Project Database - HEALTHY FUTURES€¦ · The software Geoportal Server uses US English and these...

www.healthyfutures.eu

HEALTHY FUTURES

Health, environmental change and adaptive capacity; mapping, examining & anticipating future risks of water-related vector-borne

diseases in eastern Africa

Collaborative Project Seventh Framework Programme

Cooperation

Deliverable D2.3

Project Database

Grant Agreement no. 266327

The research leading to these results has received funding from the European Community’s Seventh Framework Programme

(FP7/2007-2013) under grant agreement no 266327. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which

may be made of the information contained therein.

http://www.healthyfutures.eu/

HEALTHY FUTURES FP7: 266327 – D2.3 Project database

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Work Package WP2 - Disease information & database construction

Task Task 2.7 Creation of an online project database (information platform)

Dissemination level Public

Restricted to other programme partners (including the Commission Service)

Restricted to a group specified by the consortium (including the Commission Service)

Confidential, only for members of the consortium (including the Commission Service)

Publishing date Contractual: M36 Actual: M39

Deliverable 2.3 Version 1 Draft Final

WP/Task Leader TCD

Contact person Laragh Larsen, Stefan Kienberger

Contributors Richard Schörghofer, Stefan Kienberger

Short summary This document includes the user manual for the HEALTHY FUTURES online database and describes the objectives of the database and the design of its construction

Keywords metadata portal, online database

Document HEALTHYFUTURES_D2_3.docx

History Chart

Issue Date Changed page (s) Cause of change Implemented by

v.1 05/03/2014 all creation Richard Schörghofer

All rights reserved

This document may not be copied, reproduced or modified in whole or in part for any purpose without the written permission from the HEALTHY FUTURES Consortium. In addition to such written permission to copy, reproduce or modify this document in whole or part, an acknowledgement of the authors of the document and all applicable portions of the copyright must be clearly referenced.


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Table of Contents

1 Abbreviations ................................................................................................................. 3

2 Summary ....................................................................................................................... 4

3 Scope & Objectives ........................................................................................................ 4

4 Technical Implementation .............................................................................................. 4

4.1 Linux Server / Debian 6 .......................................................................................... 6

4.2 Apache Tomcat ....................................................................................................... 6

4.3 Esri Geoportal Server ............................................................................................. 6

4.3.1 Installation ....................................................................................................... 6

4.3.2 Configuration ................................................................................................... 7

4.3.3 Customisation .................................................................................................. 7

4.4 ApacheDS (LDAP) .................................................................................................. 8

4.5 Linux Server / CentOS – FTP ................................................................................. 8

4.6 MySQL .................................................................................................................... 8

5 Conclusion ..................................................................................................................... 8

6 ANNEX 1 ....................................................................................................................... 9

1 Abbreviations

CSW Catalogue Service for the Web

FDGC Federal Geographic Data Committee

FTP File Transfer Protocol

GIS Geographic Information System

HF HEALTHY FUTURES

HTTP Hypertext Transfer Protocol

HTML Hypertext Markup Language

ICTP International Centre for Theoretical Physics

LDAP Lightweight Directory Access Protocol

ILRI International Livestock Research Institute

IP Internet Protocol

ISO International Organization for Standardization

JSP JavaServer Pages

OGC Open Geospatial Consortium

OS operating system

PLUS Paris Lodron University of Salzburg

SQL Structured Query Language

URL Uniform Resource Locator

WAN Wide-area network

WAR Web application Archive

WP Work package

XML Extensible Markup Language


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2 Summary This deliverable produced an online database comprising data collected, quality assured and collated within Work Package (WP) 2 as well as other WPs in the HEALTHY FUTURES project. The database includes metadata of the produced output datasets as well direct access to data. Where restrictions apply, relevant contacts are identified. Initially only accessible to members of the HEALTHY FUTURES consortium and to non-consortium members of the project’s Executive Committee, the information platform will subsequently be made open access at the end of the project and will help allow access and dissemination of results and data produced in HEALTHY FUTURES. In summary, deliverable 2.3 designed the online database and developed its structure, identified a metadata profile, implemented and programmed the online database with open source software products, and currently integrates the results from the various outputs of HEALTHY FUTURES in the online database.

