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Version 2.1 by Branislav ŠIŠKA on 2022/02/25 15:09
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2 = {{id name="04.Technickéinformace-1.Hardware"/}}1. Hardware =
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5 The Clindata software runs on computer cluster located on Institute of Molecular and Translational Medicine (IMTM), Faculty of Medicine and Dentistry, Palacky University in Olomouc. The facility is secured and under global surveillance.
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8 === {{id name="04.Technickéinformace-Descriptionofhardware"/}}Description of hardware ===
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11 **Servers**
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14 Blade chassis - BM Flex System Enterprise Chassis
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17 14x Compute node IBM Flex System x240 with 10 GB virtual fabric
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20 2x CPU Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz / 8C
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23 6x DDRIII SDRAM – 8GB
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26 **Data Storages**
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29 HP 3PAR data storage 700TB.
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32 HP EML tape library
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35 **Firewall**
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38 HP F1000-S-EI VPN Firewall
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41 **~ **
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44 = {{id name="04.Technickéinformace-2.Software"/}}2. Software =
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47 === {{id name="04.Technickéinformace-Thesoftwarerequirements"/}}The software requirements ===
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49 (% style="" %)
50 The only requirement for using the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software is Internet browser which supports HTML5 standard. The list of supported browsers:
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53 * Chrome: (Current - 1) and Current
54 * Edge: (Current - 1) and Current
55 * Firefox: (Current - 1) and Current
56 * Internet Explorer: 11+
57 * Safari: (Current - 1) and Current
58 * Opera: Current
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61 (Current means the last available version of given browser)
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64 === {{id name="04.Technickéinformace-Programminglanguage"/}}Programming language ===
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67 The main programming language used for development of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) application is Java 8. Other technologies used for development are:
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70 * Spring Framework v5.
71 * HTML, CSS
72 * JavaScript
73 * jQuery
74 * jQuery UI
75 * Bootstrap
76 * MathJS
77 * Datatables
78 * SQL
79 * Oracle database
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82 === {{id name="04.Technickéinformace-Operationsystem"/}}Operation system ===
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85 Operation system installed on production servers is **RedHat Enterprise Linux 7.4.**
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88 === {{id name="04.Technickéinformace-Proxyserver"/}}Proxy server ===
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91 The **Apache HTTP Server** is used as gateway from outside world to internal application running in the production server.
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94 === {{id name="04.Technickéinformace-Applicationserver"/}}Application server ===
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97 The **ClinData** application runs on **Apache Tomcat,** which is an open-source Java Servlet Container developed by the Apache Software Foundation
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100 **~ **
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103 = {{id name="04.Technickéinformace-3.Database"/}}3. Database =
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106 === {{id name="04.Technickéinformace-TheClindataDatabase"/}}The (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) Database ===
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109 The database used for storing data from the (% style="color: rgb(23,43,77);text-decoration: none;" %)**Clindata**(%%)** **software is **Oracle Database** (commonly referred to as **Oracle RDBMS**) which is produced by Oracle Corporation. Version of database is 12.1. Standard edition.
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112 The Oracle database runs on separated Linux based server which si firewalled from external network (Internet) by hardware firewall. This database server is not accessible from outside of organization but only from enlisted inner servers (application and backup servers).
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115 **~ **
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118 = {{id name="04.Technickéinformace-4.Backup"/}}4. Backup =
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121 There are more levels of data archiving to ensure data safety and quick database recovery. Data are archived on **database level** and **operation system level**
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124 1. Database level backups
125 1*. **RMAN** utility is integral part of the Oracle database. It creates binary copy of whole database and stores it to filesystem. The RMAN utility is run **every week**. The files are stored internally on database server and are copied to two independent backup sites.
126 1*. **EXPDP/IMPDP** is data pump exporting data into text base backups. The EXPDP utility is run **every 4 hours**. The backup target is the same as with RMAN. It is stored to two independent backup sites.
