System Administrator`s Guide
Contents
1. Testing in August September 2008 revealed a number of defects Consult the XDMS Defects List for possible known problems One other source of problems is having the correct version of J argon Jargon is the API that XDMS uses to talk to SRB If the logs reveal unexpected problems connecting to SRB consider replacing the webapps xdms WEB INF lib jargon_v2 0 1lbeta jar file with a different version XDMS System Administrator s Guide v1 0 Page 20 of 24 30 Sept 2008 Maintaining XDMS Stopping and starting To stop Tomcat STOMCAT_HOME bin shutdown sh To start Tomcat cd STOMCAT_HOME bin startup sh Note The xdms log file is written to the current directory when Tomcat is started So it is best to change to the Tomcat directory first To remove just XDMS stop Tomcat then delete the xdms war file and xdms directory from Tomcat rm rf STOMCAT_HOME webapps xdms rm STOMCAT_HOME webapps xdms war To stop PostgreSQL on the database machine service postgresql stop To start PostgreSQL service postgresql start Logging There are two main logs to consider e TOMCAT_HOME logs catalina out contains messages that come directly from Tomcat e xdms log contains messages generated by XDMS itself Its location is the directory where Tomcat was started from You can configure the level and style of output messages by modifying src java log4j properties within the original XDMS source directory2. Prerequisites The following services must be installed on the installation machine itself XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 5 of 24 Service Recommended Java application server Apache Tomcat 5 5 25 but not Tomcat 6 supporting JSP 2 0 Servlet http tomcat apache org spec 2 4 Java Development Kit J2SE JDK 5 0 required to build XDMS from source J RE is sufficient for running XDMS Apache Tomcat 5 5 is the recommended tested application server Other application servers have not been tested If Tomcat is not already installed get it from http tomcat apache org download 55 cgi The Yum package tomcat5 is not recommended It has not been successfully tested with ARCHER To install these prerequisites yum install jdk These environment variables must be set on the installation machine Variable Value SCATALINA_HOME Tomcat installation directory E g usr local archer tomcat apache tomcat 5 5 26 SJAVA_HOME J DK installation directory E g usr java jdk1 5 0_16 Installation workflow The overall workflow for the installation is as follows Create directories user groups and users on the SRB Create the ICAT database Use information gathered to configure the XDMS build Build XDMS Use the generated SQL scripts to complete the creation of the ICAT database Deploy XDMS and third party components to Tomcat h
3. Warning and disclaimer During testing of ARCHER 1 0 a number of defects were discovered You should carefully read the defects list and consider whether this version of XDMS meets your needs Some of the most severe defects e The security model in XDMS ARCHER 1 0 is not suitable for a production environment You should assume that any user may view any other user s data and possibly change it e Sometimes data may be lost although the user believes it has been saved e Not all business rules of data curation are fully respected you should not assume that every dataset has full metadata or is safe from deletion or modification by unauthorised users e Not all functionality needed by all user classes is fully implemented Browsing and auditing functions are particularly limited The full defects list is available at http www archer edu au downloads 1 http epubs ccirc ac uk work details w 30324 http www itee ug edu au eresearch projects archer software php XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 3 of 24 Configuration XDMS manages datasets stored on an SRB set up by ARCHER Data Services These datasets are populated by Hermes a desktop tool DIMSIM a tool which gathers data directly from scientific instruments or by XDMS itself through its web interface XDMS metadata is stored in a PostgreSQL database known as ICAT This database can be located on any machine that the XDMS hos
