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Changes for page 04. Technical information

Last modified by Branislav ŠIŠKA on 2024/09/12 19:30
From version 5.1
edited by Branislav ŠIŠKA
on 2024/09/12 19:25
Change comment: There is no comment for this version
To version 2.1
edited by Branislav ŠIŠKA
on 2023/06/06 09:22
Change comment: There is no comment for this version

Summary

Details

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1 1  = {{id name="04.Technicalinformation-1.Hardware"/}}1. Hardware =
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3 3  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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5 5  === {{id name="04.Technicalinformation-Descriptionofhardware"/}}Description of hardware ===
6 6  
7 -**Server in virtualization system proxmox**
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11 +**Servers**
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9 -Memory: 48 GB
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14 +HPE DL385 Gen10 CTO Mod-X 8SFF Svr
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11 -Processors: 8 cores
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17 +8x HPE 16GB 2Rx8 PC4-2933Y-R
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20 +2x HPE DL385 Gen10 AMD EPYC 7302
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23 +2x HPE 240GB SATA RI SFF SC DS SSD
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13 13  **Data Storages**
14 14  
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29 +HP 3PAR data storage 700TB.
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32 +HP EML tape library
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15 15  Object storage
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17 17  **Firewall**
18 18  
19 -FortiGate 600E
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41 +HP F1000-S-EI VPN Firewall
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21 21  **~ **
22 22  
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23 23  = {{id name="04.Technicalinformation-2.Software"/}}2. Software =
24 24  
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25 25  === {{id name="04.Technicalinformation-Thesoftwarerequirements"/}}The software requirements ===
26 26  
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27 27  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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29 29  * Chrome: (Current - 1) and Current
30 30  * Edge: (Current - 1) and Current
31 31  * Firefox: (Current - 1) and Current
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33 33  * Safari: (Current - 1) and Current
34 34  * Opera: Current
35 35  
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36 36  (Current means the last available version of given browser)
37 37  
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38 38  === {{id name="04.Technicalinformation-Programminglanguage"/}}Programming language ===
39 39  
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40 40  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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42 42  * Spring Framework v5.
43 43  * HTML, CSS
44 44  * JavaScript
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50 50  * SQL
51 51  * Oracle database
52 52  
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53 53  === {{id name="04.Technicalinformation-Operationsystem"/}}Operation system ===
54 54  
55 -Operation system installed on production servers is **RedHat Enterprise Linux 9.4.**
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88 +Operation system installed on production servers is **RedHat Enterprise Linux 7.4.**
56 56  
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57 57  === {{id name="04.Technicalinformation-Proxyserver"/}}Proxy server ===
58 58  
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59 59  The **Apache HTTP Server** is used as gateway from outside world to internal application running in the production server.
60 60  
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61 61  === {{id name="04.Technicalinformation-Applicationserver"/}}Application server ===
62 62  
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63 63  The **ClinData** application runs on **Apache Tomcat,** which is an open-source Java Servlet Container developed by the Apache Software Foundation
64 64  
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65 65  **~ **
66 66  
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67 67  = {{id name="04.Technicalinformation-3.Database"/}}3. Database =
68 68  
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69 69  === {{id name="04.Technicalinformation-TheClindataDatabase"/}}The (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) Database ===
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71 71  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.
72 72  
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73 73  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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75 75  **~ **
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77 77  = {{id name="04.Technicalinformation-4.Backup"/}}4. Backup =
78 78  
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79 79  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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81 81  1. Database level backups
82 82  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.
83 83  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.
84 84  1*. **Redo Logs** are archived **every day** to filesystem.
85 85  1. Operation system backups
86 -(% style="color: rgb(23,43,77);" %)Application server is backuped up on operational system level regularly in virtualization sytem (% style="text-align: left;" %)**Proxmox**(% style="color: rgb(23,43,77);" %).
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134 +* **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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88 88  RMAN configuration file
89 89  
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90 90  CONFIGURE RETENTION POLICY TO REDUNDANCY 1; # default
91 91  CONFIGURE BACKUP OPTIMIZATION OFF; # default
92 92  CONFIGURE DEFAULT DEVICE TYPE TO DISK; # default
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102 102  CONFIGURE ARCHIVELOG DELETION POLICY TO NONE; # default
103 103  CONFIGURE SNAPSHOT CONTROLFILE NAME TO '/../../oracle/12c/dbs/snapcf_imtm.f'; # default
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105 105  EXPDP configuration file
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107 107  DIRECTORY=dtpump
108 108  DUMPFILE=registry.dmp
109 109  LOGFILE=registry.log
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112 112  JOB_NAME=registry_migration
113 113  SCHEMAS=registry,registry_aud
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115 115  = {{id name="04.Technicalinformation-05.Secureconnection"/}}05. Secure connection =
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117 117  === {{id name="04.Technicalinformation-Security"/}}Security ===
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119 119  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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121 121  === {{id name="04.Technicalinformation-Securityredirection"/}}Security redirection ===
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123 123  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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125 125  === {{id name="04.Technicalinformation-Certificate"/}}Certificate ===
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127 127  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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129 129  **~ **
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131 131  = {{id name="04.Technicalinformation-06.Authenticationandauthorization"/}}06. Authentication and authorization =
132 132  
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133 133  === {{id name="04.Technicalinformation-Usersadministration"/}}Users administration ===
134 134  
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135 135  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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137 137  The **Admin tool** is responsible for:
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139 139  * 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.
140 140  * 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**.
141 141  * Management **roles and profiles**.
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143 143  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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145 145  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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147 147  These steps must be followed to **create new account**:
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149 149  * New user asks a project owner to create new account
150 150  * The project owner asks administrator to create new account with specified privileges and roles
151 151  * The administrator creates new account and sets required privileges and roles
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152 152  * The project owner checks account setting and approve it.
153 153  * New user receives his credentials and can log in.
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155 155  === {{id name="04.Technicalinformation-Centralauthenticationservice(CAS)"/}}Central authentication service (CAS) ===
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157 157  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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159 159  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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161 161  = {{id name="04.Technicalinformation-07.PrivilegesandRoles"/}}07. Privileges and Roles =
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163 163  === {{id name="04.Technicalinformation-Accessrestrictions"/}}**Access restrictions** ===
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165 165  A user access can be restricted in two different areas:
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167 167  * restriction in **access to** ClinData **functionality**
168 168  * restriction in **access to data** stored in the ClinData software
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170 170  All restriction is set in the **IMTM Admin tool**.
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172 172  === {{id name="04.Technicalinformation-Functionalityrestrictions"/}}Functionality restrictions ===
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174 174  **Privileges**
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176 176  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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178 178  The picture shows schema of privileges in the (% style="color: rgb(23,43,77);text-decoration: none;" %)Clindata(%%) software.
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180 180  **Roles**
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182 182  Roles are virtual entities which serve as container for more privileges.
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184 184  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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186 186  * ClinData system admin - full access to all functions in ClinData, no restrictions, creating new project
187 187  * ClinData project admin - full access to all function in selected project including study designer
188 188  * ClinData project data manager - access to all functions needed to insert new/update patient’s data.
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189 189  * ClinData project data monitor - access to all functions needed for study monitoring, validation and finishing CRFs.
190 190  * ClinData project data browser - read only access to selected data.
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192 192  \\
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194 194  === {{id name="04.Technicalinformation-Datarestrictions"/}}Data restrictions ===
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196 196  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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198 198  These options can be set:
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200 200  * user can see only his data
201 201  * user can see data inserted by other user or group of users
202 202  * user can see data linked with an organization
203 203  * user can see all data in a study
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205 205  === {{id name="04.Technicalinformation-Personaldata"/}}Personal data ===
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207 207  There can be studies or registers which contain personal data. Access to this data can be restricted by special privilege.
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209 209  These options can be set:
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211 211  * user can see personal data
212 212  * user can't see personal data
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214 214  \\
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216 216  = {{id name="04.Technicalinformation-8.Logging"/}}8. Logging =
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218 218  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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220 220  There are three different types of logging mechanisms:
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222 222  * **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.
223 223  * **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:
224 224  ** create
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234 234  ** what was changed
235 235  ** what is the new value
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237 237  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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239 239  **~ **
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241 241  = {{id name="04.Technicalinformation-9.Softwaredevelopment"/}}9. Software development =
242 242  
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243 243  === {{id name="04.Technicalinformation-Issuetracking"/}}Issue tracking ===
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245 245  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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247 247  === {{id name="04.Technicalinformation-Changesmanagement"/}}Changes management ===
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249 249  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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251 251  === {{id name="04.Technicalinformation-Versioning"/}}Versioning ===
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253 253  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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255 255  === {{id name="04.Technicalinformation-Codereview"/}}Code review ===
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257 257  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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259 259  **~ **
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261 261  = {{id name="04.Technicalinformation-10.Qualityassurance"/}}10. Quality assurance =
262 262  
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263 263  === {{id name="04.Technicalinformation-Testingenvironment"/}}Testing environment ===
264 264  
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265 265  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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267 267  === {{id name="04.Technicalinformation-Unittesting"/}}Unit testing ===
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269 269  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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271 271  === {{id name="04.Technicalinformation-Applicationtesting"/}}Application testing ===
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273 273  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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275 275  === {{id name="04.Technicalinformation-Publishing"/}}Publishing ===
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277 277  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.
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