IUCLID 5 Guidance and Support
Contents
1. In this architecture the database and the application server reside on a server computer and the user works with another computer called a client It is similar to a web based application with the only difference being that the user interface of the application buttons text boxes etc is not a series of web pages but a specific Java application called UCLID 5 client that is downloaded automatically from the server This document describes how to download install and configure the necessary open source software products and the IUCLID 5 application itself on a Linux server Only the distributed installation is described The aim of this document is that a user with basic computer skills would be able to install and run IUCLID 5 The following is a list of items NOT covered in this document Complete and detailed installation and configuration procedure of the operating system GNU Linux A detailed configuration of the Database Management System PostgreSQL and the Application Server Tomcat 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 iuclid eu 1 1 Hardware requirements The server hosting IUCLID 5 must have at least e RAM 2 GB e Hard disk space 200 GB e CPU 2 GHz 32 or 64 bit architecture e Network adapter 12. vides a convenient way of managing the IUCLID 5 web application in a distributed environment To gain access to Tomcat Manager point a web browser to the address http localhost 8080 manager html 2 5 Deployment Deployment is the term used for the process of installing a web application into a web application server The web application of IUCLID 5 is published in the form of a web application archive WAR which is a file with extension war It is available from the IUCLID website http iuclid eu packaged into a file named juclid5 lt version gt _server_ lt date gt zip Download the ZIP file from the web site Unzip it and then unzip an archive within it named server zip Inside there is a file named i5server war That is the file to be deployed 2 5 1 Deployment in Tomcat Deployment of a web application into Tomcat can be done in two ways e Statically the web application is set up whilst the web application server Tomcat is not running e Dynamically one or more web applications can be managed whilst the web application server Tomcat is still running This allows IUCLID 5 to be installed on an instance of Tomcat without needing to have a break in service for any other web applications that are running on the same instance of Tomcat IUCLIDS In this installation manual only the dynamic deployment is described However the static deployment may be used instead The deployment of a web application on Tomcat is described
3. 2 2 JAVA Development Kit icsii i ucteeeeis mnnn Pivgcdaeueedcabeicadaneenel E EES EENS 3 2 3 POSIQFE SO bss souk dao a E E ERS aa thcdtagunbset tates seanetdeee 3 2 3 1 Creating the iuclidS database user cect errr eee eer eee nese een eeeeeeaieneeeeaa 4 2 3 2 Creating the iuclidS database 0 0 ccceeeee ee nner eee ae ee rere nate eres aaeeeeeeaaeeeeeeaaeeeeeaaeeeeeeaaeeeees 4 2 3 3 Set up daily backup of the database cccceccceeece cece cc eeee ce eeee ee eeceeeeeaaeeeeaeeesaeeeeaeeeeeeeesaaes 5 24 NOMGA re r a ote ae ia Sits dentaa Seated a ceaiipha sedagndsceeh A 5 2 4 1 Manual INStallation errr cass cose cays bee cash fese deus tees cash feeecens dee cauh i eacaeauveedcagh teetiuaeseeeeueh teeedeaybeeccagh ies 5 2 4 2 Memory SCUINGS 2 0 ccccceceecaeeaeeccacaneeecauaneescadeneeecaauaeeccadaneescaaaaeeseadaneeesaaaadencaganeecstaaneeneaiae 6 2 9 Deployment caisisicsseiecest csebbs ennan nn AEE dal best tadadieal aes ieee edd tested ade a eee eee 6 2 5 1 Deployment in Tomcat 0 0 rr nner rennin rete nae eeeeaaeeeeeaaeeeeeaaeeeees 6 2 6 Configuring the connection to the database cece eeee tee eee rere e titt rrtt eres eee eeee nena eeeeeeaaeneeeeaa 8 2 7 Configuring the security settings for user ACCOUNES cece cece ete eee e eet tree ee ee sete eeee nena eeeeeeaaeeeeeeaa 9 2 7 1 User account security settings defined in client properties 20 00 cece ee eeeeeeeeeeeeeeeeeneeeeeeanee
4. 5 End user Manual 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 IUCLID 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 16 IUCLIDS Note Do not click on the link Forgot your password if the First steps wizard is being run for the first time on this database This feature can work only after the wizard has been completed The use of the feature Forgot your password is explained later in this wizard at step 3 IUCLID 5 INTENNATIOWAL UNIFORM CHEMICAL INFORMATION DATADASE Please enter username and password to login local workstation Username SuperUser Password 0000 Login Cancel Forgot your password The First steps wizard then proceeds Each page of the wizard is described in a figure below Figure 4 2 Step 1 of the First steps wizard Introduction The wizard presents some useful information There a
5. 768MB RAM with 1GB RAM Administration of installed Web Start applications Start Application Manager Thu Mar 28 18 09 25 EET 2013 The page shown above page contains links that use Java Web Start technology to start a client that connects to the IUCLID 5 server and displays IUCLID 5 s graphical user interface GUI on the client machine In the example shown 15 IUCLIDS above the link under the text JUCLID 5 Client with 1GB RAM has already been followed The difference between the links in the above page is that each link passes different parameters to the IUCLID 5 server The options included are for varying amounts of memory to be allocated to IUCLID 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 downloading 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 IUCLID 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 IUCLID 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 ic