4. c cece cece eee eee teeta eee eee 16 4 Configuring database entries 0 0 00 cece cece eee e eee ee ee eee eee eee eeeeeeeaees 16 Bs BUINGING XDMS retiraron tose tila dein eee cates eee tae ae 16 Deploying XDMS ieceri teri is eee ie ey Sac it Ses Ae Co Hens ts eed a ee 18 B f re you QUO cscs srs tere ae E ease alc arnt cn ee fl nie 18 T Deploying MDE a an ies wie de E E AEEA AA EE EAEE IERTE 18 2 Registering the J NDI resource for MDE ssssssssssssssesrsrrrrrrrrrrrrrrrrrreerrrr 18 3 Deploying XDMS vrsi a us eatdice tiv cte niet aAA aaa DE AAN a ee 19 4 Optional Tweaking TomCatisicccc iv enciasecratie mn eiea coeenuersatieiey eee meedaes 19 Be Verifying riiai traii E peat ston AEA A Se eg e A Meas eaan a E R 19 Troubleshooting scaics eet ieee aa Page ads Pete ee WA a a en 19 Maintaining XDMS esei av ida ornan eaaa evades vy nati sb ee ead hed etd ey yeas ek ol des 21 Stopping and SAKE sice ee eae eee cea nay scores wile We antes toa nnr ealvtatues wean Soardee 3 tae 21 MOG GING EAEE E EE EE EEEE EEEE A tes eee ec as ede E 21 CONFIGUrIN O ae e a a a aa aA A eA E 21 Stop Tomcat redeploy the war file then restart Tomcat as described in Error Bookmark not defined Installing custom schema templates ecceeece eee eee eee eee eee eeeeeneeaes 22 Creating other grou pS oc scutes ct ri gheni tt Eni oe ot EE ENENET ENI EIEEE ETER ENERE ERRES Ena 23 Development stat S esisi tira ionian AA ose acs T a E
5. In particular lower the thresholds of each kind of logging In increasing levels of verbosity the levels are FATAL ERROR WARN INFO DEBUG Configuring When making any changes to the configuration of XDMS it is strongly recommended that you do not alter the deployed files within Tomcat i e those in CATALINA_HOME webapps xdms Instead 1 Update the configuration files in your original XDMS directory as described in section Building XDMS 2 Rebuild XDMS as described in Building XDMS 3 Stop Tomcat redeploy the file then restart Tomcat as described in Deploying XDMS Configuration of most aspects of XDMS takes place through the following files XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 21 of 24 Configuration file What it controls WEB INF classes xdms properties Locations of servers authentication SRB handle server MDE templates WEB INF classes ddm icat applicationContext xml Connection to ICAT database WEB INF classes log4j properties What to log and where to log to Installing custom schema templates By default XDMS is configured for use in crystallography and contains metadata schemas appropriate for this domain These schemas control the fields that appear in the metadata editor MDE windows To use other schemas in MDE 1 Obtain schema files in both XML and MSS format 2 Place the MSS files in the MD
6. Once it has been used for some production data it should not be changed hdl server key location Path to private key used to access handle server hdl server key passphrase Passphrase of private key if used hdl resolver url The URL of the handle server s front page In other words if you paste this value into a browser it should reach the Handle System Proxy Server page hdl base url The base URL that XDMS will be running as This is used to construct the URL that the handle will point back to To understand the significance of these fields take the following set up as an example hdl server namespace 102 100 archer hdl server key location etc grid security handlekey bin hdl resolver url http handles uni edu au hdl base url http xdms uni edu au 8080 This has the following implications XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 14 of 24 1 When a new dataset is created it will be given a handle such as 102 100 archer 2FT95S7GB 2 3 The address of the dataset in XDMS can now be found by visiting http handles uni edu au 102 100 archer 2FT95S7GB This in turn redirects to http xdms uni edu au 8080 xdms viewDatasetDetails action request hdlI d 102 100 archer 2FT95S7GB 3e Configuring the SMTP server section XDMS uses an SMTP server for several features When users click buttons such as Email Dataset Identifier W
7. http www archer edu au downloads For example mkdir xdms cd xdms wget http www archer edu au downloads xdms 1 0 tar gz tar xzf xdms 1 0 tar gz 2 Configuring ddm icat applicationContext xml The Java Spring framework needs to be configured for the ICAT database you will be using If you have not created this database yet follow the instructions in Preparing the host environment p 7 Edit the following section of src java ddm icat applicationContext xml to point to the ICAT database lt xml version 1 0 encoding UTF 8 gt lt beans xmlns http www springframework org schema beans lt ICAT Datasource gt lt bean id dataSource class org springframework jdbc datasource DriverManagerDataSource gt lt property name driverClassName value org postgresql Driver gt lt property name url value jdbc postgresql icat uni edu au icat gt lt property name username value xdms gt lt property name password value xxxxx gt lt bean gt Property name Purpose driverClassName The Java class name of the J DBC driver for the database you are using If XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 11 of 24 Property name Purpose PostgreSQL this does not need to be changed url The complete J DBC url to connect to the ICAT database Make sure the trailing icat refers to the actual name of the database y
