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IUCLID 5 Guidance and Support

1. Database connection settings for Oracle The details of the installation and configuration of Oracle database software DBMS are out of the scope of this document due to their complexity Please refer to the documentation supplied by Oracle The details of how to set up the database for IUCLID 5 are given in this section System administrator rights for the database are required If you have a database manager DBA for Oracle at your organisation ask the DBA to carry out the actions described in the rest of this section Create a user account with the following system privileges CREATE SESSION CREATE SEQUENCE CREATE TABLE CREATE VIEW The account needs to have a default tablespace with unlimited quota and autoextend set to ON The block size of the tablespace is recommended to be at least 16K to avoid the error ORA 01450 maximum key length exceeded The character set must be set using NLS_CHARACTERSET AL 32UTF8 An example of the commands required is given below CREATE tablespace jiuclid5_ts datafile iuclid5_ts dbf specify absolute path size 500M autoextend ON next 500M maxsize 2000M grant CREATE session TO iuclid5 identified BY iuclid5 grant CREATE TABLE TO 1uclid5 grant CREATE VIEW TO 1uclid5 grant CREATE sequence TO 1uclid5 ALTER USER i1uclid5 quota unlimited ON 1uclid5_ts ALTER USER 1uclid5 DEFAULT tablespace 1uclid5_ts Ensure that the IUCLID 5 database user 1ucl1d5 has been granted only the privileges
2. Attachments directory Import export directory _B B_5_B B_bB_ _68 lt Back Next gt Finis Cancel Create User Select the checkbox Create user Page 42 of 45 IUCLIDS 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 Click Set password to define a password Vv Y 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 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 within the installation files of IUCLID 5 This is documented in the relevant installation manual for your instance of IUCLID 5 Existing passwords ca
3. Ensure that the new values for Page 30 of 45 10 11 12 13 14 15 16 17 18 IUCLIDS the database connection are those for the database of the system to be upgraded Remember to transfer over any settings that relate to security 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 If the database is an Oracle database please note that the driver for Java is no longer supplied with the IU CLID 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 Install any required plug ins using the latest versions from the IUCLID web site A separate migration process is not required to upgrade to IUCLID 5 6 0 2 Changes required in the database are applied automatically when the application is first run Use the application Tomcat Manager to start the IUCLID 5 web application Run the IUCLID 5 client in the same way 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
4. 45 IUCLIDS Figure 2 35 Deploy IUCLID 5 in Tomcat upload using Tomcat Manager Context Path required AML Configuration file URL WAR or Directory URL Browse Select WAR file to upload server isserver war Browse to the file 15server 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 applications D Warning STOP IUCLID 5 must be stopped and started for changes to the server settings to take effect for example to change the settings for the connection to the database Even though Tomcat Manager can be used to stop and start only the IUCLID 5 application it is currently recommended that that is done only by stopping and starting the whole Tomcat service in Windows 2 5 3 Undeployment in Tomcat uninstall and upgrade The IUCLID 5 application is undeployed if it is to be uninstalled or upgraded Tomcat Manager is particularly useful when it comes to upgrading IUCLID 5 because it provides a reliable method of undeploying removing the previous version and deploying the new version even where both archive files have the same name In addition this can be done without shutting down Tomcat To undeploy the IUCLID 5 web application using Tomcat Manager in the application listing click the button stop for IUCLID 5 When the value in the column Running is shown as false click the button Undeploy The IUCLID 5 web appl
5. Choose the folder in which to install Apache Tomcat Setup will install Apache Tomcat in the following folder To install in a different folder dick Browse and select another folder Click Install to start the installation Destination Folder ache Software Foundation Tomcat 7 0 Space required 11 3MB Space available 5 7GB Choose the installation folder The default is shown in the screenshot above To perform the actual installation click on the button Install Page 18 of 45 IUCLIDS Figure 2 27 Installing F esgau a pr a a eee EF Ag E b F i Installing Please wait while Apache Tomcat is being installed Extract fs admin opers html Nullsoft Install System v2 46 Figure 2 28 Completing the Apache Tomcat Setup Wizard l ois a a Fl Apacn OMecadt 3 CUp o EEE Completing the Apache Tomcat Setup Wizard Apache Tomcat has been installed on your computer Click Finish to dose this wizard Show Readme http tomcat apache org Apache Tomcat Cancel The next step is to configure Tomcat When the installation process has finished a new icon Dy appears in the Windows system tray located at the bottom right corner of the screen This is Tomcat s dedicated service manager Right clicking on the icon displays a menu from which the Tomcat service can be started stopped and configured as shown in the screenshot below B
6. E EA A A E A ones 29 3 1 Upgrade from IUCLID 5 6 0 or IUCLID 5 6 0 1 to IUCLID 5 6 0 2 00 cec cence eee eeeeeeneeeeneeeees 29 3 2 Upgrade trom IUCLID 5 5X to IUCLID 5 6102 siicsccssvssaistinas ea aA a A AAEE ERREA 30 3 3 Upgrade and migration of data from IUCLID 5 4 x to IUCLID 5 6 0 2 cece cence ee ee eee eeeeeeees 31 3 4 Upgrading from IUCLID 5 2 x 5 3 x to IUCLID 5 6 0 2 0 ccc cece eee ee eee eee ea eeeea sense eeeeaeaeeeeneeeeas 33 3 5 Upgrading from IUCLID 5 0 5 1 x to IUCLID 5 6 0 2 oo cccec ccc ee eee ee eee eeeeeeeeeaeeeeeeeeeeeaeeeeaeeeeas 34 4 Initialisation of an installation Of JUCLID 5 oo cece cece cece cent renee eee ee esate eee eaeeeeeeseeaeseeeaeeeeaeeeegenees 35 4 1 Starting the MWCLID 5 CHEE siiinc csawicanusaanmenudaanbdenanusndedacwabdnadaeciwaemesnubBiapaseandaiusdee bawaddneweiessenblewanoardatast 35 A 2 TIES SUS WIZ ANG escenes cinders siot sein E E ane nese aan e a AATE nese 36 4 3 User management lt csccrninanenicasuneupntabnetasadeuneemsuanudiuaanannniubneiaciinenaantaaenadiuamnbunadahneiiGedesosamtnmeeiGeaameinn 44 5 Uminstalaton of TUCCI S sssri ka ra a e Re E E AAE E S 45 IUCLIDS Chapter 1 Introduction IUCLID 5 can be installed either as a standalone application or in a distributed multi user environment using client server architecture This document describes how to install and configure the IUCLID 5 application as a server in a distributed Microsoft Windows environment he
7. 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 e 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 e Click the Next button Page 43 of 45 IUCLIDS 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 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 Note the duration of this import process depends onthe size