3 Scope & Objectives One aim of the HEALTHY FUTURES project is to set up a metadata portal to summarize existing outcomes of different projects or topics in one inventory. First of all this speeds up the searching time. Instead of searching through many different sources, the database now stands as one source holding all the required information. Another advantage is that it reduces redundancy as the same metadata or data do not need to be uploaded again elsewhere. Additionally, the database provides an overview (cataloguing) and access to data produced in HEALTHY FUTURES (sharing & searching). The major objective of summarizing metadata and correlating data this way is to provide a standardized format that enables interoperability with other metadata systems, or systems that are able to read metadata, that uses ISO and FDGC standards. The standardized metadata is query-able via the OGC CSW standard. The portal is also a collaboration-enabled tool as users can work simultaneously and the entries are posted in near real time. There are several different roles implemented to categorize the users. The basic one is a registered user who can save and search results. Editors are those who either enter metadata from scratch or upload an existing metadata file (xml) to the Geoportal. Finally, administrators can create and manage user roles, and most importantly they make metadata records publicly accessible after quality control.

4 Technical Implementation The system and all depending applications which run this metadata portal are set up and hosted at the International Livestock Research Institute (ILRI) in Nairobi, Kenya. The link to this portal is: http://41.204.190.50/geoportal/catalog/main/home.page. The Paris Lodron University of Salzburg (PLUS) performed the portal customisations and related programming. The data is stored in a File Transfer Protocol (FTP) system that is only accessible via the portal. The International Centre for Theoretical Physics (ICTP) hosts the FTP server, as this was the only institution with enough data storage space. A technical overview is presented in Figure 1. The software Geoportal Server uses US English and these terms are used in this document to keep the original wording and to find it in the folder structure.

http://41.204.190.50/geoportal/catalog/main/home.page


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Figure 1 System architecture


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4.1 Linux Server / Debian 6 All components to run this metadata portal are hosted on a GNU/Linux server (a real physical machine) with Debian 6 as operating system. ILRI hosts and administrates/maintains this server. Debian is developed by Debian Project and is a free operating system (OS) that is called Debian GNU/Linux. The word “free” has here two meanings, first and most important it is free of charge and second it is open source, which means that you can adapt everything you like to your needs.

4.2 Apache Tomcat The installed version on this Linux server is Apache Tomcat 6.0.35. Apache Tomcat is software that is an open source web server and servlet container. The Apache Software Foundation offers this software free of charge. This server is not a physical server, but the software acts like a server on any server or client. The special thing about this web server is the possibility of hosting websites (HTTP server) as well as JavaScript files (JavaServer Pages that are translated into servlets) to display/execute them on client-side or to run tasks backend on the real Linux server. This web server provides a folder that can be accessed via the internet if the port is unlocked by the firewall. The Apache Tomcat offers several installation options. The server and especially the applications to run on this web server need a Java installation.

4.3 Esri Geoportal Server ESRI is an American company that develops geographic information system (GIS) software. ESRI is known for proprietary products but also for quality. ESRI developed the ESRI Geoportal Server that is a metadata storage system. The Geoportal Server is free of charge and open source. The server also follows the Catalogue Service for the Web standard (CSW) of the Open Geospatial Consortium (OGC). ESRI describes the Geoportal this way: “ESRI Geoportal Server is a free, open source product that enables discovery and use of geospatial resources including datasets, rasters, and Web services. It helps organizations manage and publish metadata for their geospatial resources to let users discover and connect to those resources. The Geoportal Server supports standards-based clearinghouse and metadata discovery applications.”1

4.3.1 Installation The Geoportal Server is packed into a Web application ARchive (WAR - file). To install it the .war file is put in the “webapps” folder of Apache Tomcat. The Tomcat must now be changed from stopped mode to the running mode. It is no problem if the tomcat is already running. After placing the .war file into this folder Apache Tomcat starts to deploy it and makes a new folder that is named with the name of the .war file. This creation process takes a while in the background. After approximately one minute, the installation is ready to use. By default, the Geoportal server uses a simple login feature that can be extended by the use of Lightweight Directory Access Protocol (LDAP). The Geoportal Server is now accessible via internet:

<servername> name of the server where the Apache Tomcat runs, locally this could be

localhost or the IP address (Internet Protocol, for example: 41.204.190.50).