8. Create staging area Schmod a team leader mydomain xdms staging Give rights to staging area Sls C List directories and privileges to verify the above steps After XDMS is installed you will create more users and groups 3 Creating the ICAT database XDMS stores metadata for the datasets it manages in a database structure known as ICAT which implements the CCLRC Scientific Metadata Model Version 2 You must create the ICAT database into an existing PostgreSQ installation gt http epubs cclrc ac uk work details w 30324 XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 8 of 24 If installing into SRB s PostgreSQL If you are installing ICAT into the PostgreSQL installed by SRB you must now change the security options By default they do not allow external connections at all Edit var lib psql data postgresql conf Modify the restrictions to at least allow network connections from the XDMS machine For example you could add this line listen_addresses This would allow connections from any IP address For more information see http www postgresql org docs 8 1 static runtime config connection html If installing into a machine without PostgreSQL You can install PostgreSQL as follows yum install postgresql On the database machine create a dedicated DB user for xdms to use called xams For example createuser xdms pwprompt Enter
9. E war file under test data schema 3 Place the XML files in the XDMS war file under data records 4 Re deploy both the MDE and XDMS war files See the MDE documentation for more details XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 22 of 24 Creating other groups There are three profiles used by XDMS Profile name Main purpose Assigned Specified in Team leader Create projects assign users delete records One group per XDMS installation xdms properties Project admin Create experiments One group per project Project creation page Team member Upload datafiles One group per project Project creation page To assign a user a profile 1 Create a group for the profile if it does not already exist 2 Add the user to the group 3 Link the profile to the group if needed as specified in the above table If you are using MyProxy authentication you should perform steps 1 and 2 in the LDAP The group and user changes will later be duplicated automatically in the SRB Otherwise perform these steps in SRB using mcatAdmin XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 23 of 24 Development status The XDMS source code is released under the GNU General Public License It was developed by the ARCHER project and is undergoing further development by the Monash e Research Centre You can access the latest dev
10. I T aA AEE de ete ss 24 XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 2 of 24 Introduction Intended audience This guide is intended for system administrators who will be installing and maintaining XDMS To install XDMS basic familiarity with Linux Apache Tomcat and PostgreSQL is assumed Overview XDMS is a web application that runs on an application server such as Tomcat allowing users to manage sets of data stored on an SRB Storage Resource Broker The web based front end jsp files and the Java servlet back end jar files are packaged in a single war file which is deployed to the application server Configuration takes place through several files including xdms properties and log4j properties XDMS manages two kinds of metadata about the SRB data in a database called ICAT First it implements the CCLRC Scientific Metadata Model 2 to store general information about projects experiments datasets etc Secondly it stores customisable domain specific metadata A bundled metadata editor MDE is used to edit this domain specific metadata It is delivered as a Java web application that must be deployed in the same way A J NDI resource for MDE must also be registered on the application server by adding a line to conf context xml in the case of Tomcat Security is managed by creating users and groups on the SRB Several methods of authentication are supported as described later in this section