8. 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 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 ta impart the EC inventory at a later stage using the import function from the IUCLID 5 Task panel Import EC inventory Select the import file D IUCLID ECinventory_1 1_en iSz C e a o a S a a E d 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 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 take a long time The import of the Reference substance inventory itself can take up to several hours
9. completed the installation of IUCLID 5 you should test it by starting and configuring it The config uration requires access to a legal entity file LEOX The creation of a LEOX is described on the IUCLID 5 web site where the installation software is published In addition it is recommended to upload a set of reference substances and the EC inventory which are also available from the web site http iuclid eu Vv 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 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 e To start the IUCLID 5 client as described in section Section 4 1 Starting the IUCLID 5 client a web browser is required There are no specific requirements for the browser or the computer upon which it is run For more information regarding system requirements see the FAQ on the IUCLID web site located at http iuclid eu Page 2 of 45 IUCLIDS Chapter 2 Making a fresh installation of IUCLID 5 The follow
10. defined in two settings files server properties and client properties both of which are located in the folder webapps 15server WEB INF c lasses Changes to values take effect on restarting the IUCLID 5 application on the server side 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 questi1on true 2 1 1 1 Minimum 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 Th
11. editing a settings file 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 Tip 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 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 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 Please note If your Legal entity information has not already been stored on your comp
12. of the import files It may take a considerable amount of time 2_ B 5 B 6 e B _ 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 document IUCLID 5 End 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 8080 i5server and instructions on which link to use Page 44 of 45 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 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 Page 45 of 45
13. prior to the upgrade Log in to the IUCLID 5 client as one of the users that was present before the upgrade Confirm that the version of IUCLID 5 is the new expected version This can be seen from the menu Help About Confirm that the data from the previous version is accessible in the new version 3 3 Upgrade and migration of data from IUCLID 5 4 x to IUCLID 5 6 0 2 Important Q 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 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 more than one version of IUCLID 5 and its database are to be maintained and made available on the same machine run only one at a time and use appropriate database settings to avoid conflicts Do not run more than one instance of IUCLID 5 at the same time in the same application server 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 migrate
14. shown in the commands shown above Do not grant the privileges of SELECT ANY TABLE a role DBA or direct SELECT to the secondary iuclid5 database user tables If the user 1uc11d5 has excess privileges revoke them by for example by using one or both of the following commands REVOKE CREATE SESSION FROM 1ucl1d5 REVOKE SELECT ANY TABLE FROM 1ucl1d5 The first denies access to the database whereas the second denies access to the tables 2 5 Application Server Tomcat Running IUCLID 5 in an application server allows multiple users to access a database at the same time over a network Each user accesses IUCLID 5 via a client that is run on a local machine Alternative application servers to Tomcat might work but they are not supported Page 15 of 45 IUCLIDS 2 5 1 Installation of Tomcat Tomcat can be installed either as an application that is controlled using a set of scripts or as a service under Windows The service option is convenient because it can be set up using an installer and once installed the software can be controlled using the service management tools in Windows An example of the installation as a service under Win dows is described below Download and run the Windows Service Installer of Tomcat from http tomcat apache org The first page of the installer is shown below Figure 2 21 Welcome to the Apache Tomcat Setup Wizard amp ea Welcome to the Apache Tomcat Setup Wizard This wizard will guide you
15. 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 W Tip Bear in mind that as an alternative to the upgrade scenarios described in this chapter no matter what version of IUCLID 5 is to be upgraded it is possible to perform a fresh installation of IUCLID 5 using a new database name PostgreSQL or database schema Oracle and to then transfer existing data over to it using the built in backup restore features of IUCLID 5 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 from IUCLID 5 6 0 or IUCLID 5 6 0 1 to IUCLID 5 6 0 2 The difference between IUCLID 5 6 0 or IUCLID 5 6 0 1 and IUCLID 5 6 0 2 is that some application files have changed and must therefore be patched There is no need to touch the database of 5 6 0 or 5 6 0 1 It will be used unchanged with IUCLID 5 6 0 2 A simple and reliable way to apply the patch is to replace the whole web application with the new version as described in the steps below The settings files and plug ins can be copied from the old to the new ve
16. the file browser of Windows with IUCLID 5 deployed is shown below Figure 2 33 IUCLID 5 deployed in Tomcat file browser view COW r di System C Program Files Apache Software Foundation Tomcat7 0 webapps File Edit View Tools Help Bi Organize Views Y Name Date modified Type Size _ Oserver war When IUCLID 5 is deployed in Tomcat it is shown in the list of applications in Tomcat Manager as shown below If you are unfamiliar with Tomcat Manager see Section 2 5 1 1 Tomcat Manager Page 23 of 45 IUCLIDS Figure 2 34 IUCLID 5 deployed in Tomcat application list in Tomcat Manager None specified Welcome to Tomcat true 0 Expire sessions with idle 30 minutes Start Reload Undeploy Ine Tomcat A fdocs specified Documentation me Expire sessions with idle 30 minutes Start Reload Undeploy None i5server specified IUCLIDS Server true 1 Expire sessions wath idle 30 minutes Stat Stop Reload Undeploy None Tomcat Manager memes ee manager specified Application true 1 Expire sessions with idle 2 30 minutes Alternatively deployment can be done using the deploy feature of the Tomcat Manager to upload a war file into Tomcat from a file system However before doing that the configuration of Tomcat Manager should be checked and possibly adjusted for the following reason Warning STOP By default Tomcat Manager places an upper li
