IUCLID 5 Guidance and support
Contents
1. f_f 8 Finish Cancel Activate imports 4 3 User management The installation of IUCLID 5 is now ready for hand over to whoever will be maintaining the system and whoever will be managing the user accounts The management of user accounts and their roles is described in the UCLID 5 User Manual Individual users can connect to the IUCLID 5 server using Java Web Start technology as described in section 3 1 of this document A convenient way to achieve that is for users to save onto their desktop one of the files downloaded from the default Java Web Start page The user would launch IUCLID 5 by simply double clicking on the icon on his or her desktop Alternatively the users could be supplied with the URL http lt address of your server gt S8O8O0 i5server and instructions on which link to use 30 IUCLIDS Chapter 5 Un installation of IUCLID 5 The un installation of IUCLID is a manual process UCLID can be un installed by deleting the files that were copied to the destination machine and reversing any changes made during the installation process For more details about the actions that might be required see the UCLID FAQ located at the UCLID web site http Auclid eu 312. installation software is published In addition it is recommended to upload a set of reference substances and the EC inventory These are also available from the web site at which the IUCLID 5 software is published Tip Time and IT resources can be saved by importing into IUCLID only the Reference substances you need Various different sizes of Reference substance inventory can be downloaded from the IUCLID web site There is a full set a reduced list and a function that allows you to create your own inventory using common identifiers as selection criteria such as EC Number and IUPAC name Before importing the full set consider carefully whether it is really necessary Reference substances that are not imported during the initialisation process can be imported later A simple compromise is to start with the reduced list For more information regarding system requirements see the FAQ on the IUCLID web site located at http uclid eu IUCLIDS Chapter 2 Making a fresh installation of IUCLID 5 The following chapter contains a brief description of the actions required to make a fresh installation of IUCLID 5 that runs within a web server on Windows 2 1 Operating System IUCLID 5 has been tested thoroughly using Windows server 2003 Other versions 2000 XP 2008 may be used as well In that case the file locations might be different from the ones used in this document For installation instructions please refer to the documentati
3. lt Back Next gt Cancel Create User e Select the checkbox Create user Fill in all the fields The user needs a Login name for identification during login The Full name is used for proper user identification The Assigned role is needed to administrate the access permissions In a newly installed IUCLID 5 the roles Administrator Full access and Read only are provided by default e Enter a Login name as it should be used for identification during login and the Full name used for proper user identification e Optionally click Set password and define a password e Click and highlight a role in the list of unassigned roles and assign it to the user by clicking the Right arrow Assigning a Role is needed to administrate the access permissions in a newly installed IUCLID 5 the roles Administrator Full access and Read only are provided by default Tip It is recommended to create a user with the Administrator Role regardless of whether a stand alone or a distributed version of IUCLID 5 is set up Once a user has been created the IUCLID 5 administrator in case of a distributed version can define different other user s and assign different role s to them see the IUCLID 5 User Manual 29 IUCLIDS e Assign a Legal entity normally the Legal entity imported in the third step of this wizard by clicking the green plus button and performing a search for the desired Legal entity In the Query field Legal entity nam
4. 4 2 Step 1 of the First steps wizard Introduction The wizard presents some useful information There are no actions other than to read the information Click the Next button WE First steps Welcome to IUCLID 5 Welcome to IUCLID 5 IUCLID 5 International Uniform ChemicaL Information Database is a software application to capture store maintain and exchange data on intrinsic and hazard properties of chemical substances This wizard will guide you through the different steps involved to setting up your application so that you can use it immediately We recommend that you follow the given instructions 1 Change the SuperUser password not mandatory but recommended to increase security 2 Import your Legal Entity information mandatory for running the application 3 Import the EC inventory not mandatory but strongly recommended 4 Import the Reference substance inventory not mandatory but recommended for users with gt 100 substances Create a user account and define roles strongly recommended IMPORTANT Before running this wizard please make sure your Legal Entity information has been stored on your PC information available at the IUCLID Download Website B f t_ 8 G a B8 Nex gt Cancel Introduction Figure 4 3 Step 2 of the First steps wizard Init mode New installation To initialise a new database select the button New Installationas shown below and continue to the next step ME First steps
5. Define the initialisation mode Initialisation mode New installation C Restore from backup f 2 H 6 _6 d a Cancel Init mode 25 IUCLIDS Figure 4 4 Step 2 of the First steps wizard Init mode Restore from backup To restore from a backup of a previous version of IUCLID 5 select the button Restore from backup then enter the directory containing the backup files as shown in the example below WE First steps Define the initialisation mode initialisation mode O Newinstallation Restore from backup Location to restore from DAIUCLID backup a a 8 0 8 8 0 0 i Init mode Click Next The wizard jumps to its last step where the importation of data is started as shown below Figure 4 5 Restoration from a back up Step 8 Activate imports ME First steps Start import procedure Confirm the start of the import procedure The import of the EC inventory and the Reference substance inventory is atime consuming process They run as background jobs Please do not log out from IUCLID 5 before the import confirmation pop up window appears Mote the duration of this import process depends onthe size of the import files It may take a considerable amount of time 2 B 8 6 8 B Next gt f Einish Cancel Activate imports The import may take some time Click Finish When the restoration is complete the following screen is shown Background job ended Fa Restore comp