11. ace al ae D XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 6 of 24 Preparing the host environment The host that will run XDMS must have an application server access to a prepared ICAT database and access to a prepared SRB 1 Create a team leader group on the SRB In order to create any projects in XDMS you need at least one user with a team leader access profile This profile can create or delete anything in XDMS but should not be confused with the concept of an SRB superuser XDMS profiles are mapped to SRB groups through a properties file which you will configure later Download mcatAdmin from the following address http www sdsc edu srb index php Admin_ Tool mcatAdmin is a third party SRB user and group administration tool Use it as follows 1 Create a user group for team leaders who can create projects and user groups For example team_leaders 2 Create a user in the newly created group For example team_leader Note If using MyProxy you may wish to create this user in your LDAP instead Doing so is beyond the scope of this documentation 2 Creating collections on your SRB Next you need to create the following collections 1 Common project area All validated project data will be stored in this directory Call it something like xdms project Give all access to the user you created in step 1 2 Staging area Tools that do not support XDMS n
12. ae teat da leaachbaedebeacauedeadduncite EAEE RAE Ea 9 5 Creating the ICAT database structure cccssceceniwesxetcswaniiawtiessstesteeiiecawnaexs 9 B ilding XDMS x atetvecseucasepesediennworensiesa ves echalansepeecdian A i TE ANE 11 XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 1 of 24 OV EF VIEW rine a Bato aa era r a e a n Anaa Ai Mubecd ands 11 Prerequisites isei aiia eat aE AEE AE nate la bing AE AA AATE EBA AA ia 11 1 Obtaining the XDMS Source COdG cccc cece eee ee rete eee eee eee ee eee 11 2 Configuring ddm icat applicationContext xXMl 0 cece cence eee eee eee eee 11 3 Configuring xdmMS propertieS sssssssssrrrrrrrrrt ttnt seers tease tae ecw 12 3a Configuring the SRB Se Cction c cece eee eee eee eee eee eee eee eee eee eee ees 12 3b Configuring the MyProxy SeCtION cee cece eee eee tee teeter 13 3c Configuring the Shibboleth Section cc cece cece eee eee eee teeta eee 13 3d Configuring the handle server section 0 cece ee ee cette e ete te eee ee 14 3e Configuring the SMTP Server section c ccc cece ee ee 15 3f Configuring the UQ Metadata Editor Section cece eee ees 15 3g Configuring the tree panel titles and labels SECtION ccceeeee scene eenees 15 3h Configuring the Fedora Section cccecceee eee eee eee eens eee eee e eee tetas 16 3i Configuring dataset packaging settings
13. archer ARCHER 1 0 australian research enabling environment XDMS System Administrator s Guide e Installation e Configuration e Maintenance XDMS sscssscciccdscccscrsccsscsessnccsaccssscctcedscsincnsecsscsnsssscsacendccasncscstserssccsasecsscnssansans 1 LMUPOOUCUON siosdccevacernsscaeyicrenioreyreawesduieyeaans KENAA EER E KARAD eens date 3 Intended audience i iieceducrnsvaenetrestczedentanye i aencdseraulacndia nic teeunssastet even senyenbedes 3 OVE VIEW araia e a E a E Ea tidus mauteaetas NNE aE 3 Warning and disclaimer sssssssssssssssssssrsrrrrrrrrrrannnrrrnssasttrrrrrrrrrrnnrrnnnanane 3 COMMA UNAUION irori iiaeaa eaa A DEAETE E 4 Authentication ein a a aA E a E Ea aE E 5 Do need a handle server ssssssrrrrrrrnrrrrssssrrrrrrrrrrrnnnrrrnnnsntrrerrrrrrnnnrnn 5 Do need a Fedora repository sssssssssseerirrrrrrt trint ee eee eee tenet teen ene eee eee 5 Prereg lisit S proosan dnr aE r bA Ea e aaae re a hE 5 Installation workfloW sssssssssssrrrsrrrrsrnssrttnntt tt ttn ttrt rrna rnnr nrnna nEn EEEE EEEn 6 Preparing the host environment ji s 1i2sibedececedndcadentietdhdaecneamshedbenteesdadasansatGieis 7 1 Create a team leader group on the SRB c eee cece eee 7 2 Creating collections on your SRB as cicccvsvesiscscasssssdasvasbonacitaentertatesonetnedads 7 3 Creating the ICAT Catalase csciccsssissccestacedeceneseanptenunascendedaagensecsaveneonases 8 4 B ilding XDMS ssiri adecredteicte
14. are using Copy the J DBC driver file to E common lib PostgreSQL use the J DBC driver provided with XDMS in the lib third party lib jdbc driver cp dist xdms lib third party lib jdbc driver postgresql 8 1 409 jdbc3 jar SCATALINA_HOME common 1lib SCATALINA_HO ME webapps mdelogs directory of the build 2 Copy dist xdms war to cp dist xdms war SCATALINA_HOME webapps SCATALINA_HOME webapps 3 Create this directory mkdir p CATALINA_HOME webapps mdelogs 4 Make the tomcat user the owner of it chown R tomcat tomcat SCATALINA_HOM E webapps mdelogs 4 Optional Tweaking Tomcat To be able to upload and download large files gt 20 mb through the XDMS web interface set the following line in scATALINA_HoM E bin catalina sh export JAVA_OPTS SJAVA_OPTS Xms512m Xmx1024m XX MaxPermSize 256m 5 Verifying Restart Tomcat SCATALINA_HOME bin startup sh You can verify that XDMS is installed correctly by connecting to the web server on the port it is configured for By default this is http localhost 8080 xdms You should see either the standard XDMS login screen or be redirected to a Shibboleth login screen depending on how you configured XDMS Troubleshooting If you receive an error page consult the logs See the section Maintaining XDMS for more informatio n XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 19 of 24