17. DATA Postgre SQL pgpass conf SoAPPDATA is the Application Data folder in your user profile This mechanism is used by default by all programs that use the libpg library to access the server which includes command line applications such as pg dump and pq restore other GUI applications and drivers such as psqlIODBC 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 Do not show this hint again Help Expand the tree for PostgreSQL 9 2 localhost 5432 by clicking the plus sign that has just appeared next to it as shown in the figure below Page 10 of 45 IUCLIDS Figure 2 14 Initial screen in pgAdmin Ill r E pgAcmir i LU File Edit View Tools Help Ak SE Ax TE browser Value PostgreSQL 9 2 F Hostname localhost Host Address F Port 5432 Encryption SSL Certificate File F lss Kev File 4 rr Right click on Login Roles and select New Login Role Figure 2 15 Select the option New Login Role Edit Plugins View Tools Help Pr rE ES a Servers 1 S PostgreSQL 9 2 localhost 5432 2 postgres E B Databases 1 H 5 Tablespaces 2 Login Roles otk Refresh New Login Role Object List Report Retrieving details on login roles Done Enter the name of the l
18. IUCLID 5 Guidance and Support Installation Guide for IUCLID 5 6 Client Server Architecture Microsoft Windows IUCLIDS INTERNATIONAL UNIFORM CHEMICAL INFORMATION DATABASE March 2015 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 1 INT OCON ects acess E Aicta ected ane a aka tec std daca saeco fcct mutase a Wn tatadee hc tec deo incense doen E AE R 1 1 1 Hardware requirements cccccccccccecececececececececucueaeeececeaeaeaeeeseseeesesesesesececaeusueusuegegeaeananansnsesesegegs 1 1 2 SOMWare TEQUINGIMOCMNS cesses sacs vasctacsasacenadewosn cn as e AEEA A nna daccadieenedesoesSenemasanes cna 1 2 Making a fresh installation Of IUCLID 5 oo cece cece cece cece eee e nese a eens eee ee a esse eee eee ea seta essa eseeaeneeeeaeeeaeeeees 3 Ak Operating SY SLO sarare aE Waetenien saat EA E E 3 2 2 JAVA Development KIL csccesssunanscsdudeacioensatasncaeteseetanmsmninn e AAE AEA TOA E AREAK 3 2 3 Database POStIreSQL carana ET EA EEE N 3 2 3 1 Installation of PostgreSQL s
19. Java Web Start technology to start a Java 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 above the link under the text with 71GB RAM is being hovered over Following a link downloads a file named 15client jnlp that the browser should open using Java TM Web Start Launcher The difference between the Page 35 of 45 IUCLIDS links is in the values of parameters passed to the IUCLID 5 server The options included are for varying amounts of memory to be allocated to the IUCLID 5 Java client and for different types of data compression to be employed in the connection to the application server If UCLID 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 15client jnlp from one of the links and then 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 the IUCLID 5 server without using a browser 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 then change its icon to the one that comes wit
20. L is already installed the existing installation can be used To run IU CLID 5 there is no specific need to upgrade to a higher version number of PostgreSQL If PostgreSQL is not already installed on the computer or you would like to upgrade it download the new version of PostgreSQL from the site www positgresql org download and install it The web site of PostgreSQL offers a range of alternative ways to down load and install the PostgreSQL software The screen shots shown below show the use of the one click installer avail able from the PostgreSQL web site An example of the file name of the installer is postgresqI 9 2 3 2 windows exe The default fresh installation of PostgreSQL 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 manage databases If the installer creates the database superuser postgres you will have to enter a password for it into step 4 of the one click installer as shown in the sequence of figures below Remember this password because it will be required later during the configuration of IUCLID 5 If you are unsure of what values to enter into the one click installer use the pre filled defaults Page 3 of 45 IUCLIDS Figure 2 1 Installer for PostgreSQL Setup PostgreSQL Welcome to the PostgreSOL Setup Wizard PostgreSQL Packaged by Enterprise The Enterprise Pa
21. ME First steps Import reference substance inventory Select a reference substance inventory to import into IUCLIDS The reference substance inventory is a catalogue of approximately 70 000 reference substances A reference substance is used forthe 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 D IUCLID ReferenceSubstance iS5z g Balaaa aA a Ee lt Back Next gt Cancel Reference substance inventory import Page 41 of 45 IUCLIDS Tip Time and IT resources can be saved by importing 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 r
22. a endorsed dirs C Program Files Apache Software Foundatior Dijava io tmpdir C Program Files Apache Software Foundation Tor Initial memory pool 768 ME Maximum memory pool 768 ME Thread stack size Cea Note l There are two ways of manually starting and stopping the Tomcat service under Windows 1 The service manager dedicated to Tomcat as described above 2 The service manager for all Windows services This is located in Windows at Start Computer right click Manage Computer Management Services and Applications Services Select the service that has a name beginning with Apache Tomcat Options are provided for Stop the Service Restart the Service and Start the Service 2 5 1 1 Tomcat Manager The installation of Tomcat by default includes the installation of Tomcat Manager Tomcat Manager is a web appli cation supplied along with Tomcat that provides a means of dynamically managing the running of applications within Tomcat without having to shutdown the Tomcat application server itself It provides a convenient way of managing the IUCLID 5 application in a distributed environment To gain access to Tomcat Manager point a web browser to the address http localhost 8080 manager html Log in to Tomcat Manager as an administrator using the username and password given during the installation of Tomcat On logging in the screen shown is a list of the applications currently deployed in T
23. client in the same way as before the upgrade Page 29 of 45 IUCLIDS 11 Log in to the IUCLID 5 client as one of the users that was present before the upgrade 12 Confirm that the version of IUCLID 5 is the new expected version This can be seen from the menu Help About 13 Confirm that the data from the previous version is accessible in the new version 3 2 Upgrade from IUCLID 5 5 x to IUCLID 5 6 0 2 Important Q There is no separate data migration process in upgrading from IUCLID 5 5 0 or IUCLID 5 5 1 to IUCLID 5 6 0 2 Changes required in the database are applied automatically when the upgraded application is first run The upgrade therefore consists of copying the new software from the installation package to the destination machine and then configuring it to connect to either the existing database or a copy of it If more than one version of IUCLID 5 and its database are to be maintained and made available on the same machine run only one at a time and use appropriate database settings to avoid conflicts Do not run more than one instance of IUCLID 5 at the same time in the same application server There are various different ways to manage a Tomcat application server as referred to in the section of this man ual Deployment of IUCLID 5 The following instructions are intended to give a representative example of how the IUCLID 5 software can be upgraded to IUCLID 5 6 0 2 1 Back up the database Use the built in Bac