6. architec ture of your computer from the site http Awww oracle com Follow the installation instructions provided by the vendor 2 3 PostgreSQL PostgreSQL is the database management system DBMS that IUCLID 5 uses to store all data PostgreSQL is likely to be included in your Linux distribution If PostgreSQL is not already installed it is recommend ed to install the latest version using the package management system of your Linux distribution Alternatively the installation packages are available free of charge from the following site http www postgresql org IUCLIDS You do not need to download all the installation packages The required packages have a file name that starts with postgresq1 libs postgresql server or postgresql 2 3 1 Creating the iuclid5 database user During installation process a new Linux user with name postgres is created The user postgres has no password so it is not possible to log in using this user name Its purpose is to perform database administrative tasks Commands can be run as user postgres only using the command su Change the current directory and the current user as follows cd su postgres A Note By changing the user the prompt is also changed to the sign and usually bash 3 00 is displayed Now each command you type is executed as the user postgres The first thing to do is to create a database user that allows the IUCLID 5 application to connect to the database as
7. from the IUCLID Download Website Download Website otherwise this wizard will not complete successfully and you will be forced to log out Select your Legal entity file by navigating to the desired file on your computer B Please note If your Legal entity information has not already been stored on your computer you should create it on the IUCLID Select the import file D IUCLID Leox_Manual i5z w B B 8 0 8 0 8 8 FEE rm Cca Import legal entity IUCLID 5 Import of the legal entity file completed 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 IUCLID 5 until a Legal entity has been successfully imported 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 IUCLID 5 End 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 gt First steps Import EC inventory Select the EC inventory file which you previously downloaded hae The EC inventory is the catalogue of chemical substances li
8. in detail on the web page Tomcat deployment http tomcat apache org tomcat 5 5 doc deployer howto html In essence the deployment of IUCLID 5 consists of copying the archive file i 5server war into a folder within the installation of Tomcat named webapps If Tomcat is running whilst the copying is done it automatically opens the archive and copies the content into the folder webapps In addition Tomcat automatically starts the IUCLID 5 web application When IUCLID 5 is deployed in Tomcat it is shown in the list of web applications in Tomcat Manager as shown below If you are unfamiliar with Tomcat Manager see the tip above Figure 2 1 IUCLID 5 deployed in Tomcat application list in Tomcat Manager i None a specified None docs specified i5serer None specified manager 2E specified Welcome to Tomcat Tomcat Documentation IUCLID5 Server Tomcat Manager Application true true true Io In I 2 30 minutes T 2 30 minutes 2 30 minutes Stat Stop Reload Undeploy _Expire sessions with idie 30 minutes Alternatively deployment can be done using the deploy feature of the Tomcat Manager to upload a war file into Tomcat from a filesystem However before doing that the configuration of Tomcat Manager should be checked and possibly adjusted for the following reason Warnin By default Tomcat Manager places an upper limit on the size of the war file that can be uploaded The defa
9. into IUCLID 5 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 import ing 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 iuclid 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 a Linux operating system in combination with open source components 2 1 Operating system You are free to run IUCLID 5 on the Linux distribution of your choice However only the SUSE Linux distribution has been explicitly tested Keep in mind that it is good practice to install only the required software on a server The file paths shown in this document are provided as examples and as such may differ from the values required in the actual installation 2 1 1 Opening the network port for IUCLID 5 server In order of establish the connection from the
10. not run the migration tool on that particular database Either perform a fresh installation of the new version of IUCLID 5 and transfer the data across to it using Backup Restore or perform the upgrade and migration on a duplicate of the old database If two versions of IUCLID 5 are to be run on the same computer appropriate database settings must be used to avoid conflicts Do not run two distributed versions of IUCLID 5 at the same time on the same computer There are various different ways to manage a Tomcat web application server as referred to in the section of this manual Deployment of IUCLID 5 The following instructions are intended to give a representative example of how the IUCLID 5 software can be upgraded and the data migrated from IUCLID 5 4 x to IUCLID 5 5 1 Back up the database Use the built in back up functionality of IUCLID 5 and or the back up function of the data base software for example PostgreSQL The built in backup feature is accessible by only the user SuperUser from the menu File Administrative tools Backup 2 Close all clients for IUCLID 5 3 Use the application Tomcat Manager to stop the IUCLID 5 web application 4 Copy the configuration file for IUCLID 5 server properties into a backup folder The existing plugins are compatible with IUCLID 5 5 so they can be retained for the new installation Alternatively obtain the latest versions from the IUCLID web site For example copy TOMCAT webapps i