15. ate through the normal login screen XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 13 of 24 Field Set it to apply shibboleth security y for security modes 1 or 2 n for mode 3 If n the other Shibboleth parameters are ignored allow username password srb login y for mode 1 n for mode 2 http port to block In mode 2 the port which the XDMS server is running on to bounce it from Otherwise ignored shibboleth login url In mode 2 the URL to redirect the login page towards shibboleth model unique id An identifier for the university allocated by MAMS shibboleth model unique id block chars Characters to remove from the unique ID Replaced characters are substituted with an character For example lt gt shib id trim length Maximum length for ID grid security certificate In modes 1 and 2 the security certificate used for Shibboleth cert provider Web service that provides certificates for Shibboleth 3d Configuring the handle server section This section sets up XDMS s connection to a handle server for the allocation of permanent IDs to datasets See section Do need a handle server for more information Field Set it to create dataset handle y to enable use of handle server otherwise n hdl server namespac The registered namespace you wish to use
16. atively will write to this directory Call it something like xdms staging For each directory make a note of the full name including the SRB domain For example myzone home xdms project 3 The team leader role is implemented as the owner of the project area in SRB 4 Navigate to the directory and click the key icon in the right toolbar XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 7 of 24 You can do this two ways Using inQ desktop tool InQ is a third party SRB file management tool Refer to the included help files for full documentation Note that the Name field on the initial connection screen refers to the username of an SRB superuser Download inQ from the following address http www sdsc edu srb index php nQ You can find the full name of each directory by navigating to its parent directory selecting it in the right hand pane then right clicking it and choosing Copy path to clipboard Using command line S commands You can use the S commands that are installed with SRB to create these directories directly on the SRB machine Command Explanation su srb Switch to the pre defined SRB user to load the SRB environment Sinit Prepare S commands Smkdir xdms project Create project directory Schmod a team leader mydomain xdms project Give all rights on XDMS project dir to team leader group Smkdir xdms staging
17. cation This requires two things e A MyProxy server running and accessible by XDMS e A host certificate for the MyProxy server installed on the XDMS machine somewhere It is recommended that you place this file in etc grid security certificates If MyProxy authentication is enabled all other forms of authentication are disabled Field Set it to apply myproxy security y to enable MyProxy authentication myproxy server name The name of your MyProxy host myproxy server port The port the MyProxy server is listening on 7512 by default grid security certificate myproxy The path to a host certificate for the MyProxy server For example etc grid security certificates 2920cd2a 0 3c Configuring the Shibboleth section XDMS supports Shibboleth authentication in conjunction with or as an alternative to normal website login in three modes as follows The Shibboleth functionality is untested and must be considered experimental Mode Shibboleth Web login Behaviour enabled enabled Users can authenticate through Shibboleth If they 1 v v connect directly to the site while not authenticated they can login via the normal login screen Users authenticate with Shibboleth If they attempt to 2 s 2 connect directly to the site while not authenticated they will be redirected to the configured Shibboleth login screen 3 k V Users can only authentic
18. ders srb scratch area directory The name of the staging area directory created earlier For example zonel home xdms staging srb admin email id The email address of a system administrator to send SRB related system administration messages to The following fields should not be modified unless you have specific access requirements Each field must be one of Access type Meaning read User can view but not modify the item write User can view and modify but not delete the item delete User can view modify and delete the item The Team Leader profile implicitly has delete access to all items XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 12 of 24 Property Controls srb prjt admn grp perm Access to projects for the Project Admin profile srb prjt team grp perm Access to projects for the Team Member profile srb expr admn grp perm Access to experiments for the Project Admin profile srb expr team grp perm Access to experiments for the Team Member profile srb dtst admn grp perm Access to dataset for the Project Admin profile srb dtst team grp perm Access to dataset for the Team Member profile srb dtfl admn grp perm Access to datafiles for the Project Admin profile srb dtfl team grp perm Access to datafiles for the Team Member profile 3b Configuring the MyProxy section XDMS supports MyProxy authenti