24. d from IUCLID 5 4 x to IUCLID 5 6 1 Back up the database Use the built in Backup functionality of IUCLID 5 and or the backup 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 Close all clients for IUCLID 5 Use the application Tomcat Manager to stop the IUCLID 5 web application Make a note of the plug ins that are present in the installation There is no need to keep the old plug ins because new versions will be installed The plug ins reside in the following folders where tomcat_home is the home folder of Tomcat Page 31 of 45 10 11 12 13 14 IUCLIDS client tomcat_home webapps 15server 15clientPlugins remotePlugins server tomcat_home webapps 1 5server WEB INF classes plugins Copy the configuration files for IUCLID 5 server properties and client properties into a backup folder For example where tomcat_home is the home folder of Tomcat copy the file tomcat_home webapps 15server WEB INF classes server properties in to your own folder such as tomcat_home backup Use the application Tomcat Manager to undeploy the old version of the IUCLID 5 web application Use the application Tomcat Manager to deploy the new version of the IUCLID 5 web application Stop Tomcat Copy any values that are specific to your system from the previous versions of the files se
25. d to create a new password when they next log in 2 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 Page 27 of 45 IUCLIDS 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 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 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 exp1ry 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 attem
26. d5 The encoding set under the tab Definition must be left at the default value of UTF8 Click OK Important J Make a note of the database name It is referred to later in the installation in Section 2 6 1 Database connection settings for PostgreSQL We recommend using the name 1uc11d5 If there is already a database of that name you can enter something different Page 13 of 45 IUCLIDS Figure 2 19 Enter the details of IUCLID 5 s database into pgAdmin Ill Name iudid5 OID Owner iudidS As you can see from the figure below there is now a new database named iuclid5 Figure 2 20 List of databases in pgAdmin Ill peas gpl Pes i PJA0OmMIF il File Edit Plugins View Tools Help CO 5 6 2 EE 2 w Object browser i l eem Properties Statistics Dependencies B Servers 1 Database Owner El PostgreSQL 9 2 localhost 5432 I gt judias iudid5 J E me 2 es dins T T T postgres postgres H postgres m i Tablespaces 2 i Group Roles 0 Het Login Roles 2 Database iuclids DROP DATABASE iuclids Retrieving details on database iucidS You can now close pgAdmin lIl and move directly to the installation of IUCLID 5 Page 14 of 45 IUCLIDS 2 4 Database Oracle IUCLID 5 is published with values of settings for connection to a PostgreSQL database Changing the configuration to use an Oracle database is described in Section 2 6 2
27. e aware that this is not the Tomcat Manager that is described in the next section Page 19 of 45 IUCLIDS Figure 2 29 Tomcat s dedicated service manager Configure start service Stop service Thread Dump Exit About Select Configure Under the tab General set the startup type to Automatic Figure 2 30 Apache Tomcat properties General tab Ny Apache Tomcat 7 0 Tomcat Properties al General Log On Logging Java _ Startup Shutdown Service Name Tomcat Display name Apache Tomcat 7 0 Tomcat Description Apache Tomcat 7 0 52 Server http tomcat apache Path to executable C Program Files Apache Software Foundation Tomcat 7 0 bin Tomcat Startup type Service Status Started Under the tab Java enter a value of 768 MB for both Initial memory pool and Maximum memory pool as shown below Page 20 of 45 IUCLIDS Figure 2 31 Apache Tomcat properties Java tab se Apache Tomcat 7 0 Tomcat Properties General Log On Logging Java Startup Shutdown E Use default Java Virtual Machine C Program Files Java jre bin dient jvm dll Java Classpath C Program Files Apache Software Foundation Tomcat 7 0 bin bootstrap Java Options Dcatalina home C Program Files Apache Software Foundation Tor Dcatalina base C Program Files Apache Software Foundation Tom Djav
28. e 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 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 alowercase 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 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 require
29. educed 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 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 ME 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 Importfexport directories Create user Login name Local Administrator Fullname Exam ple Password Set password C Expire password upon next login nn roles F roles ME Set password Set the password of Local Administrator Example last login Never from Nowhere 30 LEO for Manual f Helsinki f Fini Generate Set Cancel
30. er 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 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 Note aa 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 Page 36 of 45 IUCLIDS AC IUCLID 5 3 2 b A IUC LID 5 PTERAMATOHAL UHIFORH CHERECEL IHAOAFAATIOH DATADAS E Please enter username and password to login local workstation Username SuperUser 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 are no actions other than to read the
31. ering the pointer over the option Tomcat displays a message in the field Description that states installation will be done as a service Click on the button Next Figure 2 24 Configuration a Apache Tomcat Setup Configuration Options a amp Configuration k Tomcat basic configuration Server Shutdown Port 8005 HTTP 1 1 Connector Port 8080 AJP 1 3 Connector Port 8009 Windows Service Name Tomcat Create shortcuts for all users E Tomcat Administrator Login User Name admin optional Password TIL Roles manager gui Gana For IUCLID 5 the default values can be used If you want control IUCLID 5 in the application server using the Tomcat Manager which is recommended enter values for the user name and password Be careful to remember the values because they are needed to access the Tomcat Manager Click on the button Next Page 17 of 45 IUCLIDS Figure 2 25 Java Virtual Machine E Apache Tomcat Setup Java Virtual Machine path selection fog Java Virtual Machine Java Virtual Machine path selection Please select the path of a Java 5E 6 0 or later JRE installed on your system C Program Files Java jre Cancel Select the folder of the Java Virtual Machine This is likely going to be the folder of the most up to date installation of Java as in the example above Click on the button Next Figure 2 26 Choose Install Location Tal Apache Tomcat Setup o E Choose Install Location k