11. shown below The name of the user is usually iuclid5 Enter a password enter it again and then answer no to all the subsequent questions To answer no enter n and then press the enter key A Note Remember the password you give for the user iuclid5 because you will need it later createuser EP iuclid5 Enter 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 ROLE 2 3 2 Creating the iuclid5 database Create a new database specifying the owner encoding and the name of the database createdb owner iuclid5 encoding UTF 8 iuclid550 CREATE DATABASE Once the database preparation tasks are completed change back to the root user exit For security reasons by default database users are not allowed to connect to the database even if they provide the correct password However PostgreSQL can be configured to allow such a connection as described below Open the configuration file using a text editor for example nano IUCLIDS juclid5 nano var lib pgsql data pg_hba conf PostgreSQL Client Authentication Configuration File Move the cursor to the end of the file using the down arrow button until the line Pv4 local connections IPv4 local connections host all all 127 0 0 1 32 ident sameuser Insert a new line just after the
12. 00 Mbps recommended 1Gbps 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 The software prerequisites for the installation are as follows e Java Runtime Environment JRE or Java Software Development Kit SDK version 7 IUCLID 5 5 0 is compatible with Java 6 but the vendor Oracle recommends to uninstall Java SE 6 and then to install the latest update of Java 7 Various scenarios involving the use of IUCLID 5 Java 6 and Java 7 can be found in the IUCLID FAQ located at the IUCLID web site http iuclid eu e PostgreSQL 8 4 and 9 0 are supported but 9 0 is recommended IUCLIDS Tomcat 5 5 or 6 0 e The IUCLID 5 manual workstation installation package version 5 5 can be downloaded without charge from the IUCLID 5 web site e Once you have completed the installation of IUCLID 5 you should test it by starting and configuring it The con figuration requires access to at least a legal entity file LEOX The creation of a LEOX is described on the IUCLID web site where the 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 Q Time and IT resources can be saved by importing
13. 2 4 1 Manual installation Distribution independent packages can be downloaded from the Tomcat website http tomcat apache org The file to download is for example apache tomcat 5 5 26 tar gz IUCLIDS The installation of Tomcat is extracting a set of files and setting up the starting parameters Extract the downloaded archive into the directory opt use the version number of your downloaded Tomcat juclid5 tar xzf apache tomcat 5 5 26 tar gz C opt jiuclid5 It is convenient to create a version independent symbolic link pointing to the actual tomcat directory It will be used to find the location of Tomcat whichever version is installed jiuclid5 In s apache tomcat 5 5 26 opt apache tomcat jiuclid5 P ki Tomcat contains some example applications that are not needed You can delete them in order to save resources Do not delete the ROOT directory For more information visit the Tomcat website http tomcat apache org 2 4 2 Memory settings O Important IUCLID 5 requires at least 512 MB RAM to be allocated to Tomcat Check the amount of memory allocated on the server status page of the Tomcat Manager application The parameter Max Memory under JVM should show a value of at least 512 MB P Tomcat Manager Tomcat Manager is a web application supplied along with Tomcat that provides a means of dynamically managing web applications without having to shutdown the Tomcat web application server itself It pro
14. 5server WEB INF classes server properties to e backup server properties Use the application Tomcat Manager to undeploy the old verion of the IUCLID 5 web application Use the application Tomcat Manager to deploy the new version of the IUCLID 5 web application Stop Tomcat oOo N ODO A Copy any values that are specific to your system from the previous version of the file server properties to that supplied with the new version of IUCLID 5 Ensure that the new values for the database connection are those for the database of the system to be upgraded Remember to transfer over any settings that relate to security 12 IUCLIDS 9 Note that if the Oracle database is used the file server properties must contain the following entry Add it or edit the existing entry if required hibernate connection driver_class oracle jdbc OracleDriver 101f the database is an Oracle database please note that the driver for Java is no longer supplied with the IUCLID 5 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 Oracle 11g Release 2 11 2 0 2 0 the name of the driver is ojdbc6 jar 11 Copy any required plugins over from the old installation to the new one Alternatively obtain the latest versions from the IUCLID web site 12A migration process is required to upgrade to IUCLID 5 5 0 The d
15. IUCLID 5 Guidance and Support Installation Guide for IUCLID 5 5 Client Server Architecture Linux IUUCLIDS INTERNATIONAL UNIFORM CHEMICAL INFORMATION DATABASE March 2013 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 iuclid 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 gea UCU ON tay sate chee E Shee dail pcuatyae ch calves bs oo a eal daas fa Sede chess Pietagans av a edd Aes ae 1 1 1 Hardware requirement ccccecc cece ce eeee eee eee cece cece ae ee caeeee se eeecae essa eeeeaeeeeaeeesaeeeeseeeesaeeesaeeesseeesaaees 1 1 2 SoftWare requirements ccisiciees bis cicescid cade bovaeneecaeecaradsanenceessa sade NAE E AAAA AOA enfeieud dees debe EAA AE 1 2 Making a fresh installation of IUCLID 5 ooo eee EEEE ee eeaaeeeeeaaaeeeeeaaeeeeesaaeees 3 2 1 Operating SYSTEM sa ediscasedes cask bis eaes cbes ENEN ANEC dees geak EEEREN cau beanaewed Yes EEEE feds coes pies aaah EERUEO EEREN aaah beabes 3 2 1 1 Opening the network port for IUCLID 5 Server cccccececceeceeeeeeeeeeecaeeee ce eeeeeeeeaeeeeeaeeesaeeeeaes 3