19. elopment versions of the XDMS source code base at http code google com p archer xdms Javadoc documentation is generated with each build into the jardm api directory inside the generated war file and is also available at http www archer edu au downloads 8 http www archer edu au http www monash edu au eresearch XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 24 of 24
20. es project panel title The title of the project area pane project home label The name of the root node in the project area user panel titl e The title of the personal area pane user home label The name of the root node in the user s personal area staging panel title The title of the staging or scratch area pane typically used by DIMSIM or other non authenticating tools staging home label The name of the root node in the staging area XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 15 of 24 3h Configuring the Fedora section To enable datasets to be exported to a Fedora repository define it here Field Set it to fedora url URL for the Fedora repository Must include the HTTP protocol fedora username Username and password to connect to repository fedora password 3i Configuring dataset packaging settings This setting defines how XDMS splits up large files when exporting them to a Fedora repository Large files several gigabytes are known to be problematic for Fedora Testing shows that 1800 megabytes is an appropriate size Field Set it to datasetpackage splitsize The size in gigabytes at which files are split when exporting to Fedora 4 Configuring database entries To customise the possible values of lookup boxes and other values for a specific domain you should modify
21. hen exporting to Fedora has finished a notification email is sent When certain errors are encountered an email is sent to the system administrator Field Set it to smtp mail server The name of your mail host It must not require a password 3f Configuring the UQ Metadata Editor section This section forms the link between image types dataset statuses and the metadata schemas that MDE uses to edit them Each schema is an xm file which must be in the right directory of the MDE war file See Maintenance section for details The default values point to schema files distributed in the XDMS source bundle so you do not need to change these values to get XDMS running Field Set it to uq mde crystal template Schema for samples uq mde dataset DataCollection template Schema for datasets with Data Collection status uq mde dataset Processing template Schema for datasets with Processing status uq mde dataset Published template Schema for datasets with Published status uq mde dataset Solution template Schema for datasets with Solution status uq mde datafile img template Schema for img datafiles uq mde datafile mccd template Schema for mccd datafiles uq mde datafile osc template Schema for osc datafiles 3g Configuring the tree panel titles and labels section This section configures the labels of GUI elements Field Defin
22. hree modes of authentication 1 Username password Users must be maintained within the SRB itself This may be useful for short term testing 2 MyProxy Users are given a short lived certificate by a MyProxy server which authenticates against an LDAP ARCHER Data Services includes installation of a MyProxy server 3 Shibboleth experimental Users first authenticate against a Shibboleth server XDMS bounces the user to this server if they have not done so This mode is untested Do I need a handle server A handle server is used to assign permanent IDs or handles to datasets once they are ingested into XDMS If no handle server is configured XDMS can still be used but no permanent IDs will be assigned to datasets You can set up a handle server later but any datasets created before then will not retroactively receive IDs Setting up a registered handle server is a somewhat complex task involving an annual registration fee It is beyond the scope of this documentation If you do use a handle server you need a private key corresponding to it You should place this file in etc grid security See e http www handle net Ihs html overview of local handle systems e http www handle net start html guide to setting up a local handle system Do I need a Fedora repository XDMS supports exporting datasets to Fedora Digital Repository If you do not require this functionality you do not need access to a Fedora repository