6. installation will use the Java Web Start technology which depends on an installed Java Runtime Environment JRE lf you do not have a JRE installed please contact your system administrator For more information to Java Web Start please refer to http java sun com products javawebstart Current server status OK Available connections Connect without compression Install IUCLID 5 Client normal with 512MB RAM with 768MB RAM with 1GB RAM Connect with compression Install IUCLID 5 Client normal with 512MB RAM with 768MB RAM with 1GB RAM Administration of installed Web Start applications Start Application Manager The page shown above page contains links that use Java Web Start technology to start a client that connects to the IUCLID server and displays IUCLID 5 s graphical user interface GUI on the client machine In the example shown above the link under the text UCLID 5 Client with 1GB RAM has already been followed The difference between the links in the above 23 IUCLIDS page is that each link passes different parameters to the I UCLID 5 server The options included are for varying amounts of memory to be allocated to UCLID 5 and for different types of data compression to be employed in the connection to the server If IUCLID 5 runs slower than you would like and you have the available memory select a link for a larger amount of RAM The client can be run directly from a browser or by first downl
7. jar For use with Tomcat the driver must be placed in Tomcat s library folder e g Tomcat 1lib If you encounter any problems during the installation that cannot be solved using information in this manual or the documentation of third party softwares before contacting the ECHA Helpdesk please try the IUCLID FAQ located at the IUCLID web site http Auclid eu 1 1 Hardware requirements The server hosting IUCLID 5 must have at least e RAM 1 GB recommended 2 GB e Hard disk space 200 GB e CPU 2 GHz 32 or 64 bit architecture e Network adapter 100 Mbps recommended Gbps The requirements depend in part on the plugins that are in use For example using the Query Tool plugin will increase the resources required to obtain a reasonable running speed especially on a large database 1 2 Software requirements In addition to either one of the groups of software components stated above for commercial or open source the following are required e Windows 2003 Server For installation instructions please refer to the documentation of the manufacturer e The IUCLID 5 distributed installation package version 5 3 It can be downloaded without charge from the IUCLID 5 web site e Once you have completed the installation of UCLID 5 you should test it by starting and configuring it The configuration requires access to at least a legal entity file LEOX The creation of a LEOX is described on the UCLID 5 web site where the IUCLIDS
8. reflected in any other Data from an installation of IUCLID 5 1 can be transferred to an installation of UCLID 5 3 using the Backup plugin in IUCLID 5 1 followed by use of the Restore feature in IUCLID 5 3 Note that it is not possible to transfer data from either IUCLID 5 3 or IUCLID 5 2 to IUCLID 5 1 3 2 2 2 If only one computer is available for installation of IUCLID 5 If only one computer is available only one web application server can be run at a once and so only one instance of IUCLID 5 can be run at once However in this case it is possible to have two different versions of IUCLID 5 installed on one computer and to switch back and forth between them running only one at a time There are various different ways of doing that What follows is a description of one of the possible methods Before deploying an installation of IUCLID 5 3 1 In IUCLID 5 1 install and run the Backup plugin 2 In the Web Application Manager make a note of the name of the path to the application example iuclid5 1 3 In the Web Application Manager stop the IUCLIDS5 Server 4 In the computer s file system create a directory in which to store un installed web applications example uninstalled_webapps 5 In the computer s file system copy the directory noted in step 1 2 example tuclid51 to the directory just created example uninstalled_webapps 6 In the Web Application Manager un deploy the application example iuclid51 Install
9. IUCLID 5 Guidance and support Installation Guide for IUCLID 5 Version 5 3 Client Server Architecture Microsoft Windows IUCLIDS INTERNATIONAL UNIFORM CHEMICAL INFORMATION DATABASE February 2011 Legal Notice Neither the European Chemicals Agency nor any person acting on behalf of the Agency is responsible for the use which might be made of the following information A wealth of additional information on the European Union is available on the Internet It can be accessed at the addresses http tuclid echa europa eu http echa europa eu http europa eu European Chemicals Agency Reproduction is authorised provided the source is acknowledged IUCLIDS Table of Contents es UTI OC COU ea shae tyes eaten apse canoe E onus eaten te eases E E sesso ase eye ees aie sees l lA Hardware tegue MONS oong EE E E EE R Oa l Be SOM Ale a A a E E l 2 Making a fresh installation of IUCLID 3 ciccc nscnssseccemonvaxeeiies edeantpeanaeianiaceawaleriecsmitasacaseeeeenesiaaddewasenensumeraendecenees 3 Ad O TAU a SE e ea E E yee eeaaese 3 22 JAVA EVO PING Kii 2 cosattenratactanteunsiscncound eet EEEE EEE 3 2 WMS talon Ol OStOte OL 1 hasecenteusansnctutaeeeaahatacuicemunsestmanace sans eae oe eeealaeena a coensacee sda ante stetcasteeonauieenatecs 3 2 C onnsnranon OF POS fe 5 Ol bes tacnaenseiuaned ceacwareienetsancnd ean EEEE E 7 2 5 Installation of a W Cb ApplCalOm Serye sasescncdectataediiactesadedetnacehedsw bor
10. IUCLID 5 3 as described in the installation manual Note that a new database must be created It can be running on the same instance of the database software but in that case the database must have a different name When I UCLID 5 3 is running use its built in Restore feature to upload data from the back up that was created during the initialisation process step 1 1 To switch between versions of IUCLID 5 example iuclid53 gt iuclid51 1 In the Web Application Manager make a note of the name of the path to the UCLID 5 application from which you are switching example tuclid53 2 In the Web Application Manager stop that IUCLID 5 application example iuclid53 3 In the computer s file system copy the application directory of the IUCLID 5 from which you are switching example tuclid53 to the directory uninstalled_webapps 4 In the Web Application Manager un deploy the IUCLID 5 application from which you are switching example iuclid53 5 In the computer s file system move the directory of the UCLID 5 to which you are switching example tuclid51 from the directory uninstalled_webapps to the directory webapps 6 Start the IUCLID 5 application to which you are switching example iuclid51 Before switching from IUCLID 5 1 to IUCLID 5 3 consider whether you would like to transfer data from 5 1 to 5 3 If you do want to transfer data whilst you still have IUCLID 5 1 up and running use the Back up plugin to make a cop