1 http://www.esri.com/software/arcgis/geoportal


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8080 this is the default port of Apache Tomcat

http://<servername>:8080/geoportal/catalog/main/home.page

The HF portal is now available through:


4.3.2 Configuration To make the Geoportal accessible from anywhere of the world via the internet, change the port to 80, this is the default port for HTTP and is open or needs to be set open if it is not by default in the firewall. The Uniform Resource Locator (URL) then changes because the port 80 does not need to be specified any longer and a specific IP instead of local host have to be taken.


4.3.3 Customisation The Geoportal contains a Wiki where ESRI offers help for the customisation. The following topics have been customised by PLUS:

Theme: There is an option to apply a custom theme. Therefore, we have taken an existing

theme (a Cascading Style Sheets file (.css)) and applied the colours of the logo etc. The size

and type of the text can be adjusted as well as the position of the elements like the banner,

navigation bar or the footer. All design relevant modifications can be applied in this file.

gpt.xml: Here the LDAP adapter is registered, which manages user access. By default, a

simple adapter is preconfigured and used when first launching. The roles are defined inside

the xml file. When more people are using this, especially with online access, an LDAP

adapter solution is favoured.

gpt.properties: This is a file that associates textblocks to internal variables (placekeeper) that

are going to be represented on the final HTML side. There we made changes to make the

metadata requirements more comprehensive for the editors, or we adjusted general text

blocks like the footer.

Folder ‘catalog’: This folder contains all content that is presented when the Geoportal is

opened. Here is the place where the website content can be adjusted. The websites are

generated with JSP files that contains also Java code snippets.



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4.4 ApacheDS (LDAP) In order to use this Geoportal a Lightweight Directory Access Protocol (LDAP) authentication server is setup, in this case an Apache Directory Studio was chosen. The LDAP defines users and groups, the main user maintenance can be done in the Geoportal itself, which user belongs to which group. The groups also indicate the access level, normally starting from a registered user, to an editor and finally a reviewer. In this Geoportal the reviewer is also the administrator.

4.5 Linux Server / CentOS – FTP ICTP hosts the FTP server. The server is used in this project to store data that belongs to the metadata. The decision not to host it on the ILRI server was made because of the expected big amount of data and the slow internet connection. One big advantage is also that ICTP already hosts a large amount of climate data which therefore do not have to be moved. PLUS implemented the FTP upload functionality into Geoportal Server. The editor of a metadata entry can now directly upload data that belongs to this metadata. First the data has to be selected on the local computer. After selecting, the editor presses the upload button and the data are immediately available online. The data stored with the FTP can be accessed from the website (http://clima-dods.ictp.it/d10/HEALTHY_FUTURES/FTP_UPLOAD/ ) for viewing and downloading data but uploading new data is only possible if you are logged in and use an ftp program. The login process and uploading data is done by a JSP file that cannot be accessed online.

4.6 MySQL The Geoportal Server uses a MySQL database. The Geoportal could also use different up-to-date databases, but ILRI has decided to use this database. When downloading the Geoportal Server several database scripts are included that contain different SQL statements to create the required tables.