16. Pv4 local connections and type host iuclid5 iuclid5 127 0 0 1 32 md5 This line tells PostgreSQL that iuclid5 user is allowed to connect to iuclid550 database from the local computer using the encrypted password authentication IPv4 local connections host juclid550 juclid5 127 0 0 1 32 md5 host all all 127 0 0 1 32 ident sameuser Press CONTROL X to exit from the editor type y to save the file and confirm the file name by pressing the enter key Save modified buffer ANSWERING No WILL DESTROY CHANGES y Y Yes N No AC Cancel File Name to write var lib pgsql data pg_hba conf AG Get Help M D DOS Format M A Append M B Backup File AT To Files M O Mac Format M P Prepend AC Cancel Restart PostgreSQL to load the new configuration Your iuclid5 database is now ready to serve the IUCLID 5 application For more information about installing PostgreSQL and administer the server look for the http www postgresql org docs documentation page 2 3 3 Set up daily backup of the database The data you store into IUCLID 5 might be very important for your organisation A user may accidentally delete valuable data or a system failure could cause loss of data To prevent this situation and prepare a smooth recovery it is vital to schedule a daily backup 2 4 Tomcat The preferred way to install Tomcat is by using the package manager of your operating system The required version is 5 5 x or 6 0 x where x is the highest available number
17. UCLID 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 End user Manual 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 name 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 Optionally select default attachment and import export directories These settings can be changed at a later stage as described in the IUCLID 5 End user Manual 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 SuperUser is not supported r First steps Start import procedure Confirm the start o
18. access gt Administrator Read only 3 p Set password Set the password of Assigned legal entities Local Administrator Example last login Never from Nowhere 55 4 wb Ey i LEO for Manual Helsinki Finl New password Confirm new password 9 Generate Attachments directory eaj Import export directory g 8 B H 8 8 8 8 8 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 Ful name used for proper user identification e Click Set password to define a password Tip IUCLID 5 has a feature that can check the strength of passwords If the feature is turned on and the password you enter is considered to be too weak an error message is displayed that explains what a password must contain If that happens read the error message carefully then create a password that satisfies the criteria For example the default settings require the password to be at least 6 char acters in length and to contain
19. anager Context Path required XML Configuration file URL WAR or Directory URL Deploy Select WAR file to upload server iSserver_war Browse to the file iS5server war select it and then click the button Open Click on the lower of the buttons labelled Deploy Check that IUCLID 5 appears within the list of web applications Tomcat Manager can be used to stop and start the IUCLID 5 web application On the application list page there are stop and start buttons for each web application currently deployed This feature is useful for carrying out any maintenance that must be done whilst IUCLID 5 is stopped An example is the editing of settings for the connection to the database 2 6 Configuring the connection to the database The configuration of the connection from the IUCLID web application to its database is defined in the file server properties that is located in the folder webapps i5server WEB INF classes The default values are for an instance of the PostgreSQL database running on the same computer as the web application server with the values of the database name the database username and the password of that user all set to juclid5 If that configuration is used on starting the IUCLID 5 web application it will connect to the database without the need to make any changes to the configuration file If other values are required they must be entered into the file server properties Before editing the configuration file ens
20. any changes made during the installation process For more details about the actions that might be required see the IUCLID FAQ located at the IUCLID web site http iuclid eu 25
21. as before the upgrade The initialisation process is not required All of the data that was present before the upgrade should be present in the new system Therefore it should be possible to log in to any of the user accounts that were present prior to the upgrade 18Log in to the IUCLID 5 client as one of the users that was present before the upgrade 19Confirm that the version of IUCLID 5 is the new expected version This can be seen from the menu Help About 20Confirm that the data from the previous version has been successfully migrated to the new version 3 2 Upgrading from IUCLID 5 2 x 5 3 x to IUCLID 5 5 0 To upgrade from IUCLID versions 5 2 x or 5 3 x unless the database contains a very large amount of data it is recommended to use the Backup and Restore features of IUCLID 5 to transfer the data from the old installation to a fresh installation of IUCLID 5 5 0 The Backup and Restore features are described in the IUCLID 5 End User Manual Making a fresh installation is described in this manual Warning The built in Backup functionality of IUCLID 5 3 1 is known to output files in which the user accounts cannot be used on restore If you wish to use the built in Backup functionality on data in an installation of IUCLID 5 3 1 first upgrade it to IUCLID 5 3 2 The built in Backup functionality in IUCLID 5 3 2 does not suffer from this problem As an alternative to using Backup and Restore into a fresh installation it is possible to p
22. at least one uppercase letter and one lowercase letter The policy for the SuperUser is the same as that for all users The password policy is set by editing a settings file 22 IUCLIDS within the installation files of IUCLID 5 This is documented in the relevant installation manual for your instance of IUCLID 5 Existing passwords can still be used to log in even if they do not conform to the current policy When a password is created it must conform to the current password policy Y 2 If you want a use once password that is reasonably hard to guess and that definitely conforms to the password policy you can let IUCLID 5 make one for you by clicking on the button Generate It will be displayed in a new window for you to make a record of it On closing that window it will be automatically entered into the fields New password and Confirm new password Ticking the box Expire password upon next login forces whoever logs in to the account first to set their own password 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 Y k 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 I