11. Pause Restart cm ae On the Java tab type 512 MB for both Initial memory pool and Maximum memory pool Figure 2 24 Java tab Apache Tomcat Properties ed General Log On Logging Java Startup Shutdown Java Virtual Machine C Program Files Javaljdkl 5 0_17 jrelbinservertjvm dll nate Java Classpath Ci Program Files 4pache Software Foundationi Tomcat 6 0 binibootstrar Java Options Dcatalina Fome C Program Files 4pache Software Foundationi Tom Dcatalina base C Program Files 4pache Software Foundation Tome Djava endorsed dirs C Program Files 4pache Software Foundation Djaya io trpdir C Program Files 4pache Software Foundation Tom Initial memory pool o1iz ME Maximum memory pool 512 ME Thread stack size KE coe w Restart the service by right clicking on the tray icon and selecting Stop Service then Start Service Open the page http localhost 8080 manager html in your browser enter the username and password you gave to the Tomcat administrator and check the memory settings currently set for Tomcat The Max memory in the JVM section of the Server Status page should be at least 500 MB 2 6 Download IUCLID 5 Before downloading IUCLID 5 you need to register as a IUCLID user on the IUCLID website http uclid eu The application itself is packaged into the iuclid5_server zip file 2 Deployment in Tomcat Deployment is the term used for the proc
12. Request a new database by right clicking the text Databases and selecting New Database as shown in the figure below Figure 2 17 Request a new database in pgAdmin III Piel Es 22 pgAdmin III File Edit Plugins View Tools Help Tas a OPER TAS ane browser Properties Statistics Dependencies Dependents postgres postgres Reports SOL pane x Retrieving Databases details Done 0 00 secs Zi 1 IUCLIDS Enter the details you require Normally these are only name iuclid5 and owner iuclid5 The encoding should be UTF8 Click OK Important Make a note of the database name It is referred to later in the installation in section Section 2 8 Changing the database connection settings We recommend using the name iuclid5 Figure 2 18 Enter the details of IUCLID 5 s database into pgAdmin II 3 pg dmin III Ioi x 2 ve eee je on Sa T Properties Variables Privileges s Object browser Name fuclids Servers 1 Ts E l orb I T PostgreSQL 6 4 flocalhost 5432 aS Databases 1 na icis st H Tablespaces 2 Encoding uTFs Template Tablespace default tablespace gt ne Schema restriction ee Character type B Connection Limit fr IUCLID 5 2 database os HA Group Roles 0 Htt Login Roles 2 comment Retrieving Databases details Done 0 00 secs a As you can see from the figure below there is
13. Tomcat administrator Important Take note of this settings because they are required to access the Tomcat Manager to deploy and remove applications Figure 2 21 Configuration Fa Apache Tomcat Setup Configuration Options Configuration Tomcat basic configuration HTTP 1 1 Connector Port 080 Administrator Lagin User Name admin Password eeees Mullsort Install System v2 37 lt Back Cancel Select the folder of the previously installed Java Virtual Machine Figure 2 22 Java Virtual Machine A Apache Tomcat Setup Java Virtual Machine path selection l Ioj x Java Virtual Machine F Java Virtual Machine path selection Please select the path of a J25E 5 0 JRE installed on your system CiProgram Files Javaljdkl 6 0_11 Mullsort Install System v2 37 lt Back Install Cancel When the installation process is finished a new icon appears in the system tray for Tomcat right bottom corner of your screen Right click on the icon and select Configure On the General tab set Automatic startup type 14 IUCLIDS Figure 2 23 General tab x General Log On Logging Java Startup Shutdown Service Mame Tomcat Display name Apache Tomcat Description Apache Tomcat 6 0 18 Server http jitomcat apache Path to executable CProgram Filesi pache Software Foundationi Tomcat 6 0binitomecat Startup type Service Status Stopped Start Stop
14. UCLID 5 User Manual for more detail As part of the First steps wizard a legal entity must be uploaded into the IUCLID 5 installation in the form of a LEOX file Therefore before running this wizard make sure that a LEOX file for the legal entity of your company or organisation is accessible to your computer For more information see the IUCLID 5 User Manual The First steps wizard provides the option of uploading the following information to your IUCLID 5 installation For details see the IUCLID 5 User Manual e EC Inventory e Inventory of Reference substances Although these uploads are optional it is strongly recommended to do them during the first run of the First steps wizard To do so you will need to have the data accessible to your computer whilst running this wizard The First steps wizard can be run at any time but only by the SuperUser This is done from the file menu within IUCLID 5 Administrative tools Initialise When starting the UCLID 5 for the first time the only user available is an administrator named SuperUser Log in as SuperUser by entering the following case sensitive values into the login screen as shown below Username SuperUser Password root A IUCLID 5 2 0 b Please enter username and password to login ilocal workstation passnora e000 O Login Cancel 24 IUCLIDS The First steps wizard then proceeds Each page of the wizard is described in a figure below Figure
15. admin III Ioj x File Edit Plugins View Tools Help Gg k1 PER 7k m browser Froperties Statistics Dependencies Dependents Properties P No properties are available for the current selection SOL pane x Retrieving Servers details Done 0 00 secs ve Right click the text PostgreSQL 8 4 localhost 5432 that is under the word Servers highlighted in blue in the figure above Select connect as shown below Figure 2 11 Connect pgAdmin III to PostgreSQL as user postgres Pile Es 2 pgAdmin III File Edit Plugins View Tools Help RI K4 Object browser X Properties Statistics Dependencies Dependents E Servers ummm Propert a m PostgresQL 5 TTIR 4 localh ene F Description PostgresO 3 4 Cammer Hostname localhost Kem Stop Service ae 5432 Delete orop er vice postgresql a 4 Maintenance database postgres Reports FF Username postgres Store password Yes Properties Restore environment Mo E Cnnnerted Mn SOL pane x Connecting to database Failed 0 08 secs F IUCLIDS Enter the password for user postgres as given in the postgres installer Figure 2 4 Password for the database superuser postgres and the Windows service account postgres then click OK It is recommended to store the password to facilitate future access Figure 2 12 Authenticate user postgres Connect to Server Please enter pass