32. h the IUCLID 5 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 O 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 5 End us
33. ialect org hibernate dialect PostgreSQLDialect In the example configuration below the PostgreSQL database server s name is dbserver it is accepting connections on port 72345 the database name is chemdb the database user name is joe and the database user password IS XXXX hibernate connection url jdbc postgresql dbserver 12345 chemdb hibernate connection username joe hibernate connection password xxxx 2 6 2 Database connection settings for Oracle The default configuration for Oracle is shown below Un comment the lines as required hibernate hibernate hibernate hibernate hibernate hibernate hibernate connection connection connection connection username lt username gt paSSword lt password gt driver_class oracle jdbc driver OracleDriver url jdbc oracle thin localhost 1521 lt database gt hbm2dd1 auto validate dialect eu eca 1uclid server system persistence Extendedoracle9Dialect jdbc use_streams_for_binary false Page 26 of 45 IUCLIDS 2 Configuring the security settings for user accounts 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
34. ication should disappear from the application listing and its files should be deleted from the folder webapps Warning STOP An attempt to undeploy an application can fail if something prevents the deletion of the application files For example this can happen if a user with insufficient access rights is using one of the application s files For example a user whose account has insufficient rights might have a settings file open Therefore before using undeploy in Tomcat Manager check that no other applications and no file manager windows are open that are currently using files or folders of the application to be undeployed In an upgrade once the previous version of IUCLID 5 has been successfully undeployed the new version can be deployed as described above 2 6 Configuring the connection to the database The configuration of the connection from the IUCLID application to its database is defined in the file server properties that is located in the folder webapps 15server WEB INF c lasses The default values are for an instance of the PostgreSQL database running on the same computer as the application server i e localhost The values for the database name the database username and its password are all set Page 25 of 45 IUCLIDS to the value iuclid5 If that configuration is used on starting the IUCLID 5 application it will connect to the database without the need to make any changes to the configuration file If other va
35. igure 2 9 Installation of PostgreSQL complete Setup has finished installing PostgreSQL on your computer Launch Stack Builder at exit E Stack Builder may be used to download and install additional tools drivers and applications to complement your PostgreSQL installation PostgreSQL Packaged by Enterprise The Enterprise PesignesStL Company lt Back Cancel Unless you particularly want to run the Stack Builder untick the box in the screen shown above To finish the instal lation click on the button Finish 2 3 2 Configuration of PostgreSQL A new user and a new database need to be created P Tip IUCLID 5 is configured by default to connect to the database using username iuclid5 and password iuclid5 It is convenient to specify the same password now and change it later when the ap plication is set up correctly O Important Take note of the password of this user This user name and password will be needed later to connect IUCLID 5 to the database The program pgAdmin Ill can be used to create the database as follows Start pgAdmin III from the menu Start All Programs PostgreSQL9 2 After the splash screen has appeared and you have closed the pop up window that shows usage tips the following screen is shown Page 8 of 45 IUCLIDS Figure 2 10 pgAdmin Ill interface on first opening r E PUAT i LU EH ma Edit View Tools Help FE Ob ect browser E Right clic
36. ilable from the IUCLID website http iuclid eu packaged into a file named Page 22 of 45 IUCLIDS 1uclid5 lt version gt _server_ lt date gt z1p 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 15server war That is the file to be deployed Deployment of an application into Tomcat can be done in two ways e Statically the application is set up whilst the application server Tomcat is not running e Dynamically one or more applications can be managed whilst the 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 applications that are running on the same instance of Tomcat In this installation manual only the dynamic deployment is described However the static deployment may be used instead The deployment of an application on Tomcat is described 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 15server 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 application An example of what the folder webapps looks like in
37. information Click the Next button ME First steps Welcome to IUCLID 5 Welcome to IUCLID 5 IUCUD 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 Change the SuperUser password not mandatory but recommended to increase security _ Import your Legal Entity information mandatory for running the application Import the EC inventory not mandatory but strongly recommended 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 8 5 08 8 G a 8 T Fn Introduction Page 37 of 45 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 1lationas shown below and continue to the next step M First steps Define the initialisation mode initialisation mode New installation C Restore from backup 2 B 5 5 5 5 a 5 Next gt fin
38. ing 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 using Windows Server 2008 and 2012 Other versions may be used as well In that case the file locations might differ from those used in this document For installation instructions please refer to the documentation supplied by the manufacturer 2 2 JAVA Development Kit Download the JAVA Development Kit JDK 8 or JAVA Runtime Environment JRE 8 according to the architecture of the destination computer from the site http www oracle com http www oracle com IUCLID 5 6 0 2 is compatible with Java 6 but the vendor Oracle recommends to uninstall Java SE 6 and then to install the latest update of Java 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 Run the installer and follow the instructions The default parameters are appropriate for IUCLID 5 For more infor mation please refer to the documentation on the site from which the software is available 2 3 Database PostgreSQL PostgreSQL is an open source object relational database system Installation packages and more information about the software can be obtained from the site http www postgresal org 2 3 1 Installation of PostgreSQL If either version 9 0 9 1 9 2 or 9 3 of PostgreSQ
