April 03, 2008 ---------------------------------------------------------------------------- + changes in pom.xml + auto sign applet as part of maven build + copy keystore to ~/.m2/portal.keystore + define + activate the profile + to replace log4j file location at run time: + mvn clean; mvn -Denv=[dev|test|prod] install + The current Maven version does not build Eclipse 3.3 (WTP 2.x) compliant project files. To get around this, install the latest snapshot of the maven-eclipse-plugin using: 1. svn checkout http://svn.apache.org/repos/asf/maven/plugins/trunk/maven-eclipse-plugin/ maven-eclipse-plugin 2. cd maven-eclipse-plugin 3. mvn -Dmaven.test.skip=true install -U 4. add to pom.xml maven-eclipse-plugin 2.5-SNAPSHOT 2.0 5. mvn eclipse:eclipse November 28, 2007 ---------------------------------------------------------------------------- + clustalw + do not print blank files in result page + add fogbugs link for error + capture stderr from converter program + add cipres_portal link for user to sign up news and updates - add "message" when a job is timedout October 17, 2007 ---------------------------------------------------------------------------- + uploaded nexus files in admin statis page are now downdable; + add JFreeChart/cewolf plots for progress; + update charts for admin pages; October 10, 2007 ---------------------------------------------------------------------------- + add permissions.txt file to allow user run jobs with special permissions; + mark "*" in admin page to indicate those job submitted with special permissions; + round-robin to get next cluster node to run a job has been implemented. change clusternodes.txt file to list nodes to be used; + charts for admin page: + usage; + usage by datatype; + usage by ntaxa; + usage by tool selected; October 2, 2007 ---------------------------------------------------------------------------- + guigen applet is now available + support of hennig86 file format files September 18, 2007 ---------------------------------------------------------------------------- + enable guigen applet; + tmp.* files are now updated every 5 mins; + fixed window popup issue in IE; + make *.status and tmp.* files available to end users even error scenario; April 10, 2007 ---------------------------------------------------------------------------- 1 Add CIPRES_BIN_HOME env variable in .cshrc or .bashrc to pick up the location of cipres binaries including PAUP; 2 to get around the limitation of PAUP not accepting file name length > 100: + change CIPRES_WEB_HOME in .cshrc or .bashrc to a different location to short file directory path + shorten the name of UPLOADED_NEXUS_DIR variable in src/main/resources/cipres.properties 3 update the directory locations where cron job uses to remove files: crontab -e April 17, 2007 ---------------------------------------------------------------------------- 1. Terri made changes to *garli* command files to increase the memory to 2G to fix the memory problem on large dataset; availablememory = 2048 2. handle files without a starting tree... (-DtreeInferTool=paup-infer.xml) 3. allow user upload PHILIP format file; 4. Add StartTime, StopTime for each analysis run (input.xml) 5. make *.status file" downloadable; 6. change to in command files: recidcm3_garli-gtr-g.xml recidcm3_garli.xml recidcm3_paup.xml recidcm3_raxml.xml rid3-rax-12.5-pct.xml rid3-rax-25-pct.xml rid3-rax-50-pct.xml 7. add 12.5%, 25%, 50% for PAUP(recidcm3_paup.xml), GARLI(recidcm3-garli-gtr-g.xml) based methods: change SetMaxTaxaSubsetSize=20 to SetMaxTaxaSubsetPercent=(12.5, 25, 50) rid3-paup-12.5-pct.xml rid3-paup-25-pct.xml rid3-paup-50-pct.xml rid3-garli-gtr-g-12.5-pct.xml rid3-garli-gtr-g-25-pct.xml rid3-garli-gtr-g-50-pct.xml 8. make email field a required field 9. remove "-i 10" parameter value (delete -i 10 from both Large Tree Inference and Small Tree Infererence for ridcm3-raxml: recidcm3_raxml.xml: -i 10 recidcm3_raxml.xml: -i 10 rid3-rax-12.5-pct.xml: -i 10 rid3-rax-12.5-pct.xml: -i 10 rid3-rax-25-pct.xml: -i 10 rid3-rax-25-pct.xml: -i 10 rid3-rax-50-pct.xml: -i 10 rid3-rax-50-pct.xml: -i 10 0. provide viewJobs.jsp link under "Admin" to show list of portal jobs status 1. remove breadcrumb trails when viewing "Admin" pages (decorators/main.jsp) 2. fix problem of using symbolic link to view NexusFiles.xml