127 1*. **Redo Logs** are archived **every day** to filesystem.
128 1. Operation system backups
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131 * **IBM Tivoli Storage Manager** (TSM Admin) is enterprise solution from IBM for backups and recovery of physical or virtual servers. The backup created by TSM Admin includes redo logs, RMAN and EXPDP exports. It runs **every day** and the backup data is stored to disk array.
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134 RMAN configuration file
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137 CONFIGURE RETENTION POLICY TO REDUNDANCY 1; # default
138 CONFIGURE BACKUP OPTIMIZATION OFF; # default
139 CONFIGURE DEFAULT DEVICE TYPE TO DISK; # default
140 CONFIGURE CONTROLFILE AUTOBACKUP ON;
141 CONFIGURE CONTROLFILE AUTOBACKUP FORMAT FOR DEVICE TYPE DISK TO '%F'; # default
142 CONFIGURE DEVICE TYPE DISK PARALLELISM 1 BACKUP TYPE TO BACKUPSET; # default
143 CONFIGURE DATAFILE BACKUP COPIES FOR DEVICE TYPE DISK TO 1; # default
144 CONFIGURE ARCHIVELOG BACKUP COPIES FOR DEVICE TYPE DISK TO 1; # default
145 CONFIGURE MAXSETSIZE TO UNLIMITED; # default
146 CONFIGURE ENCRYPTION ALGORITHM 'AES128'; # default
147 CONFIGURE COMPRESSION ALGORITHM 'BASIC' AS OF RELEASE 'DEFAULT' OPTIMIZE FOR LOAD TRUE ; # default
148 CONFIGURE RMAN OUTPUT TO KEEP FOR 7 DAYS; # default
149 CONFIGURE ARCHIVELOG DELETION POLICY TO NONE; # default
150 CONFIGURE SNAPSHOT CONTROLFILE NAME TO '/../../oracle/12c/dbs/snapcf_imtm.f'; # default
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153 EXPDP configuration file
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156 DIRECTORY=dtpump
157 DUMPFILE=registry.dmp
158 LOGFILE=registry.log
159 CONTENT=ALL
160 COMPRESSION=NONE
161 JOB_NAME=registry_migration
162 SCHEMAS=registry,registry_aud
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165 = {{id name="04.Technickéinformace-05.Secureconnection"/}}05. Secure connection =
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168 === {{id name="04.Technickéinformace-Security"/}}Security ===
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171 As the (% style="color: rgb(23,43,77);text-decoration: none;" %)**Clindata**(%%)** **application is **web-based** application there is need to **secure communication** between **server** and **client's computer**. It is done by using **HTTPS** communication protocol which is encrypted using Transport Layer Security **(TLS).** This protocol is widely used for all secure transactions on the Internet (payment, emails etc.) and is considered as safe and unbreakable. It protects against man in-the middle attacks. Communication without the security layer (HTTP) is can be interfered by attackers, they can listen to it or change it.
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174 === {{id name="04.Technickéinformace-Securityredirection"/}}Security redirection ===
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177 All user requests coming via unsecured **HTTP** protocol are automatically **redirected** to secure **HTTPS** protocol. All communication between client and server is secured and there is no way how to connect to the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software via unsecured connection.
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180 === {{id name="04.Technickéinformace-Certificate"/}}Certificate ===
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183 The secured communication requires a certificate stored on the web server. The certificate must be signed by **trusted certificate authority**. The (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) server uses the certificate digitally signed by **TERENA** authority.
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186 **~ **
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189 = {{id name="04.Technickéinformace-06.Authenticationandauthorization"/}}06. Authentication and authorization =
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192 === {{id name="04.Technickéinformace-Usersadministration"/}}Users administration ===
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195 All user using the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) application must be registered before they can log in. There is no possibility to get unauthorized access to the server even for some demonstration purposes. There is a specialized application for user management - IMTM Admin tool.