39. ish 7 Cancel_ 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 M First steps Define the initialisation mode Initialisation mode O New installation Restore from backup Location to restore from D IUCLID backup o o 8 0 8 3 0 2 na Init mode Click Next The wizard jumps to its last step where the importation of data is started as shown below Page 38 of 45 IUCLIDS Figure 4 5 Restoration from a backup 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 Note the duration of this import process depends onthe size of the import files It may take a considerable amount of time o 2 0 0 88 0 0 o gt Cnr Activate imports The import may take some time Click Finish When the restoration is complete the following screen is shown Background job ended Fa m Restore completed successfully Figure 4 6 Step 3 of the First steps wizard Change password If the password for SuperUser has neve
40. k the text PostgreSQL 9 2 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 Ill to PostgreSQL as user postgres Edit View Tools Help cS BEEF a Pos tgreSOL 9 2 fozalhnet n477 PostgreSQL 9 2 Refresh Connect Delete Drop Reports Retrieving details on server localhost Done Page 9 of 45 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 the user postgres i Connect to Server Please enter password for user postgres on server PostgreSQL 9 2 localhost Store password If you elect to save the password the following warning might be displayed Click OK Figure 2 13 Saving passwords Warning 2 Guru Hint Saving passwords Sox Saving passwords WARNING 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 PostgreSQL s pgpass mechanism to store your passwords On nix systems the password will be stored in lt pgpass whilst on Windows systems it will be stored in APP
41. kup functionality of IUCLID 5 and or the backup 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 Close all clients for IUCLID 5 Use the application Tomcat Manager to stop the IUCLID 5 application on the server side Make a note of the plug ins that are present in the installation There is no need to keep the old plug ins because new versions will be installed The plug ins reside in the following folders where tomcat_home is the home folder of Tomcat client tomcat_home webapps 15server 15clientPlugins remotePlugins server tomcat_home webapps 1 5server WEB INF classes plugins Copy the configuration files for IUCLID 5 server properties and client properties into a backup folder For example where tomcat_home is the home folder of Tomcat copy tomcat_home webapps 15server WEB INF classes server properties to e backup server properties Use the application Tomcat Manager to undeploy the old version of the IUCLID 5 web application Use the application Tomcat Manager to deploy the new version of the IUCLID 5 web application Use the application Tomcat Manager to stop the newly deployed IUCLID 5 web application Copy any values that are specific to your system from the previous versions of the files server properties and client properties to those supplied in the new version of IUCLID 5
42. lues are required they must be entered into the file server properties ad Important Make sure that there are no spaces after the username and password values in the properties file For any change in a configuration file to take effect the IUCLID 5 application must pass through the start process This can be done either individually for IUCLID 5 by re starting it using the Tomcat Manager or by re starting the whole Tomcat service The IUCLID 5 server records its activities in log files The configuration file for the logging is 15server logging properties which is located in the folder WEB INF classes The default location of the logs is in the top level directory of the Tomcat installation Consult the content of the logs if you encounter any errors that you cannot explain If you are following this manual to perform a fresh installation all the software has now been installed What remains is some configuration as described in Section 2 7 Configuring the security settings for user accounts and Sec tion 4 1 Starting the IUCLID 5 client 2 6 1 Database connection settings for PostgreSQL The default configuration for PostgreSQL is shown below Settings for using hibernate hibernate hibernate hibernate hibernate PostgreSQL connection connection url jdbc postgresql localhost 5432 iuclid5 username i1ucli1d5 connection password 1uclid5 connection driver_class org postgresq Driver d
43. mented or added as shown above 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 15server log and 1uclidMT 1og The default location of these files is on the top level directory of the Tomcat installation The file 1 5server log contains statements about the start and end of the migration process The file 1uc11dMT log 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 Page 32 of 45 15 16 17 18 19 20 21 IUCLIDS integration database scripts ScriptUtils Checking Database Status Ceu eca iuclid server integration database scripts migrate_schemav51_to_schemav55 xml integration database scripts ScriptUtils Upgrading table integration database scripts Scriptutils 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
44. migrated are written to 1ucl1dMT log 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_schemav55_patch xml integration database scripts ScriptUtils Upgrading table integration database scripts ScriptUtils Database 1s up to date If the migration is interrupted or fails for whatever reason the database must be restored from the backup and the migration started again Note The entries in the log files shown above state schemav55 rather than schemav56 because the migration process is only to IUCLID 5 5 There is no data migration process in upgrading from IU CLID 5 5 x to IUCLID 5 6 0 2 Changes required in the database to convert from IUCLID 5 5 x to IUCLID 5 6 0 2 are applied automatically when IUCLID 5 6 0 2 is first run When the migration finishes successfully stop the new version of the IUCLID 5 web application by stopping Tomcat Set IUCLID 5 to start not in its update mode by commenting out the line edited previously database update startup true Start Tomcat Run the IUCLID 5 client in the same way 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 i
45. mit on the size of the war file that can be uploaded The default value of the limit is smaller than the size of the file 15server 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 lllegalStateException 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 xm to values that are larger than the size of the war file The default values are shown below lt multipart config gt lt 50MB max gt lt max fi le 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 An example of the new values required is shown below The value is a 1 followed by 8 zeroes lt max f1i 1e size gt 100000000 lt max fi 1e size gt lt max request s1ze gt 100000000 lt max request si1ze 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 Page 24 of
46. n 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 Tip 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 e Ticking the box Expire password upon next login forces whoever logs in to the account first to set their own 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 P 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 End user Manual 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
