Manual

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Introduction
Installing Databrowse
Getting Started
Databrowse Configuration Options
Databrowse Library
Databrowse Plugin Format
- Plugin File Structure
- File Contents
Included Databrowse Plugins
License and Third-Party Components

Databrowse: An extensible data management platform

Tyler J. Lesthaeghe

tylerl@iastate.edu

Nathan D. Scheirer

scheirer@iastate.edu

Department of Aerospace Engineering and

Center for Nondestructive Evaluation

Iowa State University of Science and Technology

Ames, Iowa 50011

June 27, 2018

Version 0.8

Databrowse: An Exensible Data Management Platform

2012-2016 Iowa State University Research Foundation, Inc.

Redistribution and use in source and binary forms, with or without modiﬁcation, are permitted provided

that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the

following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and

the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or

promote products derived from this software without speciﬁc prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”

AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IM-

PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE

LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUEN-

TIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS

OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER

CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

This material is based on work supported by the Air Force Research Laboratory under Contract #FA8650-

10-D-5210, Task Order #023, and performed at Iowa State University.

DISTRIBUTION A. Approved for public release: distribution unlimited; 19 Aug 2016; 88ABW-2016-4051.

This material is based on work supported by NASA under Contract NNX16CL31C and performed by Iowa

State University as a subcontractor to TRI Austin.

Approved for public release by TRI Austin: distribution unlimited; 01 June 2018; by Carl W. Magnuson

(NDE Division Director).

Contents

1 Introduction 5

1.1 Motivation .............................................. 5

1.2 Implementation............................................ 5

1.2.1 XML.............................................. 5

1.2.2 XSLT ............................................. 6

1.3 DatabrowsePlugins ......................................... 6

2 Installing Databrowse 9

2.1 DatabrowsePlatforms ........................................ 9

2.2 DatabrowseServer .......................................... 9

2.2.1 Software Requirements and Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . 9

2.2.2 Installation on Unix-based Platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

2.3 CEFDatabrowse ........................................... 12

2.3.1 Software Requirements and Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . 12

2.3.2 Installation .......................................... 13

3 Getting Started 15

3.1 FeaturesofInterest.......................................... 15

3.2 CreatingNewDirectories ...................................... 16

3.3 UploadingFiles............................................ 17

4 Databrowse Conﬁguration Options 18

4.1 databrowse wsgi.conf ....................................... 18

4.2 iconmap.conf ............................................. 19

4.3 hiddenfiles.conf .......................................... 19

5 Databrowse Library 20

6 Databrowse Plugin Format 21

6.1 PluginFileStructure......................................... 21

6.2 FileContents ............................................. 21

6.2.1 init.py .......................................... 21

6.2.2 db plugin name.py ..................................... 21

6.2.3 dbs stylesheet name.xml ................................. 24

6.2.4 handlers.py ......................................... 25

7 Included Databrowse Plugins 26

7.1 ChecklistEditor ........................................... 26

7.2 ChecklistViewer ........................................... 26

7.3 Datacollectv1Viewer ........................................ 27

7.4 Datacollectv2Viewer ........................................ 27

7.5 DataguzzlerDataFile ........................................ 27

7.6 DataguzzlerSettingsFile ...................................... 28

7.7 DataTable .............................................. 28

7.8 Default ................................................ 28

7.9 Directory ............................................... 29

7.10FileOperations............................................ 29

7.11GenericBinaryFile.......................................... 29

7.12GenericHDF5File.......................................... 30

7.13GenericWSGIApplication ..................................... 30

7.14GenericXMLFile .......................................... 30

7.15ImageViewer............................................. 31

7.16MercurialRepository......................................... 31

7.17MovieViewer............................................. 31

7.18MultimediaDirectory ........................................ 32

7.19OﬃceViewer ............................................. 32

7.20PDFViewer.............................................. 33

7.21PlainTextFile ............................................ 33

7.22SolidWorksViewer .......................................... 33

7.23SpecimenManagementPlugin.................................... 34

7.24SpecimenDirectoryPlugin ..................................... 34

7.25 Specimen Group Management Plugin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

7.26SVGViewer.............................................. 35

7.27 Transducer Management Plugin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

7.28TransducerDirectoryPlugin..................................... 35

7.29TriggerLogPlugin.......................................... 35

7.30TriggerLogDirectoryPlugin .................................... 35

7.31WebPageViewer........................................... 36

7.32SDTFileViewer ........................................... 36

8 License and Third-Party Components 37

8.1 BSD3-ClauseLicense ........................................ 38

8.2 GNUGeneralPublicLicensev3................................... 39

8.3 GNU Lesser General Public License v3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

8.4 MITLicense.............................................. 51

8.5 ZopePublicLicensev2.1....................................... 52

8.6 ApacheLicensev2.0 ......................................... 53

1 Introduction

Databrowse is an extensible web-based platform for data viewing, manipulation, and management. At the

most basic level, Databrowse is a ﬁle browser; however, simple plugins enable Databrowse to represent data

of a variety of formats in a consistent way, enabling rapid viewing and transformation of those views to

narrow in on features of interest. The plugin architecture enables Databrowse to be adapted to support any

data format in which knowledge of the data format is available. Data from multiple sources or formats can

be pulled together into combined representations and then further transformed as desired. Furthermore, all

of these transformations are performed in real time.