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198 The **Admin tool** is responsible for:
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201 * Management of **institutions, companies, hospitals** and their departments. There can be unlimited number of organization levels, for example a university can have such structure university-faculty-department-laboratory. Each organization level can obtain different set of privileges and roles.
202 * Management of **users**. Every user is identified by email address as login and password. Users are assigned to their organizations. Users can work on more projects with different roles. It is allowed by** user profiles**. Number of profiles for a user is not limited. Each profile can have different set of **privileges and roles**.
203 * Management **roles and profiles**.
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206 The Admin database with user's data is stored in the Oracle database as separated schema. Access to this schema is restricted only for admin users. The server with the Oracle database is firewalled out of public network and not accessible from Internet.
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209 An account for new user can be created **only by administrator**. There is no way that user could create his account on its own.
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212 These steps must be followed to **create new account**:
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215 * New user asks a project owner to create new account
216 * The project owner asks administrator to create new account with specified privileges and roles
217 * The administrator creates new account and sets required privileges and roles
218 * The project owner checks account setting and approve it.
219 * New user receives his credentials and can log in.
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222 === {{id name="04.Technickéinformace-Centralauthenticationservice(CAS)"/}}Central authentication service (CAS) ===
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225 The (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) application must be connected with data from the IMTM Admin to control accounts, roles and privileges. It is done by integrating of the CAS technology into the ClinData software. The CAS technology consists of CAS Server and CAS Client.
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228 The CAS server is responsible for authenticating users and granting accesses to applications. The CAS clients protect the CAS applications and retrieve the identity of the granted users from the CAS server.
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231 = {{id name="04.Technickéinformace-07.PrivilegesandRoles"/}}07. Privileges and Roles =
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234 === {{id name="04.Technickéinformace-Accessrestrictions"/}}**Access restrictions** ===
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237 A user access can be restricted in two different areas:
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240 * restriction in **access to** ClinData **functionality**
241 * restriction in **access to data** stored in the ClinData software
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244 All restriction is set in the **IMTM Admin tool**.
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247 === {{id name="04.Technickéinformace-Functionalityrestrictions"/}}Functionality restrictions ===
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250 **Privileges**
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253 Access privileges determine which (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) objects a user can browse or edit. Each functionality in the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software is reflected in corresponding privilege so the access to everything is controlled. Any user or group of users can have access to any privilege granted or restricted.
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256 The picture shows schema of privileges in the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software.
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259 **Roles**
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262 Roles are virtual entities which serve as container for more privileges.
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265 There are predefined roles and users, or groups of users can be assigned to them. The most frequently used roles are:
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268 * ClinData system admin - full access to all functions in ClinData, no restrictions, creating new project
269 * ClinData project admin - full access to all function in selected project including study designer
270 * ClinData project data manager - access to all functions needed to insert new/update patient’s data.
271 * ClinData project data monitor - access to all functions needed for study monitoring, validation and finishing CRFs.
272 * ClinData project data browser - read only access to selected data.
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275 \\
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278 === {{id name="04.Technickéinformace-Datarestrictions"/}}Data restrictions ===
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281 Default setting for accessing of data in the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software is maximally restricted. A user can see only data he inserted himself. By default, he doesn't see any data inserted by any other user. Access to any other data must be explicitly permitted.
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284 These options can be set:
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287 * user can see only his data
288 * user can see data inserted by other user or group of users
289 * user can see data linked with an organization
290 * user can see all data in a study
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293 === {{id name="04.Technickéinformace-Personaldata"/}}Personal data ===
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296 There can be studies or registers which contain personal data. Access to this data can be restricted by special privilege.
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299 These options can be set:
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302 * user can see personal data
303 * user can't see personal data
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306 \\
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309 = {{id name="04.Technickéinformace-8.Logging"/}}8. Logging =
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312 The ClinData software **records everything** happening in the system. Admin user can browse these records in user friendly way and analyze potential problems, watch user activities etc.