23. atabase and all the data it contains are migrated from the previous to the new version by running IUCLID 5 in update mode only once IUCLID 5 is instructed to start in update mode by the line shown below in the file server properties database update startup true The line is supplied although commented out in the file server properties in the installation package for the new version of IUCLID 5 To run in update mode the line must be either uncommented or added as shown above 13 To begin the migration start Tomcat This automatically starts the new version of the IUCLID 5 web application Dependent on the quantity of data in the database and the system resources available the migration process can take from minutes to many hours It is essential that the migration process is not interrupted The progress of the migration can be monitored from the log files iSserver log and iuclidMT 1log The default location of these files is on the top level directory of the Tomcat installation The file iSserver 1log contains statements about the start and end of the migration process The file 1uc1idMT 10g contains full details If you need to know what happened during the migration process check those files first At the start of the process the following entry is shown integration database scripts ScriptUtils Checking Database Status Ceu eca iuclid server integration database scripts migrate_schemav51_to_schemav55 xml integration data
24. base scripts ScriptUtils Upgrading table integration database scripts Scriptutils Je she ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale ale KKK RRR RR RR KKK Database changes are being applied now This process might depending on the size of your database take some time several minutes to perhaps hours Please do NOT shutdown the system as this might result in an inconsistent database state As the migration proceeds details of which data are being migrated are written to iuclidMT 1log The end of a successful migration is indicated by the following entry integration database scripts ScriptUtils Database update successfully finished integration database scripts ScriptUtils Checking Database Status Ceu eca iuclid server integration database scripts migrate_schemav51_patch xml integration database scripts ScriptUtils Upgrading table integration database scripts ScriptUtils Database is up to date 13 IUCLIDS If the migration is interrupted or fails for whatever reason the database must be restored from the back up and the migration started again 14When the migration finishes successfully stop the new version of the IUCLID 5 web application by stopping Tomcat 15Set IUCLID 5 to start not in its update mode by commenting out the line edited previously database update startup true 16Start Tomcat 17 Run the IUCLID 5 client in the same way
25. ce 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 5 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 hitp lt address of your server gt 8080 i5server An example of the page displayed is shown below Figure 4 1 Example default page for Java Web Start of IUCLID 5 IUCLID 5 Welcome to the IUCLID 5 Server IUCLID 5 Version IUCLID5 release 5 5 0 IUCLIDS PUCLIDS retease 5 5 0 buid of 2013 03 28T14 00 23Z Install IUCLID 5 Client Component The server does not feature an interactive web frontend In order to connect to the IUCLID5 database please install the client application locally via the link below This installation vall use the Java Web Start technology which depends on an installed Java Runtime Environment JRE If 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
26. e a long time The import of the Reference substance inventory itself can take up to several hours E First steps Import reference substance inventory Select a reference substance inventory to import into IUCLID 5 hae 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 If 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 v Import reference substance inventory Select the import file D IUCLID ReferenceSubstance i5z bs g B B B lt Back Next gt Cancel Reference substance inventory import Tip Time and IT resources can be saved by importing into IUCLID 5 only the Reference substances you need Various different sizes
27. erform step wise upgrades in which the database is migrated from IUCLID 5 2 x 5 3 x to 5 4 x to 5 5 0 For example this method might be required if the amount of data is so large that it makes use of the Backup feature impractical If you choose the migration method obtain the installation packages to perform the required upgrades and then proceed as per the instructions included therein Note that the plugins for IUCLID 5 2 x 5 3 x are not compatible with IUCLID 5 5 Therefore they must not be copied over to the new installation Compatible versions can be downloaded from the IUCLID web site 3 3 Upgrading from IUCLID 5 0 5 1 x to IUCLID 5 5 0 To upgrade from 5 0 5 1 x no migration process is available and so the method of using Backup then Restore into a fresh installation must be used In IUCLID 5 0 5 1 x there is no built in Backup function Instead the functionality is provided by a plugin Backup Plug in 5 0 3 that is available on the IUCLID web site under downloads for IUCLID 5 1 1 14 IUCLIDS Chapter 4 Initialisation of an installation of IUCLID 5 This chapter describes the configuration that is required to create a working IUCLID 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 5 During initialisation from scratch reference substan