5 Conclusion The HEALTHY FUTURES metadata portal is currently available and will now be filled with data entries by the different partners in the consortium. Therefore a user manual has been designed which is attached to this deliverable as Annex 1. Once the database is filled, the portal will be made accessible to the public which will be accompanied by dissemination in different newsletters etc. Currently links have been established to the Eastern African Community (EAC) and its activities in regard to climate change adaptation to maintain long term sustainability of the portal.

http://clima-dods.ictp.it/d10/HEALTHY_FUTURES/FTP_UPLOAD/

http://clima-dods.ictp.it/d10/HEALTHY_FUTURES/FTP_UPLOAD/


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6 ANNEX 1

FUTURE WITH GEOINFORMATION > www.uni-salzburg.at/zgis/

Salzburg, 21.03.2014

Metadata

Catalogue

Editor manual

Organisation Paris-Lodron Universität Salzburg (PLUS)

Department of Geoinformatics (Z_GIS)

International Livestock Research Organisation

(ILRI)

University of Rwanda, Centre for Geographic

Information Systems (UR-CGIS)

Author(s) Richard Schörghofer

Stefan Kienberger

Period 06-12/2013

Delivery date 25.02.2014

Status V2

Distribution level Project Internal

European Union’s Seventh Framework Programme (FP7/2007-2013)

The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013)

FUTURE WITH GEOINFORMATION > www.uni-salzburg.at/zgis/ 2

"The only way to discover the limits of the possible

is to go beyond them into the impossible"

(Arthur C. Clarke)

For Data Publisher

Table of Contents

TABLE OF CONTENTS ........................................................................................................................................ 2

1 INTRODUCTION ....................................................................................................................................... 3

2 ADD AND MANAGE THE METADATA ....................................................................................................... 4

2.1 ADD/CREATE OR UPLOAD NEW METADATA ...................................................................................................... 4

Add metadata manually ................................................................................................................................. 5

Enter/Change metadata ................................................................................................................................. 7

Upload existing metadata to the geoportal ................................................................................................. 10

2.2 MANAGE YOUR METADATA ........................................................................................................................ 11

3 SEARCH METADATA ...............................................................................................................................13

Step1: Navigate to the search page .............................................................................................................. 13

Step2: Execute the search ............................................................................................................................. 14

4 STANDARD VALIDATION OF A XML FILE TO UPLOAD TO THE GEOPORTAL..............................................15

Step1: Select the file ...................................................................................................................................... 15

Step2: Validation........................................................................................................................................... 15

5 OTHER INFORMATION ............................................................................................................................17

Personal Information .................................................................................................................................... 17

6 CONTACT ................................................................................................................................................18


1 Introduction

Geoportal is a Free and Open Source Software (FOSS) that enables discovery and use of

geospatial resources including datasets, rasters, and web services. It helps manage and publish

metadata for geospatial resources to let users discover and connect to those resources. The

Geoportal supports standards-based clearinghouse and metadata discovery applications.

The HEALTHY FUTURES metadata portal is available using the following link

http://41.204.190.50/geoportal/catalog/main/home.page (Figure 1).

Figure 1: The public metadata entry site

To ensure interoperability with other catalogue services on the web (e.g. Climate Adapt), the

created metadata follows international standards.

Opens the

search site

Opens the add

metadata site

(Login required)



The ISO 19139 Metadata Standard has been taken and extended to achieve the potential

connection to other portals.

Searches on all publicly available metadata entries can be requested without registering at the

application as shown in Figure 18. Subsequently, search results are presented in a list. By

default a metadata record is presented in "simple-view" presenting only the abstract and some

contact info. By choosing another view-mode the user is able to view all the entered attributes.

2 Add and manage the metadata

This section includes a description on how to add new metadata records. It is possible to create

this manually step-by-step or to upload existing metadata information directly as a XML

file.There is also a description on how to edit your created metadata entries.

2.1 Add/Create or Upload new metadata

You must be logged in.

Choose the ‘Add HF-Metadata’ tab on the main site


This is the entry site (Figure 2) of the geoportal where you can start adding (creating or

uploading) new metadata records.