16. ctionality of UCLID and or the back up function of the database software for example PostgreSQL 2 Remove the executable program files for the previous version of IUCLID Note that the plugins for IUCLID 5 2 x are not compatible with IUCLID 5 3 Therefore they must not be copied over to the new installation 3 Copy the executable program files for the new version of IUCLID to the installation destination 4 Adapt the configuration files for UCLID if necessary Note that if the Oracle database is used the file server properties must contain the following entry hibernate connection driver_class oracle jdbc OracleDriver The previous value was hibernate connection driver_class oracle jdbc driver OracleDriver 5 Migrate the database by running IUCLID in update mode only once This is done as follows First ensure the UCLID web application is stopped Uncomment the following line in the file server properties database update startup true Start the application wait for the migration to finish then stop the application Comment out the previously edited line in the file server properties database update startup true 6 Once the migration process has been completed successfully the new version of IUCLID can be started and checked before being entered into production 3 1 1 Examples of the upgrade and migration processes per type of web application server The detailed actions required for step 2 5 above depend on the particula
17. dea cseadmcdoinonane senses a teudadantiacmeenacsuasenecaasaeteen edt 30 eG OE LO Gs Do eee tern ttn Meernn E er ore 31 iii IUCLIDS Chapter 1 Introduction IUCLID 5 can be installed as standalone or in a multi user environment This document describes how to install and configure the IUCLID 5 application in a distributed Microsoft Windows environment IUCLID 5 can be installed with the following open source components e JDK 1 6 or higher Installation packages can be downloaded from http www java com e Tomcat 5 5 x or 6 0 x where x is the latest version Installation packages can be downloaded from http tomcat apache org e PostgreSQL 8 2 8 3 or 8 4 recommended but not 9 Do not use PostgreSQL 9 Installation packages can be downloaded from http www postgresql org For a I UCLID 5 installation using commercial software the following components can be used e JDK 1 6 or higher Installation packages can be downloaded from http www java com e BEA WebLogic Server 9 0 http www oracle com bea e Oracle 10g or higher Installation packages can be downloaded from http www oracle com The Oracle driver for Java is no longer supplied with the UCLID installation package The correct driver for the combination of Java and Oracle versions in use must be obtained from the oracle web site and installed in the appropriate folder For example for Java 1 6 and Oracle 11g Release 2 11 2 0 2 0 the name of the driver is ojdbc6
18. e enter the name of the desired Legal entity or an asterisk as wildcard and click the Search button In the Query results list click the desired entry and then click the Assign button e Optionally select default attachment and import export directories These settings can be changed at a later stage as described in the UCLID 5 User Manual e Click the Next button Figure 4 11 Step 8 of the First steps wizard Start import procedure If you have selected an EC Inventory and or Reference substances inventory file s during the wizard steps you can now run the imports Click the button Execute imports Note again that these imports can take up to several hours depending on your machine speed and the amount of data you are importing Then click the button Finish If you have launched any imports you will now have to wait until the imports are completed Afterwards you should log out and then log in again as a user for the newly defined account Remember general working as Super User is not supported WE First steps Start import procedure Confirm the start of the import procedure The import of the EC inventory and the Reference substance inventory is atime consuming process They run as background jobs Please do not log out from IUCLID 5 before the import confirmation pop up window appears Note the duration of this import process depends onthe size of the import files It may take a considerable amount of time f _B b B B
19. e settings have to be adjusted Open the server properties file in the webapps i5server WEB INF classes directory The server properties file is the configuration of the IUCLID 5 server In order to connect to the database correctly it is necessary to modify the server properties configuration file The default configuration file contains settings in order to connect to a PostgreSQL database on the same computer Usually it is sufficient to specify the database password it Settings for using PostgreSQL mibo rao tee eon e a a E aea ae oe eaa eda hibernate connection username iuclid5 hibernate connection password i1uclidd5 hibernate connection driver_class org postgresgl Driver hibernate dialect org hibernate dialect PostgreSQLDialect If your database server is running on another computer or database name or the username is different modify the settings accordingly For example if your database server s name is dbserver PostgreSQL is accepting connections on port 12345 the database name is chemdb and the user is joe with password xxxx your configuration is 16 IUCLIDS iberna te COM erro ici Goce cmekme cel Clocetion ko or elnomele hibernate connection username joe hibernate connection password xxxx Important Make sure that there are no spaces after the username and password values in the properties file The IUCLID 5 server registers the activities into a log file which helps the system administrator The configurati
20. e your own inventory using common identifiers as selection criteria such as EC Number and IUPAC name Before importing the full set consider carefully whether it is really necessary Reference substances that are not imported during the initialisation process can be imported later A simple compromise is to start with the reduced list 28 IUCLIDS Figure 4 10 Step 7 of the First steps wizard Create user account and assign role Create a new user account and define its user access rights by assigning it a role It is essential to create a new user because general working within IUCLID 5 with the SuperUser is not supported Only one user can be created per run of the First steps wizard WE First steps Create user account and assign role It is recommended to create a user account before running IUCLIDS The SuperUser account is for user administration only and therefore to run IUCLID 5 we strongly recommend that you create your own user account by selecting the following tick box Assign your role and legal entity and specify the attachments and Import export directories Create user Login name Local Administrator Full name Example Set password Unassigned roles Assigned roles Full access Read only p Set password P Set the password of Local Administrator Example last login Never from Nowhere gE H8 LEO for Manual 7 Helsinki f Fin l coool attachments directory LG Import export directory HB B MEA