23. ms war deployable application and third party components to be deployed META INF sql Scripts to create the ICAT table structure and to populate it with default values sxrc XDMS source code LICENSE Full text of the GPL licence under which XDMS is released README Overview of the product and its directory structure XDMS System Administrator s Guide v1 0 Page 17 of 24 30 Sept 2008 Deploying XDMS To deploy XDMS you will Copy the bundled metadata editor MDE war file to the application server 2 Register a JNDI resource for MDE 3 Copy the XDMS war file to the application server 4 Optionally configure Tomcat for large file uploads 5 Restart Tomcat and verify that XDMS is running Before you begin Ensure that the scATALINA_HOME variable points to your Tomcat installation For example export CATALINA_HOME usr tomcat apache tomcat 5 5 26 Stop Tomcat if necessary SCATALINA_HOME bin shutdown sh If you wish to use a port other than 8080 for XDMS edit SCATALINA_HOME conf server xml NOW 1 Deploying MDE The Metadata Editor MDE is a bundled J ava servlet which must also be installed in Tomcat First copy the following files Copy file To dist xdms lib third party lib uq mde archer server SCATALINA_HOME common 1lib metaservice jar dist xdms lib third party lib ugq mde org json jar SCATALINA_HOME common 1lib dist xdms lib third
24. ou created username password The login and password of the dedicated user for the ICAT database which you set up earlier 3 Configuring xdms properties The xdms properties file controls almost all the configuration of XDMS You should now go through each section configuring as appropriate Section Modify this section SRB Always MyProxy If using a MyProxy server for authentication Shibboleth If using Shibboleth for authentication Handle Server If using a Handle Server for storing dataset identifiers SMTP Server Always to allow XDMS to send mail UQ Metadata Editor If using any metadata schemas other than default crystallography ones Tree panel titles Only for cosmetic purposes Fedora Repository If using a Fedora repository to export data to Dataset Packaging Only to tweak the treatment of large datafiles 3a Configuring the SRB section Field Set it to srb host Name of the machine hosting the SRB server srb port Port to connect to the SRB server on Typically 5544 srb resource SRB Resource to use Typically demoResc or lt servername gt Disk srb common project directory The name of the common project directory on the SRB created earlier For example zonel home xdms project directory super admin group The name of the user group for team leaders created earlier For example team_lea
25. party lib uq mde mde war STOMCAT_HOME webapps Note The destination directory depends on the application server In particular Tomcat 5 5 uses SCATALINA_HOME common lib whereas Tomcat 6 0 uses sCATALINA_HOME 1lib cp dist xdms lib third party lib uq mde archer server metaservice jar SCATALINA_HOME common 1lib cp dist xdms lib third party lib uq mde org json jar SCATALINA_HOME common 1lib cp dist xdms lib third party lib uq mde mde war SCATALINA_HOME webapps 2 Registering the J NDI resource for MDE In order for XDMS and other applications to be able to use MDE it must be registered as a J NDI resource For Tomcat add the following lt resource gt tag to SCATALINA_HOME conf context xml lt Context gt XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 18 of 24 lt Resource name bean RecordBrokerFactory auth Container type au edu archer metadata spi MetadataServiceProvider factory au edu archer metadata spi recordbroker RecordBrokerFactory gt lt Context gt 3 Deploying XDMS If your DBMS is not PostgreSQL you need to obtain the type 4 J DBC driver for it delivered as a jar file The J DBC driver for PostgreSQL is included J DBC drivers can be obtained from http developers sun com product jdbc drivers Proceed as follows Example command Step 1 SCATALINA_HOM If you