47. n to any of the user accounts that were present prior to the upgrade Log in to the IUCLID 5 client as one of the users that was present before the upgrade Confirm that the version of IUCLID 5 is the new expected version This can be seen from the menu Help About Confirm that the data from the previous version has been successfully migrated to the new version 3 4 Upgrading from IUCLID 5 2 x 5 3 x to IUCLID 5 6 0 2 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 Page 33 of 45 IUCLIDS a fresh installation of IUCLID 5 6 0 2 The Backup and Restore features are described in the IUCLID 5 End user Manual Making a fresh installation is described in this manual D Warning STOP 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 perform step wise upgrades in which the database is migrated from IUCLID 5 2 x 5 3 x to 5 4 x to 5 6 0 2 For example this method might be required if the amo
48. ogin role We recommend using a name of i1uc11id5 Page 11 of 45 IUCLIDS Figure 2 16 Create a new login role i e a user with the name iuclid5 Br membership Variables Security Labels Role name OID The login role can have a password set although this is optional The password is entered under the tab Definition Figure 2 17 Set the password of the new login role This step is optional Password ooeneee Password again seeeee Account expires 26 03 2013 Connection Limit Page 12 of 45 IUCLIDS Important J Make a note of the user name and if set the password They are referred to later in the installation in Section 2 6 1 Database connection settings for PostgreSQL We recommend using 1ucl1id5 as the name of the login role and for the password Request a new database by right clicking the item Databases and selecting New Database as shown in the figure below Figure 2 18 Request a new database in pgAdmin Ill tF pgAdmin M File Edit Plugins View Tools Help Oia d Object browser Properties Statistics Dependencies Server Groups ee Servers 1 Database bate El F PostgreSQL 9 2 localhost 5432 postgres postgres G 3 Refresh H T Tablespal 2 Group Re E Login Rol A iudid He postgres Mew Database Reports Retrieving details on databases Done Enter the details you require Normally these are only name iuclid5 and owner iucli
49. omcat Immediately after a fresh default installation of Tomcat the following screen is shown Page 21 of 45 IUCLIDS Figure 2 32 IUCLID 5 Tomcat Manager default administrator screen immediately after installation S Apache Software Foundation ttp www apache org Tomcat Web Application Manager pee List Applications HTML Manager Help Manager Help server Status Welcome to Tomcat E e minutes Mone speciied Tomcat Documentation a wee minutes Start Stop Reload Undeploy imanager None specified Tomcat Manager Application true 1 O m se E E Expire sessions with iiie 2 20 Mone spected This diagnostic check will tigger a full garbage collection Use it with extreme caution on production systems Apache TonmcatT 0 21 1 6 0_22 b04 Sun Microsystems linc Copyright 19982071 Apache Software Foundation Before attempting to deploy IUCLID 5 check the memory settings for Tomcat To do that using Tomcat Manager from the page shown above click on the link Server Status and then check the field JVM The value of Max memory should be at least 742 MB Deploying IUCLID 5 in Tomcat is described in the next section 2 5 2 Deployment in Tomcat Deployment is the term used for the process of installing an application into an application server The application of IUCLID 5 is published in the form of a web archive file WAR which is a file with extension war It is ava
50. pts 3 Max number of attempts to answer the reset question max failed answer attempts 3 2 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 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 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 2 3 Maximum number of attempts to log in This feature is used to prevent the combination of user name and password from being obtained 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 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 Page 28 of 45 IUCLIDS Chapter 3 Upgrade This document describes the process of obtaining an installation of IUCLID 5 6 0 2
51. r 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 M First steps Change the SuperUser password For security reasons it is recommended to change the SuperUser s password and specify a security question g It is not secure as itis now 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 a B B 5 5 f 8 I Finish Cancel J Change 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 Page 39 of 45 v IUCLIDS 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 letter The policy for the SuperUser is the same as that for all users The password policy is set by
52. reafter referred to as Windows and how to launch a client to connect to it 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 At least 2 GB on the mother board 4 GB if PostgreSQL is run on the same machine as IUCLID 5 e Hard disk space 200 GB e CPU Intel Pentium Dual 1 8 GHz e Network adaptor 100 Mbps recommended 1Gbps The requirements depend in part on the plug ins that are in use For example using the Query Tool plug in will increase the resources required to obtain a reasonable running speed especially on a large database There are no specific hardware requirements to run the IUCLID 5 client 1 2 Software requirements Operating system e The IUCLID 5 server can be hosted under Microsoft Windows Server 2008 or 2012 Other versions 2003 may be used but note that the testing has been done with 2008 and 2012 The IUCLID 5 client can be run under Windows 7 or 8 IUCLID 5 can be installed with the following open source components e Java SE Runtime Environment 7 or 8 IUCLID 5 6 0 2 is compatible with Java 6 but the vendor Oracle recom mends to uninstall Java SE 6 and then to install the latest update of Java Variou
53. rsion of IUCLID 5 1 Back up the database Use the built in Backup functionality of IUCLID 5 and or the backup 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 application on the server side as described in Sec tion 2 5 1 1 Tomcat Manager 4 Copy the configuration files and the folders that contain the plug ins into a backup folder These are indicated below where tomcat_home is the home folder of Tomcat tomcat_home webapps 15server WEB INF classes server properties tomcat_home webapps 15server WEB INF classes client properties tomcat_home webapps 1 5server WEB INF classes plugins tomcat_home webapps 15server 15clientPlugins remotePlugins 5 Use the application Tomcat Manager to undeploy the old version of the IUCLID 5 web application 6 Use the application Tomcat Manager to deploy the new version of the IUCLID 5 web application 7 Use the application Tomcat Manager to stop the newly deployed IUCLID 5 web application 8 Copy the configuration files and the folders that contain the plug ins from the backup folder into the location they were in before the upgrade shown above in step 4 9 Use the application Tomcat Manager to start the IUCLID 5 web application 10 Run the IUCLID 5