21. ess of installing a web application into the Tomcat server 15 IUCLIDS Web application deployment may be accomplished in two ways e Statically the web application is set up before Tomcat is started e Dynamically in conjunction with the Tomcat Manager web application or manipulating already deployed web applications You can find more information about how to deploy a web application on tomcat on the Tomcat deployment http tomcat apache org tomcat 5 5 doc deployer howto html web page In this document only the Dynamic deployment is described However also the static deployment may be used The deployment of IUCLID 5 actually consists of copying the i5server war archive into the webapps directory of Tomcat Figure 2 25 UCLID 5 Deployment amp C Program Files Apache Software Foundation Tomcat 6 0webapps File Edit View Favorites Tools Help G Bak O iF lE Search Folders i S x I m Folder E g Tomcat 6 0 O host manager File Folder gt bin idserver File Folder conf fan File Folder ib File Folder 9 logs fhiSserver war S7 784KB WAR File temp o webapps Note When IUCLID 5 is started the first time it creates new tables in the database which might take up to 30 seconds 2 8 Changing the database connection settings If the username password and name of the database are all iuclid5 the application will start normally otherwise it cannot connect to the database and the databas
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23. leted successfully OK 26 IUCLIDS Figure 4 6 Step 3 of the First steps wizard Change password If you have not yet changed the default password of the SuperUser to a more secure value than root the traffic light in the wizard screen will be yellow To change the password check the box Change SuperUser password enter the old password root and then enter the new password After confirming the password click the button Next WE First steps Change the SuperUser password For security reasons it is recommended to change the SuperUser s password g it is not secure as it is now a Change SuperUser password Old password New password Confirm new password We strongly recommend that you change the SuperUser password since each IUCLID 5 installation uses an identical default password To change your password please tick the checkbox g C n a i a a E a a E Cancel Change password Figure 4 7 Step 4 of the First steps wizard Import Legal Entity To import a Legal entity see the IUCLID 5 User Manual select its LEOX file by browsing to the file The browsing is accessed by clicking on the folder icon to the right of the field Select the import file Click the Next button The Legal entity is imported immediately ME First steps Import legal entity In order to run IUCLID 5 you have to import your Legal entity obtained from the IUCLID Download Website Download Website otherwise this wizard
24. me being It can be deleted in the future when you are absolutely sure that it is no longer needed What follows is some information and advice as to how you can manage more than one version of IUCLID 5 As stated above each installation of IUCLID 5 must have its own database and its own web application server A new database must be created for IUCLID 5 3 because the structure of the database differs from that of previous versions This requirement can be met in a variety of different ways The following sub sections describe some common sets of circumstances The database for IUCLID 5 3 can be run on the same instance of the database software as a previous version of IUCLID 5 however it must have a unique name within that instance of the database software When IUCLID 5 3 is run for the first time on an empty database it will automatically create all the correct tables 21 IUCLIDS 3 2 2 1 If more than one computer is available for installation of IUCLID 5 Each instance of UCLID 5 that is running in an application server is installed on a separate computer and has its own database In this case the instances of IUCLID 5 can point to databases that are either running on the same computers as the respective IUCLID 5s or on a central instance of the database software that contains a separate database for each of the instances of IUCLID 5 In all of these cases each instance of IUCLID 5 is independent of all others such that a change to one is not
25. mmenting the following line in the file server properties database update startup true 11 Start the IUCLID 5 server by starting Tomcat and wait until the IUCLID database has been migrated This can be followed from logs During the migration the IUCLID server status is Unavailable 12 Stop the IUCLID 5 server by stopping Tomcat 13 Set IUCLID 5 to start not in its update mode by commenting out the line edited in step 10 19 IUCLIDS database update startup true 14 Start the IUCLID 5 server by starting Tomcat 3 1 1 2 Upgrade and migrate from IUCLID 5 2 to IUCLID 5 3 under BEA WebLogic Server l 2 Close all clients for IUCLID 5 Shutdown the IUCLID 5 server for example by shutting down BEA WebLogic Server Copy the configuration file server properties into a backup folder For example copy c program files IUCLID5 i5server server properties to e backup server properties Delete the folder with the old UCLID 5 program For example trdc program files IUCLID5 i5server Copy the file i5server war into the folder ITUCLID5 For example copy 15server war to c program files IUCLID5 Create a folder mkdir idserver Move into the new folder cd i15server Unzip the WAR file to this folder unzip i5server war Copy the file server properties from the backup folder into the folder sTOMCAT S webapps i5server WEB INF classes For example copy e backup server