28. etter The policy for the SuperUser is the same as that for all users The password policy is set by editing a settings file within the installation files of UCLID 5 This is documented in the relevant installation manual for your instance of IUCLID 5 Existing passwords can still be used to log in even if they do not conform to the current policy When a password is created it must conform to the current password policy Q IUCLID 5 has a feature that allows a user to log in by answering a security question instead of providing the password for the account Users define their own questions and answers from within their own accounts However the SuperUser is a special case because the question and answer can be defined before logging in for the first time The question and answer are entered into the fields shown above in step 3 of the wizard To use the feature to log in a user clicks on the link Forgot your password which is situated at the bottom right of the login page 19 IUCLIDS Figure 4 7 Step 4 of the First steps wizard Import Legal Entity To import a Legal entity see the IUCLID 5 End 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 E First steps Import legal entity In order to run IUCLID 5 you have to import your Legal entity obtained
29. f the import procedure de 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 on the size of the import files It may take a considerable amount of time p B B p g p p A lt Back Finish Cancel Activate imports 23 IUCLIDS 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 IUCLID 5 End user Manual Individual users can connect to the IUCLID 5 server using Java Web Start technology as described in Section 4 1 Starting IUCLID 5 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 8080 i5server and instructions on which link to use 24 IUCLIDS Chapter 5 Un installation of IUCLID 5 The un installation of IUCLID 5 is a manual process IUCLID 5 can be un installed by deleting the files that were copied to the destination machine and reversing
30. ined by trial and error The value is the maximum number of successive unsuccessful attempts there can be to log in to an account before it is suspended 2 7 2 4 Maximum number of attempts to answer the security question This feature is used to prevent the security question from being answered by trial and error The value is the maximum number of successive unsuccessful attempts there can be to answer the security question before the account is suspended 11 IUCLIDS Chapter 3 Upgrade This document describes the process of obtaining an installation of IUCLID 5 5 0 that contains all the data from a previous version The details of how to proceed depend on the version being upgraded There is a chapter specific to each scenario To see the current version of IUCLID 5 log in to the application then click Help and select About Before starting the upgrade it is important to backup the database Use the built in Backup functionality of IUCLID 5 and or the backup functionality of the database Making only a copy of the file system on which IUCLID 5 is installed is not recommended as a means of backing up 3 1 Upgrade and migration of data from IUCLID 5 4 x to IUCLID 5 5 0 0 Important The migration process changes the IUCLID 5 database such that it can no longer be used with previous versions of the IUCLID 5 application Therefore if you would like to be able to continue to use a database with the previous version of IUCLID 5 do
31. lation Restore from backup a 8 5 5 8 5 a 8 PES Cites Init mode 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 p First steps Define the initialisation mode Initialisation mode Newinstallation Restore from backup Location to restore from D IUCLID backup 8 B 8 f8 8 B f 8 lt Back Next gt Cancel 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 backup Step 8 Activate imports lt First steps Start import procedure Confirm the start of the import procedure dab 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 a a a 0 6 08 0 0 ee Activate imports The import may take some time Click Finish When the restoration is complete the following screen is shown Background job ended x Restore completed successfully C 18 IUCLIDS Fig
32. mum password length This feature is used to prevent the use of overly weak passwords for user accounts The password of a user account must contain at least this number of characters If an attempt is made to create a password with fewer characters an informative error message is given and the user is presented with an opportunity to try again The security policy is applied to passwords only when they are created Therefore if the minimum length of passwords is increased users can still log in using existing passwords even if they are now considered to be too short The IUCLIDS user manager can force a user to create a new password by ticking a box for the account in the IUCLID 5 client The user is then required to create a new password when they next log in 2 7 1 2 Minimum number of character sets in passwords This feature is used to prevent the use of overly weak passwords for user accounts The password of a user account must contain at least one character from all the character sets The value is an integer from 1 to 4 A value of 1 means only character set 1 a value of 2 means both character sets 1 and 2 etc The four character sets are 1 a lowercase letter a z 2 an uppercase letter A Z 3 a digit 0 9 4 a non alphanumeric symbol amp _ For example if the value is 3 a password of AdkbScfw is rejected for being too weak but AdkbSc37 is accepted because it contains at least one character from
33. 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 21 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 p First steps Create user account and assign role It is recommended to create a user account before running IUCLID 5 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 v Create user Login name Local Administrator Full name Example Password Set password Expire password upon next login Unassigned roles Assigned roles 3 3 Full
34. on that comes with the installation Double clicking on the icon then launches the IUCLID 5 GUI Once you see the login page you are ready to go through the First steps wizard as described in the next section 4 2 First steps wizard When you start IUCLID 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 IUCLID 5 End user Manual a Important 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 IUCLID 5 End 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 End user Manual The First steps wizard provides the option of uploading the following information to your IUCLID 5 instal lation For details see the IUCLID