Figure 2: Main page for creating and uploading metadata

Choose either

manually

editing or

uploading an

existing

metadata

XML file



Add metadata manually

You must be logged in

1. Select “Add metadata manually” (Figure 3)

2. Select the button “Proceed” (Figure 3)

Figure 3: Add metadata manually

3. Select the Metadata standard on the criteria that describe best your data (Figure 4)

4. Select the button “Proceed” (Figure 4)

Figure 4: Selection of the metadata standard

Standards description1:

Dublin Core: This standard is mostly used to describe documents and other objects in the

internet. Author is the „Dublin Core Metadata Initiative“ (DCMI).

FGDC: The standard is called ‘Content Standard for Digital Geospatial Metadata’ (CSDGM).

Since the author is the ‘Federal Geographic Data Committee’ (FGDC), the standard is better

known as FGDC metadata standard. This standard is mostly used in North America, but is also

1 http://www.fgdc.gov/metadata/geospatial-metadata-standards

http://www.fgdc.gov/metadata/geospatial-metadata-standards


used in the rest of the world. The newest FGDC standard generation will be based on ISO

19115.

ISO 19115: The basic ISO metadata standard for the description of geographic information and

services.

ISO 19119: Extensions of the service metadata model. An affiliate standard that supports the

detailed description of digital geospatial services including geospatial data portals, web

mapping applications, data models and online data processing services. The standard can be

used in conjunction with ISO 19115 to document services associated with a specific data

set/series or independently to document a service.

ISO 19115 – 2: Extensions for imagery and gridded data. The basic ISO 19115 metadata

standard plus extended elements for the description of imagery, gridded data and data collected

using instruments, e.g. monitoring stations and measurement devices. These extensions also

include improved descriptions of lineage and processing information.

Dublin Core standard:

The Dublin Core standard needs a minimum of mandatory fields that are marked with *

(asterisk)

The Dublin Core requires also the type specification of the Service URL, choosing the

“Resource Typ” which belongs to the URL

Figure 5: Example of a required field (‘Title’) using the Dublin Core standard

FDGC and ISO standards:

The other standards indicate with a yellow warning triangle where to enter the required

“minimum” values (see Figure 6)


Enter/Change metadata

If the metadata record contains the minimum required information to fulfill the standard, no

warning triangle (Figure 6) and no associated error message will appear.

Figure 6: This metadata record doesn’t fit the standard

Additionally you can add a link/URL to data that is accessible via the internet below the section

with the metadata information entered so far (Figure 7).

If you know the URL you can skip the first 3 steps and jump to the 4th step.

If you don’t have data online accessible, it is possible to upload the data to our FTP server

(hosted at ICTP) and get an URL from this uploaded data.

Only one data set per each upload is possible.

The size is limited to one GB.

Allowed formats: no restrictions by now!

1. Select the ‘Choose/Upload/Search’ button – depending depends on your browser – and

select the file you wish to upload from your computer.

Figure 7: File Upload section below the main metadata specifications

The record is missing still some values to fit the

minimum requirement of the standard


2. When the data is selected the file name appears as in Figure 8 (display depends on your

browser). The ‘Upload File’ button uploads the data and an URL link of the data will be

generated.

The uploaded data is public and can be accessed by everyone who knows the URL.

Figure 8: The selected file is ready to be uploaded

3. When the upload is finished, an URL link to the data is shown in the box below (Figure

9).

Figure 9: Result box with the generated URL where the data can be downloaded from

4. Copy the URL (Figure 9) and paste it into the box as shown in Figure 10: In the

‘Distribution’ tab check both the ‘Distribution’ and the ‘Online’ checkboxes and insert

the URL into the text field.

The file name or the file path is

displayed when it is selected.


Figure 10: How data can be linked to the metadata


Upload existing metadata to the geoportal

You must be logged in

On this page (Figure 11) you can upload metadata records in XML format which correspond to

the metadata standards. You are able to validate the standard compliancy before uploading by

using the ‘Validate' button. XML files that follow standards such as FGDC, ISO-based profiles,

Dublin Core, etc are uploadable. When using the ‘Upload’ button, the XML file is automatically

validated before it is inserted into the geoportal. Only correct XML files will be uploaded.