26. must be transferred manually from the old to the new database as described in the sub section below Each installation of IUCLID 5 must have its own database and its own web application server There can be more than one database running on a single instance of the database software but each web application server cannot be used to run more than one IUCLID 5 application at once 3 2 1 Migration of data to IUCLID 5 3 from IUCLID 5 0 or 5 1 Before starting to install IUCLID 5 3 all the data must be exported from IUCLID 5 1 x using the Back up plugin that is available on the IUCLID web site The export process is essential because the exported data will later be imported into IUCLID 5 3 When it is run the Back up plugin asks the user to create and enter a single password This will become the password for all the user accounts in the new installation with the exception of the account SuperUser which has a default password of root To import the exported data into IUCLID 5 3 use the built in Restore feature of IUCLID 5 3 that can be found from the menu File Administrative tools This feature allows the upload of data that was exported using the Back up plugin on 5 1 x Note that it is not possible to transfer data from either IUCLID 5 3 or IUCLID 5 2 to IUCLID 5 1 3 2 2 Database configuration for running IUCLID 5 3 and a previous version at the same time If you already have a previous version of IUCLID 5 it is recommended to keep it for the ti
27. nces EINECS the European List of Notified Chemical Substances ELINCS and the No Longer Polymers list NLP published in the Official Journal of the European Communities Each substance listed in the inventory has an EC number and an EC name allocated by the European Commission lf you want to use the EC inventory in your IUCLID 5 installation please download it from the IUCLID Download Website and save the file on your hard disk To import the EC inventory in IUCLID 5 using this wizard please tick the import box Select the import file by navigating to the desired file on your computer Note it is possible to import the EC inventory at a later stage using the import function from the IUCLID 5 Task panel Import EC inventory Select the import file DAIUCLIDYECinventory_1 1_en i52z e a a l a a E a a E lt Back Next gt Cancel EC inventory import Figure 4 9 Step 6 of the First steps wizard Import reference substance inventory Reference substance inventory import Select the file for the Reference substance inventory see the UCLID 5 User Manual The Reference substance inventory will not be imported immediately The import will start at the end of the first steps wizard together with the EC Inventory import Depending on your machine speed and the size of the inventory this bulk operation may take a long time The import of the Reference substance inventory itself can take up to several hours ME First steps Impo
28. now a new database named iuclid5 12 IUCLIDS Figure 2 19 List of databases in pgAdmin III If pgAdmin III OF x File Edit Plugins View Tools Help Tas ac OPER Ze Object browser Properties Statistics Dependencies Dependents San E J Postaresol 8 4 s Eo 98 iuclids iuclidS IUCLID 5 2 database postgres postgres c H epa 3 Ag Group Roles 0 i cA Login Roles 2 Retrieving Databases details Done 0 00 secs a You can now close pgAdmin III and move directly to the installation of IUCLID 5 2 5 Installation of a Web Application Server Here is described the installation of the Tomcat Web Application Server BEA Web Logic can be used instead 2 5 1 Tomcat Download the Windows Service Installer of Tomcat 6 0 from http tomcat apache org At Choose Components step select also the Service and Native components Figure 2 20 Choose Components la x Check the components you want to install and uncheck the components you don t want to install Click Next to continue Select the type of install Custom Or select the optional a F Tomcat components you wish ko i install Choose Components Choose which Features of Apache Tomcat you want to install Description Position your mouse Over a component to seg its description Space required 9 8MB Mullsort Install system ve ar lt Back Cancel 13 IUCLIDS Type a name and password for the
29. nstall Setup is now ready to begin installing Postgres BitRock Installer IUCLIDS Figure 2 8 Installation of PostgreSQL in progress Installing Please wait while Setup installs PostgreSQL on your computer Installing Unpacking C Program Files PostgreSQL 8 4 bin pgAdmin3 exe Completing the PostgreSQL Setup Wizard Setup has finished installing PostgreSQL on your computer E Launch Stack Builder at exit Stack Builder may be used to download and install additional tools drivers and applications to complement your PostgreSQL installation PostgreSQL Packaged by EnterprisepB The Enterprise Postgres Company Cancel 2 4 Configuration of PostgreSQL A new user and a new database need to be created Tip IUCLID 5 is configured by default to connect to the database using username iuclid5 and password iuclids5 It is convenient to specify the same password now and change it later when the application is set up correctly Important J Take note of the password of this user This user name and password will be needed later to connect IUCLID 5 to the database IUCLIDS The program pgAdmin III can be used to create the database as follows Start pgAdmin III from the menu Start All Programs PostgreSQL 8 4 After the splash screen has appeared and you have closed the pop up window that shows usage tips the following screen is shown Figure 2 10 pgAdmin IIT interface on first opening I pg
30. oading a file from one of the links and running that Depending on your browser settings when you click on one of the links above you will see either a dialogue box or UCLID 5 will run and you will see the login page The browser dialogue asks whether you would like to save a file or run it straight away The choice is yours A convenient way to access UCLID 5 is to download one of the files from the default page save it to the desktop of your local machine used to access IUCLID 5 and give it the IUCLID 5 icon that comes with the installation Double clicking on the icon then launches the UCLID 5 GUI Once you see the login page you are ready to go walk through the First steps wizard as described in the next section 4 2 First steps wizard When you start I UCLID 5 for the first time the First steps wizard is run automatically It guides you through the steps required to make a working user account and to upload the data required to use IUCLID 5 in a practical setting The settings that relate to user accounts can also be changed after having run the wizard using the features described in the UCLID 5 User Manual Important O This wizard allows a single user account to be created per run This user is in addition to the SuperUser account that comes with the installation It is essential to have at least one user account in addition to SuperUser because SuperUser should be used only for the special tasks that only it can carry out See the I
