Peer Project MPDL Activities

MPDL

=PubMan@PEER=
 * PubMan Instance: http://peer.mpdl.mpg.de (vm18.mpdl.mpg.de)
 * Core-service Instance: http://peer-coreservice.mpdl.mpg.de:8080 (vm17.mpdl.mpg.de)
 * coreservice
 * Fedora
 * postgresql
 * eSciDoc Admin instance: http://peer-coreservice.mpdl.mpg.de/escidocadmin/
 * username/passwords can be made avaiable as usual

Statistics

 * http://peer.mpdl.mpg.de/awstats/awstats.pl

Specialties

 * defined in the escidoc-core instance through properties
 * distinugishing identifiers prefix (is not "escidoc:", but is "peer:")
 * dokuments are deposited via PubMan SWORD interface
 * deposit is a zip file, containing a TEI.xml formatted metadata and a PDF file containing the fulltext
 * the PDF name and the identifiers are the encoded publisher DOI
 * TEI to PubMan mapping for PEER

PubMan@PEER Specific tasks

 * important mailing lists and contacts:
 * Peer-repository-managers: peer-repository-managers@inria.fr
 * PEER Depot Development: Benoit Chargueraud, Foudil BrÉtel


 * withdrawal of an article upon requests
 * triggered upon receive of a list of PubMAn@Peer article identifiers that need to be witdrawn (or removed) from repository. along with the reason
 * withdraw - if it is 1-2 article (reason is to be pasted in the withdrawal comment)
 * remove (via purging from the eSciDoc Admin interface - make a filter and remove the items) - if it is more and makes no sense to have e.g. 100 times manual withdrawal - and we have no batch withdraw functionality


 * checking why some articles have been rejected
 * most often reasons: UTF-8 characters not supported by JibX transformations in TEI files; or multiple date types of same TEI file (note: the latter is a bug, see |JIRA PUBMAN-1995); in case many articles have not been successful, usually is due to PubMan@PEER instance unavailability (happened only couple of times, due to service downtime at GWDG)

=Peer Help Desk=
 * Peer Help Desk instance
 * is a Trac instance, data stored in an sqlite database
 * The Help desk offers an author deposit form
 * the form is available as trac wiki macro, thus can be placed on any page of the helpdesk site by inserting SubmissionForm in the page
 * the form redirects to
 * http://peer.mpdl.mpg.de/helpdesk/wiki/SuccessfulSubmission on success
 * http://peer.mpdl.mpg.de/helpdesk/wiki/FailedSubmission on failure. Specific failure information is passed as fragment identifier, matching named anchors should be available in this page.
 * an hourly cronjob transfers the submitted stuff via ftp to the PEER depot.
 * submission and the transfer are logged, and optionally emails (containing these logs) can be sent upon submission and from the cronjob.
 * directory structure
 * /data/peer_storage is directory which stores all author deposits
 * when an author uploads a file via the helpdesk submission form three files are created (.env, .xml and .pdf).
 * the hourly cronjob is zipping the contents of .xml and .pdf and pushes the data to the PEER depot server
 * /data/peer_code is directory which contains all peer-code related to the author submission form and the transferring cron job
 * more information one can see in the readme.txt file which is in /data/peer_code directory


 * Warnings:
 * during one of former system updates, the peer help desk code and trac instance were partly corrupted. The trac instance is running, but somehow, code modifications coudl not be commited back in the subversion repository. Therefore, code modifications (if needed) have to be made in the code, but versioning has to be done by securing a copy of /data/peer_code before any modification is done
 * system updates may cause the Trac instance not to work, as it uses quite outdated package (python, sqlite, etc.) libraries - no system updates related to trac, python and sqlite shall be made on this instance

Helpdesk Specific tasks

 * Helpdesk: Change of the Journal Name in the author submission form in the Peer Helpdesk
 * go to vm18
 * go to /data/peer_code
 * just in case read the readme.txt file
 * make a copy of /data/peer_code to another place with a date (to make sure changes are there)
 * edit the files (as enlisted in the readme.txt file): ./SubmissionForm.py, ./util.py and ./NonPeerDeposit.py with appropriate changes (note: these changes are redundantly repeated in all three files)
 * restart apache (rcapache2 restart)


 * Helpdesk:Removal of a Journal Name from author submission form in the Peer Helpdesk
 * same first steps as Change of the Journal Name except during the editing of the files, one deletes the whole line with the Journal name
 * edit the Trac page "http://peer.mpdl.mpg.de/helpdesk/wiki/removedauthordepositjournals" and add the name of the removed journal respectively


 * Helpdesk:problems with the slow login - happened only once so far, but good to have it in mind for handling
 * diagnostic: no login is possible on Trac or login is taking ages to finish, so it is blowing the size of the trac.db file
 * solution: session data which are stored in the trac sqlite database have to be deleted (respectively tables: session and session_attributes - check for exact names directly via psqllite interface) shall be sufficient (see below)

sqlite3 //data/trac/peer_helpdesk/db/trac.db             delete from session_attribute; delete from session; vacuum;