54. rver properties and client properties to those 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 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 If the database is an Oracle database please note that the driver for Java is no longer supplied with the IU CLID 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 Install any required plug ins using the latest versions from the IUCLID web site A migration process is required to upgrade to IUCLID 5 6 0 2 The database 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 uncom
55. s 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 For Java the requirement for the IUCLID 5 client is the same as that for the server e Tomcat 7 or 8 Installation packages can be downloaded from http tomcat apache org e PostgreSQL 9 0 9 1 9 2 and 9 3 are supported PostgreSQL 9 3 is recommended Installation packages can be downloaded from hitp www postgresql org As an alternative to the free database software PostgreSQL the commercial database software Oracle can be used You do not need both PostgreSQL and Oracle e Oracle 11g or 12c Oracle 10g is not supported Installation packages can be downloaded from http www oracle com The Oracle driver for Java is no longer supplied with the IUCLID 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 For use with Tomcat the driver must be placed in Tomcat s library folder e g Tomcat 11b Page 1 of 45 IUCLIDS The following essential components can be downloaded without charge from the IUCLID 5 web at the at http iuclid eu Before downloading them you must register as a user on the site e The IUCLID 5 distributed installation package version 5 6 0 2 e Once you have
56. srseisararesrirriiranniin kann aa kaTa erana 3 2 3 2 COMMGUIATOM Or POSTGFES OL serisinin hoa ia aaa aaaea aaa 8 24 Database Oracle necinimecrrnrrsiins rinne a AEO aAA EESE AAEE EART 15 2 5 Applicaton Server TOMCADL s2ccscosincaesiansncadanaeewsaticnadaccaanevenendaudadaadevess achadacemanesedalncwandecmadetatsucnasescdacsss 15 Zilia MS tANAUIOMGOM TOMCA esnaera a I a E EEEE EEEE 16 25 2 Deployment m VOMICAL siiosi cuit innsntocsiseincedaunubsaaniaistndudunenddeaclgns Ea aE a a N EERTE ERNER 22 2 5 3 Undeployment in Tomcat uninstall and upgrade cccc cece ec eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneeeeees 25 2 6 Configuring the connection to the database ccc cece ccee sec ee eee ee sense eee eeeeaeseeeeeeeeeeeeeeaeeeeaeeeneeees 25 2 6 1 Database connection settings for PostgreSQL cc ccc cec ccc eec eee eeeeeeeceen eee eceeaeeeeseeaeeeeseeseeaes 26 2 6 2 Database connection settings for Oracle cccccccccec eee ee eee ee eee eeeeeeeeea essen eseeseaeseeaeeeeaeaeeeaes 26 2 Configuring the security settings for user accounts ccccceceeeec eee ec eee eeeee essen ee eeeeaeseeaeeeeeeaeeeeaeeeees 27 2 1 User account security settings defined in client PropertieS cceececec eee eeeeeeeeeaeeeeaeeeeeeeees 27 2 7 2 User account security settings defined in server properties ccccececseceeeeeeeeeeeeeeeeeeeneeeeaes 28 ig MIAO Sa NEEN AE EA A E A ENESA E EAE EN atone EE
57. stqreSQL Company Please specify the directory where PostgreSQL will be installed Installation Directory C Program Files PostareSQL 9 2 BitRock Installer Page 4 of 45 IUCLIDS Figure 2 3 Data directory for PostgreSQL he Setup Data Directory Please select a directory under which to store your data Data Directory Program Files PostgreSQL 9 datal BitRock Installer lt Back Next gt cancel _ Figure 2 4 Password for the database superuser postgres and the Windows service account postgres ee Setup Password Please provide a password for the database superuser postgres Password eeeeneee Retype password seeee8 BitRock Installer lt Back Next gt Cancel Page 5 of 45 IUCLIDS Figure 2 5 Port number for PostgreSQL Please select the port number the server should listen on Port 5432 BitRock Installer Select the locale to be used by the new database duster Locale Default locale BitRock Installer Page 6 of 45 IUCLIDS Figure 2 7 Confirm installation of PostgreSQL Ready to Install Setup is now ready to begin installing PostgreSQL on your computer BitRock Installer Figure 2 8 Installation of PostgreSQL in progress Please wait while Setup installs PostgreSQL on your computer Installing Unpacking C Program doc postgresql himl gistimplementation html BitRock Installer Page 7 of 45 IUCLIDS F
58. 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 the IUCLID 5 client Connect to the application with a browser by entering the address http lt address of your server gt 8080 5server 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 6 0 2 MACS ALDA G wl of SSH 10T TS Fz 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 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 F M apo 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
59. through the installation of Apache Tomcat It is recommended that you dose all other applications before starting Setup This will make it possible to update relevant system files without having to reboot your Click Next to continue kL o v r 0 A T pe 4 E 8 A ker Apache Tomcat A Click on the button Next Figure 2 22 Licence Agreement Press Page Down to see the rest of the agreement Version 2 0 January 2004 BaF htto www apache org icenses TERMS AND CONDITIONS FOR USE REPRODUCTION AND DISTRIBUTION License shall mean the terms and conditions for use reproduction and distribution as defined by Sections 1 through 9 of this document If you accept the terms of the agreement dick I Agree to continue You must accept the agreement to install Apache Tomcat Nullsoft Install System v2 46 If you accept the licence click on the button Agree Page 16 of 45 IUCLIDS Figure 2 23 Choose Components a Apache Tomcat Setup al Choose Components d Choose which features of Apache Tomcat you want to install Check the components you want to install and uncheck the components you don t want to install Click Next to continue Description Or select the optional Tomcat components you wish to H Install the Tomcat install Servlet container as a Windows service Space required 11 3MB For IUCLID 5 the default values can be used Hov
60. unt 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 plug ins for IUCLID 5 2 x 5 3 x are not compatible with IUCLID 5 6 Therefore they must not be copied over to the new installation Compatible versions can be downloaded from the IUCLID web site 3 5 Upgrading from IUCLID 5 0 5 1 x to IUCLID 5 6 0 2 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 plug in Backup Plug in 5 0 3 that is available on the IUCLID web site under downloads for IUCLID 5 1 1 Page 34 of 45 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 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
61. uter you should create it on the IUCLID 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 Select the import file D IUCLID Leox_Manual i5z B B_t _B _ fB_f_ _ 68 lt Back Next gt Cancel Import legal entity IUCLID 5 m gt Import of the legal entity file completed Late Important At least one Legal entity must be imported successfully before this wizard can be completed If there is 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 Page 40 of 45 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 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 ME 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

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