31. on file for setting the logging is i5server logging properties in the WEB INF classes directory Start Tomcat using the Tomcat server icon All the software has now been installed What remains is some configuration as described in the next section 17 IUCLIDS Chapter 3 Upgrade This chapter describes how to upgrade a previous version of UCLID 5 to IUCLID 5 3 Dependent upon the version of UCLID 5 that is being upgraded to IUCLID 5 3 there are two main scenarios in the upgrade process One is to upgrade from any version 5 2 whereas the other is to upgrade from 5 0 or 5 1 These are each described in a dedicated sub section of this chapter In all scenarios before starting the upgrade it is important to back up the database Use the built in back up functionality of IUCLID and or the back up functionality of the database Making only a copy of the file system on which IUCLID is installed is not recommended as a means of backing up 3 1 Upgrading from IUCLID 5 2 to IUCLID 5 3 for client server architecture This section is relevant only if the upgrade is from IUCLID 5 2 For earlier versions see the next section The version can be seen from within the interface of IUCLID 5 To see the version start UCLID 5 log in then click Help and select About The upgrade process can be summarised by the steps shown below Detailed step by step examples are given in following subsections 1 Back up the database Use the built in back up fun
32. on of the manufacturer 2 2 JAVA Development Kit Download the JAVA Development Kit JDK 6 or JAVA Runtime Environment JRE 6 according to the architecture of your computer from http java sun com jJavase downloads index jsp Select the latest available update Run the installer and follow the instructions The default parameters are appropriate for IUCLID 5 For more information please refer to the installation instructions http java sun com javase 6 webnotes install index html 2 3 Installation of PostgreSQL If PostgreSQL 8 2 8 3 or 8 4 are not already installed on the computer download 8 4 from the site www postgresql org download and install it Do not use PostgreSQL 9 The web site of PostgreSQL offers a range of alternative ways to download and install the PostgreSQL software The screen shots shown below show the use of the one click installer available from the PostgreSQL web site for PostgreSQL 8 4 An example of the file name of the installer is postgresqlI 8 4 7 1 windows exe If version 8 2 8 3 or 8 4 of PostgreSQL is already running as a service with a user postgres the existing installation can be used although the latest 8 4 is recommended The default fresh installation of PostgreSQL 8 4 made using the one click installer automatically starts PostgreSQL as a service creates the user postgres if necessary and supplies administration tools e g pgAdmin III that can be used to create the database If the installer create
33. pgAdmin III 4 pgAdmin III Ioj x Eile Edit wiew Tools Help Object k Froperties Statistics Dependencies Dependents Fa S fi Lo L 5 4 da aeg 5432 ag postares postgres H ae Teena er 42 Group Roles 0 Login Roles 1 SOL pane x Retrieving Databases details Done 0 00 secs a Right click on Login Roles and select New Login Role Figure 2 15 Select create a new user option i pgAdmin III jo x File Edit ma wiew Tools Help Object browser Properties Statistics Dependencies Dependents ee e Q PostgreSQL 8 4 localhost 5432 E B Databases 1 H A Tablespaces 2 vn Group Roles 0 Refresh New Login Role Object list report SQL pane x Retrieving Login Roles details Done 0 00 secs a Enter the role name iuclid5 Set the password 10 IUCLIDS Important Make a note of the user name and password They are referred to later in the installation in section Section 2 8 Changing the database connection settings We recommend using iuclid5 as both the user name and the password Figure 2 16 Create new role i e a user with name iuclid5 New Login Role Properties Role privileges Role membership Variables SQL Role name fuclids DID an login Password Password again Account expires Connection Limit Role for IUCLID 5 application comment Use replication m ma A
34. properties to STOMCAT webapps i5server WEB INF classes server properties 10 Note that if the Oracle database is to used the file server properties must contain the following entry hibernate connection driver_class oracle jdbc OracleDriver The previous value was hibernate connection driver_class oracle jdbc driver OracleDriver 20 IUCLIDS 11 Set IUCLID 5 to start in its update mode by uncommenting the following line in the file server properties database update startup true 12 Start the IUCLID 5 server and wait until the IUCLID database has been migrated This can be followed from logs During the migration the IUCLID server status is Unavailable 13 Stop the IUCLID 5 server 14 Set IUCLID 5 to start not in its update mode by commenting out the line edited in step 11 database update startup true 15 Start the IUCLID 5 server 3 1 2 Starting IUCLID 5 after migration using the server method If the migration process has been carried out successfully you can now connect to the newly installed UCLID in the same way as before the upgrade The initialisation process is not required All of the data that was present in the upgraded system should be present in the new system Therefore it should be possible to log in to any of the user accounts from the previous system 3 2 Upgrading from IUCLID 5 0 or 5 1 to IUCLID 5 3 O Important There is no automatic upgrade of the database from IUCLID 5 0 5 1 to IUCLID 5 3 The data
35. r web application server in use Examples are given below for the web application servers relevant to this document 18 IUCLIDS 3 1 1 1 Upgrade and migrate from IUCLID 5 2 to IUCLID 5 3 under Tomcat l 2 Close all clients for IUCLID 5 Shutdown the IUCLID 5 server for example by shutting down Tomcat Copy the configuration file server properties into a backup folder For example copy TOMCAT webapps i5server WEB INF classes server properties to e backup server properties Delete the folder with the old IUCLID 5 program For example rd sTOMCAT webapps i5server Copy the file i5server war into the folder webapps For example copy 15server war to STOMCAT webapps Start Tomcat and it will automatically unpack and start the application The content of the war file will be extracted to a folder For example STOMCAT S webapps i5server Shutdown Tomcat Copy the file server properties from the backup folder into the folder sTOMCAT S webapps i5server WEB INF classes For example copy e backup server properties to STOMCAT webapps i5server WEB INF classes server properties Note that if the Oracle database is to used the file server properties must contain the following entry hibernate connection driver_class oracle jdbc OracleDriver The previous value was hibernate connection driver_class oracle jdbc driver OracleDriver 10 Set IUCLID 5 to start in its update mode by unco
