows gives access to data belonging to non-public studies Initial Comment: The phylows API, even without a special access parameter, is giving access to data from studies that are still either "in progress" or "ready" (but not "published"). For example, this URL resolves, when it ought not to: http://treebasedb-dev.nescent.org:6666/treebase-web/phylows/study/TB2:S44 ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-01-15 14:24 Message: Fixed as of revision 446. For unpublished studies, the x-access-code parameter is required, otherwise the user is redirected to the accessviolation.html error page. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-01-15 14:24 Message: Your bug has been resolved. Thanks for the report. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2931595&group_id=248804 |
|
From: <rv...@us...> - 2010-01-15 14:19:25
|
Revision: 446
http://treebase.svn.sourceforge.net/treebase/?rev=446&view=rev
Author: rvos
Date: 2010-01-15 14:19:19 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Changed access violation jsp
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/accessviolation.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/accessviolation.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/accessviolation.jsp 2010-01-15 13:56:27 UTC (rev 445)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/accessviolation.jsp 2010-01-15 14:19:19 UTC (rev 446)
@@ -1 +1,8 @@
-<h2><strong>Sorry! your action is not authorized.</strong></h2>
\ No newline at end of file
+<%@ include file="/common/taglibs.jsp"%>
+<head>
+ <title>Access denied</title>
+ <content tag="heading">Access denied</content>
+</head>
+<body>
+ <strong>Sorry! your action is not authorized.</strong>
+</body>
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 13:56:35
|
Revision: 445
http://treebase.svn.sourceforge.net/treebase/?rev=445&view=rev
Author: rvos
Date: 2010-01-15 13:56:27 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Now a priori explicitly denies access to unpublished studies.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2010-01-15 13:32:07 UTC (rev 444)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2010-01-15 13:56:27 UTC (rev 445)
@@ -91,15 +91,13 @@
theStudy = getStudyService().findByID(studyID);
if (theStudy == null) { throw new UnknownStudyError(); }
LOGGER.debug("formBackingObject found study " + theStudy);
- /*
if ( ! theStudy.isPublished() ) {
- String hashedId = theStudy.getNamespacedGUID().getHashedIDString();
- String xAccessCode = request.getParameter(Constants.X_ACCESS_CODE);
- if ( ! hashedId.equals(xAccessCode) ) {
- throw new RestrictedStudyError();
- }
+ // we assume access is denied, unless specifically granted!
+ setAuthorizationChecked(false);
}
- */
+ else {
+ setAuthorizationChecked(true);
+ }
}
theTree = null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 13:32:14
|
Revision: 444
http://treebase.svn.sourceforge.net/treebase/?rev=444&view=rev
Author: rvos
Date: 2010-01-15 13:32:07 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Removed early throwing of RestrictedStudyError
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2010-01-15 12:41:32 UTC (rev 443)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2010-01-15 13:32:07 UTC (rev 444)
@@ -91,6 +91,7 @@
theStudy = getStudyService().findByID(studyID);
if (theStudy == null) { throw new UnknownStudyError(); }
LOGGER.debug("formBackingObject found study " + theStudy);
+ /*
if ( ! theStudy.isPublished() ) {
String hashedId = theStudy.getNamespacedGUID().getHashedIDString();
String xAccessCode = request.getParameter(Constants.X_ACCESS_CODE);
@@ -98,6 +99,7 @@
throw new RestrictedStudyError();
}
}
+ */
}
theTree = null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-15 12:36:35
|
Revision: 442
http://treebase.svn.sourceforge.net/treebase/?rev=442&view=rev
Author: rvos
Date: 2010-01-15 12:18:59 +0000 (Fri, 15 Jan 2010)
Log Message:
-----------
Changed the way the study id is fetched from the request inside isReviewerAccessGranted, turned on logging.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-14 19:57:17 UTC (rev 441)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/BaseFormController.java 2010-01-15 12:18:59 UTC (rev 442)
@@ -183,33 +183,28 @@
Object xAccesCodeObject = pRequest.getSession().getAttribute(Constants.X_ACCESS_CODE);
if ( xAccesCodeObject != null ) {
String storedHashedStudyId = xAccesCodeObject.toString();
- //LOGGER.info("x-access-code="+storedHashedStudyId);
- if ( ! TreebaseUtil.isEmpty(storedHashedStudyId) ) {
- Long studyId = ControllerUtil.getStudyId(pRequest);
- //LOGGER.info("studyId="+studyId);
- TreebaseIDString tbidstr = new TreebaseIDString(Study.class,studyId);
- //LOGGER.info("TreebaseIDString="+tbidstr);
- NamespacedGUID nsguid = tbidstr.getNamespacedGUID();
- //LOGGER.info("NamespacedGUID="+nsguid);
- String computedHashedStudyId = nsguid.getHashedIDString();
- //LOGGER.info("computedHashedStudyId="+computedHashedStudyId);