26. password for new role Enter it again Shall the new role be a superuser y n n Shall the new role be allowed to create databases y n n Shall the new role be allowed to create more new roles y n n Create a database called icat owned by the xdms user For example su postgres createdb icat 0 xdms 4 Building XDMS Now that you have created the ICAT database you have all the information required to configure the XDMS build script Follow the instructions in section Building XDMS p 11 then return here to continue the installation 5 Creating the I CAT database structure The build process generates two SQL scripts in the dist xdms sql directory File Purpose dist xdms sql xdms_icat_ddl sql Creates the ICAT database table structure dist xdms sql xdms_icat_dml sql Populates the ICAT database table structure with values Again this user can be called anything but must be referred to in the configuration file It is not strictly necessary to create a dedicated user but it is recommended 7 Any name can be used The choice of name must be reflected in the J DBC URL specified in step Building XDMS XDMS System Administrator s Guide v1 0 Page 9 of 24 30 Sept 2008 Run these scripts on the ICAT database For example 1 Copy xdms_icat_ddl sql and xdms_icat_dml sql to your PostgreSQL machine 2 Run the two files in order on the database s
27. t can access Typically the database PostgreSQL hosting MCAT which was installed at the time of SRB is used Creating the ICAT table structure is part of the XDMS installation Before installing XDMS install ARCHER Data Services using the ARCHER Data Services Installation Guide This will set up the infrastructure required by XDMS In particular your target machine needs access to the following Service Purpose Required Installed in ADS SRB repository Stores the datasets f of being managed PostgreSQL Will host ICAT which V stores CCLRC metadata v for datasets see note Shibboleth server Provides authentication x if using Shibboleth MyProxy server Provides MyProxy authentication to SRB Handle server Provides permanent IDs x k for datasets Fedora repository Destination for k publishing datasets SMTP server Sends mail on user K request Note ICAT is a database schema implemented in PostgreSQL ARCHER Data Services installs PostgreSQL as part of SRB You can use this same PostgreSQL to host ICAT In the tested ARCHER configuration the components are laid out on two servers as follows XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 4 of 24 Fedora MyProxy Browser MyProxy PostgreSQL cert MCAT Archer data services Front server Back server Authentication XDMS supports t
28. the file build config db xdms_icat_dml sql Table name Contains STUDY_STATUS Statuses of projects INVESTIGATION_TYPE Types of experiments FACILITY_USER Managers available to be selected for each project DATASET_TYPE Types for the Create a new Dataset folder page DATASET_STATUS Statuses also for this page DATAFILE_FORMAT Not used TOPIC Topics for the Create an experiment folder page You will use this script to create the ICAT database After the database is created you should maintain these tables by modifying the database directly 5 Building XDMS Before running the build ensure that e ant is installed and is on the PATH e The sJAVA_HOME environment variable points to the directory of a JDK You can verify this as follows ant version Apache Ant version 1 6 5 compiled on April 4 2007 echo SJAVA_HOME usr java jdk1 5 0_16 XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 16 of 24 To run the build run the default ant target from within the root directory of the XDMS source directory ant This produces a new directory dist which contains a zip file This zip file contains the complete distribution of compiled Java classes and other files configured for your environment Directory Contains doc User manual developer manual and javadoc source code documentation lib The xd
29. u postgres psql dbname icat file xdms_icat_ddl sql username xdms psql dbname icat file xdms_icat_dml sql username xdms Note The XDMS user must have read and write access to all ICAT tables If using a different method to create the database and tables you can grant access with this SQL command GRANT ALL PRIVILEGES ON DATABASE icat to xdms Note An Ant build target clean icat db setup can be used to automate this process Before using it configure the appropriate values in user properties This target must be used with caution as it first destroys the existing icat database with no confirmation prompt XDMS System Administrator s Guide v1 0 30 Sept 2008 Page 10 of 24 Building XDMS Overview The process of building XDMS from source code includes first configuring several property files The end product is a single war file which can be deployed with no further configuration Prerequisites As XDMS is Java based it can be built on any platform including Windows This document assumes it is being built on a Unix environment however Install these products on your build machine before commencing Product Purpose Source Ant 1 7 1 Driving the build process ant apache org Java JDK 1 5 Compiling the source code java sun com javase downloads index jsp For example yum install ant jdk 1 Obtaining the XDMS source code Download the source code bundle from
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