36. rt reference substance inventory Select areference substance inventory to import into IUCLIDS The reference substance inventory is a catalogue of approximately 70 000 reference substances A reference substance is used for the identification of substances and contains information such as CAS Numbers IUPAC names SMILES and InChl notations structural formula and the EC inventory information The reference substance inventory is publicly available and can be downloaded entirely or partially lf you want to use the reference substance inventory in your IUCLID 5 installation please download it from the IUCLID Download Website and save the file on your hard disk To import the reference substance inventory in IUCLID 5 using this wizard please tick the import box Select the import file by navigating to the desired file on your computer Note It is possible to import the reference substance inventory at a later stage using the import function from the IUCLID 5 Task panel Import reference substance inventory Select the import file DAIUCLID Referencesubstance i5z a B b 5B _6 G _ B lt Back Next gt Cancel Reference substance inventory import Tip Time and IT resources can be saved by importing into UCLID only the Reference substances you need Various different sizes of Reference substance inventory can be downloaded from the UCLID web site There is a full set a reduced list and a function that allows you to creat
37. s the superuser postgres you will have to create a password for it as shown in the figure below and enter it later into the configuration file for UCLID 5 Figure 2 1 Installer for PostgreSQL version 8 4 Setup PostgreSQL Welcome to the PostgreSQL Setup Wizard PostgreSQL Packaged by EnterprisepB The Enterprise Postgres Company IUCLIDS Figure 2 2 Installation directory for PostgreSQL BitRock Installer Please select a directory under which to store your data C Program Files PostgresOL s BitRock Installer IUCLIDS Figure 2 4 Password for the database superuser postgres and the Windows service account postgres Please provide a password for the database superuser postgres and service account postgres If the service account already exists in Windows you must enter the current password for the account If the account does not exist it will be created when you dick Next Password pion Retype password BitRock Instale Figure 2 5 Port number for PostgreSQL Please select the port number the server should listen on Port EEE BitRock Installer IUCLIDS Figure 2 6 Set the default locale for PostgreSQL Advanced Options Select the locale to be used by the new database duster Default locale Install pl pgsal in template1 database BitRock Installer Ready to I
38. will not complete successfully and you will be forced to log out Please note If your Legal entity information has not already been stored on your computer you should create it on the IUCLID Select your Legal entity file by navigating to the desired file on your computer Select the import file DAIUCLID Leox_Manual i5z 2 5 B 6 8 a 8 l lt Back Next gt Cancel Import legal entity IUCLID 5 Import of the legal entity file completed ox Important You must import at least one Legal entity in order to succeed with this wizard If you have no Legal entity in the IUCLID 5 system the traffic light in the wizard screen will be red The First steps wizard will be automatically launched when you log in to UCLID 5 until a Legal entity has been successfully imported 27 IUCLIDS Figure 4 8 Step 5 of the First steps wizard Import EC Inventory EC inventory import To import the EC inventory select the file for the EC inventory see the UCLID 5 User Manual The EC Inventory will not be imported immediately The import will start at the end of the First steps wizard Depending on your machine speed and the size of the inventory this import can take some time e g up to half an hour WE First steps Import EC inventory Select the EC inventory file which you previously downloaded The EC inventory is the catalogue of chemical substances listed on the European Inventory of Existing Commercial chemical Substa
39. word For user postgres on server PostgresO_ 6 4 localhost esses M Store password Help OK Cancel When you elect to save the password the following warning may be displayed Click OK Figure 2 13 Saving passwords Warning Ca Guru Hint Saving passwords Mie x Saving passwords WARHIHG You have opted to save your password It will be stored in plain text in your home directory on nix systems or in your user profile on Windows If you do not want this to happen please press the Cancel button pgAdmin uses PostgreSGL s pgpass mechanism to store your passwords On nix systems the password will be stored in pgpess whilst on Windows systems it will be stored in APPDATA PostgreSQL pgnass cont Mo4PPDATA is the Application Data folder in your user profile This mechanism is used by default by all programs that use the libpq library ta access the server which includes command line applications such as pg_durmp and pq restore other GUI applications and drivers such as psqlODBC This means that those applications may automatically connect to the server using your stored password If you do not want this to happen you should not use the Store Password option in pgAdmin T Do not show this hint again Help OK Cancel Expand the tree for PostgreSQL 8 3 localhost 5432 by clicking the plus sign that has just appeared next to it as shown in the figure below IUCLIDS Figure 2 14 Initial screen in
40. y of your data The copy can then be imported into UCLID 5 3 using IUCLID 5 3 s built in Restore feature 22 IUCLIDS Chapter 4 Initialisation of an installation of IUCLID 5 This chapter describes the configuration that is required to create a working I UCLID 5 system from an installation of IUCLID 5 that has an empty database There are two scenarios either to create a working installation from scratch or to load data from a back up that was made using the built in back up function of IUCLID During initialisation from scratch reference substance data and a legal entity are uploaded into the database and the required user accounts can be created For initialisation from back up make sure that the back up files are accessible from the system on which IUCLID will be initialised What to do in each scenario is described in the rest of this chapter 4 1 Starting IUCLID 5 Connect to the application with a browser by entering the address http lt address of your server gt SO8O0 i5 server The following page is displayed Figure 4 1 The default page for Java Web Start of IUCLID 5 IUCLID 5 Welcome to the IUCLID 5 Server IUCLID 5 Version IUCLID5 release 5 2 0 IU LIDS IU CLIDS release 5 2 0 build of 2010 02 11715 05 3352 Install IUCLID Client Component The server does not feature an interactive web frontend In order to connect to the IUCLIDS database please install the client application locally via the link below This
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