- if ( storedHashedStudyId.equals(computedHashedStudyId) ) {
- reviewerAccessGranted = true;
- saveMessage(pRequest,"You are in reviewer access mode.");
- //LOGGER.info("x-access-code matches computed hashed study id");
- //LOGGER.info("Reviewer access is granted");
- }
- else {
- //LOGGER.info("x-access-code doesn't match computed hashed study id");
- //LOGGER.info("access denied");
- }
+ LOGGER.info("x-access-code="+storedHashedStudyId);
+ Long studyId = Long.parseLong(pRequest.getParameter("id"));
+ LOGGER.info("studyId="+studyId);
+ TreebaseIDString tbidstr = new TreebaseIDString(Study.class,studyId);
+ LOGGER.info("TreebaseIDString="+tbidstr);
+ NamespacedGUID nsguid = tbidstr.getNamespacedGUID();
+ LOGGER.info("NamespacedGUID="+nsguid);
+ String computedHashedStudyId = nsguid.getHashedIDString();
+ LOGGER.info("computedHashedStudyId="+computedHashedStudyId);
+ if ( storedHashedStudyId.equals(computedHashedStudyId) ) {
+ reviewerAccessGranted = true;
+ saveMessage(pRequest,"You are in reviewer access mode.");
+ LOGGER.info("x-access-code matches computed hashed study id");
+ LOGGER.info("Reviewer access is granted");
}
else {
- //LOGGER.info("x-access-code is empty");
+ LOGGER.info("x-access-code doesn't match computed hashed study id");
+ LOGGER.info("access denied");
}
}
else {
- //LOGGER.info("No x-access-code parameter supplied");
+ LOGGER.info("No x-access-code parameter supplied");
}
return reviewerAccessGranted;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-01-14 20:44:53
|
Bugs item #2932317, was opened at 2010-01-14 15:44 Message generated for change (Settings changed) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2932317&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: internals Group: None Status: Open >Priority: 3 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Nobody/Anonymous (nobody) Summary: Drop the org.cipres.framework dependency Initial Comment: The dependency in treebase-core on framework-1.0.1.jar <dependency> <groupId>org.cipres</groupId> <artifactId>framework</artifactId> <version>1.0.1</version> <scope>compile</scope> </dependency> is likely deprecated and should be dropped. This transpired during conf call discussion 2010-01-14 and is related to disabling the test org.cipres.treebase.service.nexus.NexusParserTest.testLoadPhyloDataSet() in SVN commit 441. References to this JAR date to days when TB considered using CIPRES'es CORBA facilities. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2932317&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-01-14 20:44:25
|
Bugs item #2932317, was opened at 2010-01-14 15:44 Message generated for change (Tracker Item Submitted) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2932317&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: internals Group: None Status: Open Priority: 5 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Nobody/Anonymous (nobody) Summary: Drop the org.cipres.framework dependency Initial Comment: The dependency in treebase-core on framework-1.0.1.jar <dependency> <groupId>org.cipres</groupId> <artifactId>framework</artifactId> <version>1.0.1</version> <scope>compile</scope> </dependency> is likely deprecated and should be dropped. This transpired during conf call discussion 2010-01-14 and is related to disabling the test org.cipres.treebase.service.nexus.NexusParserTest.testLoadPhyloDataSet() in SVN commit 441. References to this JAR date to days when TB considered using CIPRES'es CORBA facilities. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2932317&group_id=248804 |
|
From: <yo...@us...> - 2010-01-14 19:57:24
|
Revision: 441
http://treebase.svn.sourceforge.net/treebase/?rev=441&view=rev
Author: youjun
Date: 2010-01-14 19:57:17 +0000 (Thu, 14 Jan 2010)
Log Message:
-----------
block three unit tests no longer suitable
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/service/matrix/RowSegmentServiceImplTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java 2010-01-14 19:33:26 UTC (rev 440)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java 2010-01-14 19:57:17 UTC (rev 441)
@@ -517,6 +517,7 @@
/**
* Run the void findTreeBlocksByNexusFileName() method test
*/
+ /*this test failed be cause treeBlock may not have tree inside
public void testFindTreeBlocksByNexusFileName() {
String testName = "findTreeBlocksByNexusFileName";
if (logger.isInfoEnabled()) {
@@ -565,7 +566,7 @@
logger.info(testName + " - end "); //$NON-NLS-1$
}
}
-
+ */
/**
* Test topological search
* @author mjd
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/service/matrix/RowSegmentServiceImplTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/service/matrix/RowSegmentServiceImplTest.java 2010-01-14 19:33:26 UTC (rev 440)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/service/matrix/RowSegmentServiceImplTest.java 2010-01-14 19:57:17 UTC (rev 441)
@@ -127,6 +127,7 @@
* Run the createRowSegments test.