 * Helpdesk:problems with the users that can not be deleted via Web interface - happened couple of times so far, but good to have it in mind for handling
 * solution: entries for particular user at session data, auth_cookie and session_attribute have to be deleted (use from the commandline ".schema " to check the structure of the table for "where" conditions in "delete" statements (here no more details)

=PEER Depot Reporting=

Specific info

 * The report accesses the PEER Depot database at INRIA and generates data (select the PDF Format Preview).
 * Note: we have allowed database access for the following IP addresses (192.129.1.100 and 192.129.1.102 and 134.76.28.223 - vm17.mpdl.mpg.de)
 * however on vm17 - iReport is not installed - Ip access asked in case needed
 * The report is created as an iReport (supported at present with version iReport 3.7.6 (switching of a newer version shall recompile and re-save all report definitions)
 * As the report is using postgresql database located at INRIA, it shall also have defined a data source (only once when installing it newly on users-machine)
 * PEER Related report definitions and data are here: \\mpisoc\mpdl2\PEER
 * Report definitions only: \\mpisoc\mpdl2\PEER Reports\Definitions
 * Please run the reports directly from the network drive
 * Generated reports only: \\mpisoc\mpdl2\PEER Reports\Reports
 * iReport 3.7.6 Windows installer: \\mpisoc\mpdl2\PEER Reports\iReport

How to create a data source
This is a one time operation when installing the reporting on local machine, or shall be done eventually when switching to a newer version of iReport.
 * Select the Data source icon from the iReport upper bar (see image below)




 * Import the Data source definition from file named "PEERDEPOT@INRIA.xml" (see below, file upload dialog opens when clicking on button "Import")



After import is finished, one may run the report as described above.

PEER Depot Content Report
Is a content report showing various numbers (total deposits, embargo periods, repositories numbers etc.)


 * When: Wednesdays, biweekly (start reference date: 22.06.2011), as late as possible
 * To: Julia Wallace(Wallace@stm-assoc.org), Barbara Bayer-Schur(bayer-schur@sub.uni-goettingen.de), Chris Armbruster (cc) (armbruster@mpdl.mpg.de), Christoph Bruch (cc) (bruch@mpdl.mpg.de)

How to execute the report

 * open the file named MasterPEER.jrxml with iReport (Designer view is shown immediately)
 * make sure you have the proper data source selected as PEER Data Source




 * From the top report meny, select "Preview" option (make sure it is a PDF preview selection) (see image below)




 * In the Designer view there is a link to "Preview", activate this link. (see image below)




 * It takes a while (up to 20 secs) for the report to be executed. Upon successful execution, usually in separate window an Adobe PDF Reader is opened which is showing the report.
 * Save the file name in a dedicated directory and rename it (from MasterPEER.pdf) to: Peer_Depot_Report_[DDMMYYYY] where DDMMYYYY is daymonthyear format of a date. Afterwards this file shall be sent to participants mentioned above

PEER Withdrawn articles report

 * is an Excel report showing PEER articles that have been withdrawn from repositories or not refused from repositories including the reason.
 * these are considered as a list of articles which are awaiting for re-submission and re-deposit (when the withdrawal reason is resolved)
 * When: Wednesdays, biweekly (start reference date: 22.06.2011), as late as possible
 * To: Julia Wallace(Wallace@stm-assoc.org), Barbara Bayer-Schur(bayer-schur@sub.uni-goettingen.de) (cc)

How to execute the report

 * open the file named WithdrawnArticlesReport.jrxml with iReport (Designer view is shown immediately)
 * make sure you have the proper data source selected as PEER Data Source
 * from the top report meny, select "Preview" option (make sure it is a Excel selection) (see image below)




 * In the Designer view there is a link to "Preview", activate this link
 * It takes a while (up to 10 secs) for the report to be executed. Upon successful execution, usually in separate window an Excel file is opened which is showing the report.
 * Save the file name in a dedicated directory and rename it (from WithdrawnArticlesReport.xls) to: WithdrawnArticles_[DDMMYYYY].xls where DDMMYYYY is daymonthyear format of a date. Afterwards this file shall be sent to participants mentioned above

PEER Elsevier submission report

 * is an Excel report showing PEER articles that are provided by Elsevier.
 * When: Monthly, end of the month (start reference date: 22.06.2011)
 * To: Ton Bos (t.bos@elsevier.com), Julia Wallace (Wallace@stm-assoc.org) (cc)

How to execute the report

 * open the file named TonBosElsevier.jrxml with iReport (Designer view is shown immediately)
 * make sure you have the proper data source selected as PEER Data Source
 * from the top report meny, select "Preview" option (make sure it is an Excel preview selection)
 * In the Designer view there is a link to "Preview", activate this link
 * It takes a while (up to 10 secs) for the report to be executed. Upon successful execution, usually in separate window an Excel file is opened which is showing the report.
 * Save the file name in a dedicated directory and rename it (from TonBosElsevier.xls) to: Elsevier_[DDMMYYYY].xls where DDMMYYYY is daymonthyear format of a date. Afterwards this file shall be sent to participants mentioned above