Figure 11: Upload and Validate your metadata

1: Select a

file on the

local disc

2a: Inserting a XML file to the geoportal

2b: OPTIONAL: Standard validation

of the XML file


2.2 Manage your Metadata

After adding at least one metadata record, you are able to manage the created metadata.

Select the ‘ADMIN’ tab in the main bar, and then select the ‘Manage’ tab from the subbar

(Figure 12).

Figure 12: Manage your Metadata

The Metadata can be assigned with four different status

Set as Published (Figure 13)

Set as Incomplete (Figure 14)

Set Access Level (Figure 15)

Delete (Figure 16)

“Set as Published” is the default after creation and means that the metadata is complete

Figure 13: Publish the Metadata

The

metadata

you have

created!

2. Select

the tab

“Manage”

1. Select

the tab

“ADMIN”


Figure 14: Mark your Metadata as Incomplete

Figure 15: Provide other publishers access to your Metadata

If you don’t select a group with limited access permission levels (which is the default), the

metadata can be accessed by anyone (once it ischecked and released by the administrator).

‘gpt_publishers’ are editors (higher access level than ‘gpt_registeredUsers’)

‘gpt_registeredUsers’ are able to log in without additional rights (not used in the project

so far)

Finally, there is also an option to delete metadata entries. The publishers can only delete their

own created metadata records, but the administrators are able to delete metadata from other

users.

Figure 16: Delete Metadata


3 Search Metadata

No Login required to see approved metadata records

With Login, all metadata records are displayed

Step1: Navigate to the search page

Select the search tile (left symbol: magnifier) (Figure 17) on the home screen of the geoportal.

When moving with the mouse over the tile, it will dim. Clicking on this image opens the search

page.

Figure 17: Click on the search tile


Step2: Execute the search

In the search field (Figure 18) you can enter a specific term you are looking for, or leave it blank

to get all records. On the right side appears a list of records that belong to your search criteria.

Figure 18: Search page and result list

Options on the metadata:

Open: Opens the related dataset for downloading

Preview: Gives a online preview in a new map window of the downloadable dataset

Metadata: Displays the metadata information with a style

Metadata XML: Displays the metadata information in raw XML

Zoom To: Zooms to the region where the metadata record belongs to

Select the “Search” button

Result list


4 Standard validation of a XML file to upload

to the geoportal

Registered users can only validate XML files (existing metadata records from other

platforms) (see Figure 20)

Publisher and administrators also have this functionality(see Figure 19, Figure 11 to get

an idea where this function is)

When the validation is successful, a green notifier appears with the corresponding information.

If the validation detects an error in the XML file, a red notifier appears with the related error

information.

Step1: Select the file

Select the “Select file” button and choose the file on your local disk.

Step2: Validation

Select the “Validate” button to run the test if the XML file fits the standards of the geoportal. If

the validation is successful, the file can be uploaded (Upload existing metadata to the

geoportal).

If you are a publisher (more rights than registered users) or administrator you can validate the

metadata XML file in the upload section. (Figure 19)

Figure 19:Validation of a XML file in the Upload section for publishers or administrator

Step 1

Step 2


If you are a registered user only (lowest rights in the geoportal), you get a “VALIDATION” tab

(Figure 20) where you can select the XML file for validation. The metadata will not be stored in

the geoportal, it will be only validated!

Figure 20: Validation of an XML file for registered users

Step 1

Step 2


5 Other Information

Personal Information

When choosing the “My Profile” button (Figure 21) in the upper right corner, you can modify

your personal information. The username is not changeable once it has been set by the

administrator.

Figure 21: My Profile


6 Contact

Richard Schörghofer

University of Salzburg

Interfaculty Department of Geoinformatics

[T] +43 662 8044 7592

[E] [email protected]

Dr. Stefan Kienberger

University of Salzburg

Interfaculty Department of Geoinformatics

[T] +43 662 8044 7567

[E] [email protected]

mailto:[email protected]

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