*
*/
+ /* this test can not be done without headless mesquite enviroment
public void testCreateRowSegments() throws Exception {
String testName = "testCreateRowSegments";
@@ -245,4 +246,5 @@
logger.info(testName + " verified.");
}
}
+ */
}
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java 2010-01-14 19:33:26 UTC (rev 440)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java 2010-01-14 19:57:17 UTC (rev 441)
@@ -21,6 +21,7 @@
*
* Creation date: Apr 18, 2006 2:50:18 PM
*/
+ //cipres datatype will not be used anymore
public void testLoadPhyloDataSet() throws Exception {
String testName = "loadPhyloDataSet";
if (logger.isInfoEnabled()) {
@@ -30,14 +31,14 @@
File nexusFile = new File(getClass().getResource(TEST_NEX_FILE).toURI());
assertTrue("Test File " + TEST_NEX_FILE + " cannot be found.", nexusFile.exists());
- PhyloDataset data = new PhyloDataset(nexusFile);
+ /*PhyloDataset data = new PhyloDataset(nexusFile);
DataMatrix matrix = data.getDataMatrix();
assertTrue("Empty matrix.", matrix != null);
Tree tree = data.getFirstTree();
assertTrue("Empty tree.", tree != null);
-
+ */
if (logger.isInfoEnabled()) {
logger.info(testName + " - end "); //$NON-NLS-1$
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <vga...@us...> - 2010-01-14 19:33:33
|
Revision: 440
http://treebase.svn.sourceforge.net/treebase/?rev=440&view=rev
Author: vgapeyev
Date: 2010-01-14 19:33:26 +0000 (Thu, 14 Jan 2010)
Log Message:
-----------
Marking META-INF/context.xml as svn-ignored -- forgot in my previous commit
Property Changed:
----------------
trunk/treebase-web/src/main/webapp/META-INF/
Property changes on: trunk/treebase-web/src/main/webapp/META-INF
___________________________________________________________________
Added: svn:ignore
+ context.xml
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-01-14 16:12:34
|
Revision: 439
http://treebase.svn.sourceforge.net/treebase/?rev=439&view=rev
Author: rvos
Date: 2010-01-14 16:12:28 +0000 (Thu, 14 Jan 2010)
Log Message:
-----------
Now throws exception if access isn't granted through x-access-code
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2010-01-14 15:59:53 UTC (rev 438)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2010-01-14 16:12:28 UTC (rev 439)
@@ -70,6 +70,7 @@
class NoStudySpecifiedError extends Error { }
class UnknownStudyError extends Error { }
+ class RestrictedStudyError extends Error { }
Study theStudy = null;
CharacterMatrix theMatrix = null; // XXX What if it isn't a CharacterMatrix?
@@ -90,6 +91,13 @@
theStudy = getStudyService().findByID(studyID);
if (theStudy == null) { throw new UnknownStudyError(); }
LOGGER.debug("formBackingObject found study " + theStudy);
+ if ( ! theStudy.isPublished() ) {
+ String hashedId = theStudy.getNamespacedGUID().getHashedIDString();
+ String xAccessCode = request.getParameter(Constants.X_ACCESS_CODE);
+ if ( ! hashedId.equals(xAccessCode) ) {
+ throw new RestrictedStudyError();
+ }
+ }
}
theTree = null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
1 message has been excluded from this view by a project administrator.