file. Replace it with PerformanceAction and performance.jsp files April 20, 2007 (Friday)~ --------------------------------------------------------------------------------- <<<<<<< .mine 1. remove the "report an issue" and "request a feature" button and replace with Ashton's links instead per Mark Miller's request; ======= 0. change availablememory = 2048 to availablememory = 2056 1. remove the "report an issue" and "request a feature" button and replace with Ashton's links instead per Mark Miller's request; Move links to the left of page instead of center of page. 2. Add Web Count which is a global variable for the web portal in -DgroupLabel property when calling RunServiceApp() so backend can keep track of the job; 3. display intermediate results files for user to download. 4. send email to user of URL so they can view the intermediate results April 23, 2007 (Monday)~ -------------------------------------------------------------------------------- 0. build and install cipres on cipres14; 1. implemented sychronized method for webcount; 2. move admin* pages to /admin directory so secure page can be managed easily; 3. FileAction, ProcessRequestAction, add a "DEBUG" flag set environment variable (DEBUG) in Eclipse; value can be anything (true, TRUE); as long as this "DEBUG != null", FileAction and ProcessRequestAction will use my cipres-framework-stub code for testing instead of the actual code; TO DO: +. webinfo.properties: webCount -> WebCount; reset value to "1" when reachese Integer.MAX; +. make job status table columns sortable and searchable; (maybe replace using mysql) --------------------------------------------------------------------------------- April 24, 2007 (Tuesday), April 25, 2006 (Wednesday) -------------------------------------------------------------------------------- 1. separate NexusFiles.xml into NexusFiles.xml.(paup/raxml/garli) to make it more readable; 2. add "DATATYPE" to mapping.xml for "DATATYPE" (DNA vs Amino Acid): list of analysis depends on the uploaded nexus files's datatype; list of tools for a selected analysis depends on the "tool" attribute if RunNexusReader return datatype of: NULL, or anything other than "DNA_DATATYPE" or "AA_DATATYPE", set datatype= ANY_DATATYPE; 3. add "treeinfer" to mapping.xml to indicate which paup infer xml to use (the web will pass paup_infer.xml if paup if chose, otherwise, quick_paup_infer.xml) RunServiceApp() will ignore this parameter if the nexus file already has a starting tree 4. add "timeout" to mapping.xml for each tool (in minutes); Terri removed in all command files 5. update mapping.xsd for the abvove changes (add 3 required attributes) 6. Mark holder make the following changes to paup.xml: I have made the PAUP command in the *paup*xml files in cipres-web/src/main/resources/conf more thorough. Specifically it is now: Set maxtrees = 1000; and in the context of ab initio tree searching (rather than improving a current tree), the starting tree is coming from Hsearch start=stepwise addseq=random nreps=200 I think that in the context of getting a starting tree for an ML run (e.g. using GARLI when the user has uploaded a file without a tree in it), then we shouldn't spend too much time getting a good parsimony tree. Thus, I have added a quick_paup_infer.xml file. This has the old, quick and dirty search settings and should be used when we are just getting a tree so that we can use GARLI. April 30, 2007 (Monday) ---------------------------------------------------------------------------- + update raxml to 2.2.3 from 2.2.1 (see Holder's email dated 04/24/2007): /projects/cipres/bin/RaXMLHPC2.2.3 May 3, 2007 (Thursday) ----------------------------------------------------------------------------- + change the return MIME-type in DownFileAction to "text/plain" so end users won't be told they are download a binary file; + change package name (from org.cipres.helpers to org.cipres.portal) for RunServiceApp and RunNexusReader + also change tryit script and Performance; + eanble recidcm3-raxml using for nexus files with at least 500 taxa: + 500 - 1000: 50% subproblem size + 1001 - 2000: 25% subproblem size + 2001 - 3000: 16% subproblem size + 3001 - 5000: 6.25% subproblem size ? replace to_nexus.py to philip_to_nexus to convert philip to nexus files; + 5001 + : 6.25% subproblem size