35. ration as described in Section 2 7 Configuring the security settings for user accounts and Sec tion 4 1 Starting IUCLID 5 2 7 Configuring the security settings for user ac counts IUCLID 5 has features designed to control the level of security of authentication of user accounts The level of security can be tailored to that required for the particular instance of IUCLID 5 For example when setting passwords for their user accounts users can be forced to enter values that have a minimum strength The values of the parameters that determine the level of security are defined in two settings files server properties and client properties both of which are located in the folder webapps 7i 5server WEB INF classes Changes to values take effect on restarting the server software of IUCLID 5 The security features are described below grouped together by settings file 2 7 1 User account security settings defined in client properties The settings are shown below as they appear in the settings file that is supplied with the installation of IUCLID 5 The values are shown set to the hard coded defaults If a line is commented out the default value is used A value of zero 0 disables a feature The minimum length for a new password password min length 6 The minimum number of character sets used in the password password min charsets 2 If a secure question system is enabled password use secure question true 2 7 1 1 Mini
36. re no actions other than to read the information Click the Next button 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 5 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 a a a 0 8 0 0 8 Introduction 17 IUCLIDS Figure 4 3 Step 2 of the First steps wizard Init mode New installation To initialise a new database select the button New Instal lationas shown below and continue to the next step ee gt First steps Define the initialisation mode initialisation mode Newinstal
37. s 9 2 7 2 User account security settings defined in server properties 0 cc eeeeeceeeeeeeenneeeeeeaaeeeeeeaaeeees 10 3 Upgrade secarei ieina k EENE advances EE ai DANETAN ENTAR RO AEON EAEE EET bed AETERNA EAEN ERTEN 12 3 1 Upgrade and migration of data from IUCLID 5 4 x to IUCLID 5 5 0 siisessersssrreessrrerssrrrrsrrrresenne 12 3 2 Upgrading from IUCLID 5 2 x 5 3 x to IUCLID 5 5 0 ooersiriiiiicnriniiniceniktnn diie iN ENEE 14 3 3 Upgrading from IUCLID 5 0 5 1 x to IUCLID 5 5 0 ooo nee eeee ee ereeeeaeeeeeeea 14 4 Initialisation of an installation of IUCLID 5 oo i terre aan reer aaneeeeeaaeeeeeeaaeeeeeeaaeeeees 15 471 Starting JUCEID 2S saasaa atanena aaia naaa E anesthe aaadees ausdind wi sabessandease i EEEE AaS 15 4 2 First Steps Wizard sinesmenei ece cecedccke hace guuacdie a feldaaee lad aedaeldeads bide cade aaae 16 4 3 User management 4 2 ceenatec saps cccas ate adevags de cndephadac abe atcha adehacaags EENAA EAEE NAERAA ETEEN EAEAN 24 5 Un installation of IUCLID S secssic ia vocestevciek tae vaca ties iden ini get Ales cent aaes cack dah Wawa REE REEE ERRAT each a EEEE 25 IUCLIDS Chapter 1 Introduction IUCLID 5 has two different installation architectures Standalone installation The IUCLID 5 application connects directly to the database which usually resides on the same computer Using this installation only one user can work simultaneously on the same database Distributed installation
38. sets 1 2 and 3 If an attempt is made to create a password that does not comply an informative error message is given and the user is presented with an opportunity to try again The security policy is applied to passwords only when they are created Therefore if the minimum number of character sets allowed within passwords is increased users can still log in using existing passwords even if they are now considered to contain too few character sets The user manager can force a user to create a new password by ticking a box for the account in the IUCLID 5 client The user is then required to create a new password when they next log in 2 7 1 3 Security question This feature is designed to allow an alternative method of user authentication to the user name password combi nation It can help to reduce the resources required for user management by preventing account blocking due to forgotten passwords Each user can define their own security question and a secret answer This is done from the graphical user interface of the client after the user has logged in A user can log in by answering their question correctly instead of supplying the password The question is answered via a link on the log in page Forgot your password The feature is turned on or off for the whole instance of IUCLID 5 using a value of true or false 2 7 2 User account security settings defined in server properties The settings are shown below as they appear in the se
39. sted on the European Inventory of Existing Commercial chemical Substances 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 If 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 v Import EC inventory Select the import file D IUCLID ECinventory_1 1_en i5z E B 5 f 8 3 f 8 lt Back Next gt Cancel EC inventory import 20 IUCLIDS 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 IUCLID 5 End 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 tak
40. ttings file that is supplied with the installation of IUCLID 5 The values are shown set to the hard coded defaults If a line is commented out the default value is used A value of zero 0 disables a feature A suspended account can be un suspended by a user with user management rights Account expiry in days A value of zero 0 disables the feature account expi ry 180 Password expiry in days Zero 0 disables the feature password expiry 90 Max number of attempts before the account is disabled Zero 0 disables the feature max failed login attempts 3 Max number of attempts to answer the reset question max failed answer attempts 3 2 7 2 1 Account expiry period This feature is used to automatically suspend an account that has not been used for a long time If the period between two successive successful log in attempts exceeds the value the account is suspended 2 7 2 2 Password expiry period This feature is used to prevent users from using the same password for long periods It defines the life span of a password After the password has been in use for the period the user is prompted to change the password when 10 IUCLIDS they next log in The period is counted from the time of first logging in to the account then after that from the time of changing the password 2 7 2 3 Maximum number of attempts to log in This feature is used to prevent the combination of user name and password from being obta