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315 There are three different types of logging mechanisms:
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318 * **Software logging** is done on programming language level and is very detailed. The log files contain data about internal state of the whole system in time of logging event. This approach is designed for detailed analyses of problems which happened in past.
319 * **Access logging** is designed for controlling of user’s activities. The access record contains data about who did an action and when. It logs all actions done on all objects in the system. Object can be study, patient, CRF form, file. These actions are logged:
320 ** create
321 ** open
322 ** change
323 ** add
324 ** remove
325 ** delete
326 ** export
327 * **Auditing** is focused to changes done in CRF forms. It records complete history of what was changed by users. One record contains data about:
328 ** when the change was done
329 ** who changed the data
330 ** what was changed
331 ** what is the new value
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334 The important information is that the ClinData software** doesn't delete any record**. Every record in the database has system **flag ACTIVE**. Deleting of the row just sets this **ACTIVE** flag to **false**. The inactive rows are not displayed in the ClinData software but are still stored in the database.
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337 **~ **
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340 = {{id name="04.Technickéinformace-9.Softwaredevelopment"/}}9. Software development =
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343 === {{id name="04.Technickéinformace-Issuetracking"/}}Issue tracking ===
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346 Any problem found in the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software is documented and created as a **new issue in JIRA software**. JIRA software is developed by Atlassian and is an issue tracking tool. The new issue is analyzed, and priority is assigned.  The list of issues is sorted by priorities and processed by developers. When a serious problem is fixed then it is published in new version of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software. The issue is also closed as done in JIRA.
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349 === {{id name="04.Technickéinformace-Changesmanagement"/}}Changes management ===
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352 All requests for changes planned in the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software are stored in JIRA. When a new request is coming then it is analyzed, time estimation is done, and priority assigned. The list of issues is sorted by priorities and processed by developers.
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355 === {{id name="04.Technickéinformace-Versioning"/}}Versioning ===
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358 The source code of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software is stored in** GIT repository** which allows tracking of changes in files. There is possibility to browse history of any source code file in the repository. Every change is also documented so it is easy to understand the development cycle.
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361 === {{id name="04.Technickéinformace-Codereview"/}}Code review ===
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364 Any change done in source code of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software must be **reviewed** by another developer. This process is called **code review**. This process minimizes number of bugs in source code because everything is double checked. **Bitbucket software** (developed by Atlassian) is used for code reviews. It prevents developers from using not proven code in public versions of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software.
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367 **~ **
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370 = {{id name="04.Technickéinformace-10.Qualityassurance"/}}10. Quality assurance =
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373 === {{id name="04.Technickéinformace-Testingenvironment"/}}Testing environment ===
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376 All new versions of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software must be tested and proven as functional and correct before they are published. There is a special environment which is used form testing of the new version before it is published. The testing environment must be similar to production environment to avoid configuration issues.
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379 === {{id name="04.Technickéinformace-Unittesting"/}}Unit testing ===
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382 Unit testing is a software testing method by which individual units of source code are tested to determine whether they are fit for use. There are actually more than one thousand-unit tests in the source code of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software. All critical parts of the source code are covered by unit test close to 100%. Overall source code is covered by unit test by more than 85%. Any problem in unit testing is blocker for publishing of the version of the software.
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385 === {{id name="04.Technickéinformace-Applicationtesting"/}}Application testing ===
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388 The whole application is tested by application exploratory testing before it is published. The application testing is done in testing environment. Any problem in application testing is blocker for publishing of the version.
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391 === {{id name="04.Technickéinformace-Publishing"/}}Publishing ===
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394 Publishing process means that a new version of the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software is being released and made accessible for users. The Bamboo software (developed by Atlassian) is used for building and publishing new versions. Unit testing is also involved in publishing of the new version. In case of any problem in any unit test the whole publishing, process is interrupted, and an notification email is sent to responsible persons.