41. ult value of the limit is smaller than the size of the file 1uclid war If the size limit is exceeded the following error is given The server encountered an internal error that prevented it from fulfilling this request Excep tion java lang llegalStateException org apache tomcat util http fileupload FileUploadBase SizeLimi tExceededException the request was rejected because its size XXX exceeds the configured maximum 52428800 The solution is to increase the size of the limit by increasing the values of the parameters max file size and max request size in the settings file tomcat7 webapps manager WEB INF web xml to values that are larger than that they exceed the size of the war file The default values are shown below lt multipart config gt lt 50MB max gt lt max file size gt 52428800 lt max file size gt lt max request size gt 52428800 lt max request size gt lt fi le size threshold gt 0 lt fi le size threshold gt lt multipart config gt IUCLIDS An example of the new values required for IUCLID 5 5 0 is shown below lt max fi 1e size gt 100000000 lt max fi le size gt lt max request size gt 100000000 lt max request size gt Once you are sure that the file size limit is large enough in Tomcat Manager click on the button Browse that is under the lower of the two options deploy options WAR file to deploy as shown below Figure 2 2 Deploy IUCLID 5 in Tomcat upload using Tomcat M
42. ure 4 6 Step 3 of the First steps wizard Change password If the password for SuperUser has never been changed from its default value of root the traffic light in the wizard screen will be yellow To change the password check the box Change SuperUser password enter the current password and then the new password and then the new password again To proceed click the button Next gt First steps Change the SuperUser password For security reasons it is recommended to change the SuperUser s password and specify a security question p It is not secure as it is now M Change SuperUser password Old password New password Confirm new password Question Answer 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 B B B B B B B lt Back Next gt Change password Q IUCLID 5 has a feature that can check the strength of passwords If the feature is turned on and the password you enter is considered to be too weak an error message is displayed that explains what a password must contain If that happens read the error message carefully then create a password that satisfies the criteria For example the default settings require the password to be at least 6 characters in length and to contain at least one uppercase letter and one lowercase l
43. ure that no clients are connected to the IUCLID 5 web application and then stop the application using Tomcat Manager The default configuration for PostgreSQL is shown below Settings for using PostgreSQL hibernate connection url jdbc postgresql localhost 5432 iuclid550 hibernate connection username iuclid5 hibernate connection password iuclid5 hibernate connection driver_class org postgresql Driver hibernate dialect org hibernate dialect PostgreSQLDialect For example if the PostgreSQL database server s name is dbserver it is accepting connections on port 12345 the database name is chemdb with a database user named joe with a password xxxx the configuration is IUCLIDS hibernate connection url jdbc postgresql dbserver 12345 chemdb hibernate connection username joe hibernate connection password xxxx O Important Make sure that there are no spaces after the username and password values in the properties file After editing the configuration file start the IUCLID 5 web application server using Tomcat Manager The IUCLID 5 server records its activities in a log file The configuration file for the logging is i5server logging properties which is located in the folder WEB INF classes If you encounter any errors that you cannot explain consult the content of the log file If you are following this manual to perform a fresh installation all the software has now been installed What remains is some configu
44. workstation computer to the server the server s firewall must be con figured to allow the IUCLID 5 server to accept connections on port 8080 It is not recommended to completely disable the firewall In CentOS for example the system config secu ritylevel tui tool allows you to easily modify the firewall settings On other Linux distributions please refer to the documentation of the operating system system config securitylevel tui Be cautious You should not trust any network interface In the Allow incoming section set SSH secure shell and 8080 port For security reasons do not allow any other traffic such as telnet http or ftp Before you start the installation procedure you have to download the required components for IUCLID 5 In order to select the correct files you should know the architecture platform of your server computer Please consult the user manual of your computer If the Linux operating system is already installed write the following command The command will write the platform s name on the screen for example 7386 uname 1 1386 2 2 JAVA Development Kit The simplest way to install Java is using the package manager of your operating system In this way you do not need to download Java manually In case no appropriate Java runtime environment is available in the package manager download the JAVA Develop ment Kit JDK 7 or JAVA Runtime Environment JRE 7 according to the operating system distribution and
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