1.1 Motivation

Databrowse was originally developed to aid in viewing and analyzing data collected in the ﬁeld of nonde-

structive evaluation (NDE). NDE is a broad, highly interdisciplinary ﬁeld related to the development of

measurement techniques that ﬁnd and characterize material ﬂaws and condition. Some well known NDE

techniques include visual/liquid penetrant inspection, magnetic particle inspection, ultrasonics, radiography,

and eddy current testing.

NDE techniques are capable of generating considerable amounts of data in very short periods of time.

However, many industrial NDE inspections today produce a simple pass/fail response as a result of a testing

process. Recorded raw data is often viewed as useless, or potentially even a liability, unless we have ways

to extract useful information. Ultimately, the problem of ﬁnding a needle in a haystack is particularly

challenging, especially if you do not know what you are looking for.

Even in research scenarios where we desire to collect large quantities of data to examine speciﬁc items,

handling large quantities of data can still be a challenge. As a part of a recent modeling eﬀort related

to development of a forward model for vibrothermography, a nondestructive testing technique that utilizes

vibration-induced heating to located cracks in materials, the need became apparent for better tools and data

management practices. It was known at the beginning of the work that a considerable amount of data was

to be generated. In the end, a ﬁnal data table containing almost 25,000 entries was generated, along with

over 0.5 TB of raw data.

The authors sought to develop a tool that would help in the short term for dealing with the latter problem,

while serving as a spring board to further work toward dealing with the former problem. Databrowse was

the resulting tool.

1.2 Implementation

1.2.1 XML

Databrowse represents data as XML. XML (eXtensible Markup Language) is a standard that allows text

data to be hierarchically structured utilizing arbitrarily deﬁned tags. Special engines can then be used to

parse and manipulate such structured data. Figure 1 shows an example of a simple data set being structured

and stored in an XML format. The ﬁrst line of the sample XML ﬁle shows an experiment tag, and the

last line shows that tag being closed. Everything contained between the opening and closing tags can be

described as children. In this context, our measurements are children of the experiment. Thus, a hierarchical

data structure can be developed. Subsequently, we have represented all of the individual parameters for each

measurement as children of that measurement.

We can take it a step further and indicate that one of these parameters could have multiple values, as

seen with the voltage data. This is one major advantage of this type of data structure, as our spreadsheet

style data table does not necessarily make representing this type of data structure easy. We have made it

work here with a comma list of values in our data table; however, this does not work so easily with more

complicated data.

Furthermore, XML tends to work very nicely as a way of representing most data, since many frequently

used data formats internally represent data in a natural hierarchical structure, often as a convenient way

of dealing with the issue just described. Therefore, conversion to XML, if even required, is generally very

straightforward. Once represented as XML, Databrowse is able to leverage the power and speed of the open

# Sample Voltage Result

A-001

A-002

B-004

1V, 2V, 3V

1.5V

1.5V, 3V

Simple Experimental Data Table

</voltages>

</measurement>

</voltages>

</measurement>

</voltages>

</measurement>

</experiment>

Converted and Stored in a

Simple XML Representation

Opening Tag

Closing Tag

Parent

Children

Tag Name

Attribute

Attribute Name

Attribute Value

Figure 1: Sample XML Data

source XML engine libxml2. The result is being able to parse and transform considerable amounts of data

in seconds.

It is important to note that raw binary waveforms are not intended to be represented as XML; however,

pieces of them might be. More typically though, a plugin would utilize an interface provided by Databrowse

that enables the creation of images of such data. Such an image can be generated in real time and served to

the web browser by Databrowse. This would not be limited to images. Any format that could be displayed

in a web browser could be used, such as videos, animations, or any format that can use a web browser plugin

to display.

1.2.2 XSLT

Databrowse utilizes XSLT to transform data. XSLT (eXtensible Stylesheet Language Template) provides

an interface by which the user can deﬁne a set of transformations to be applied to XML data. In other

words, XML data and XSLT templates designed to act on that data are provided to the XSLT engine and

the engine will output a new set of XML data based on the transformation provided. This behavior can be

seen in Figure 2, where our sample data from Figure 1 has been transformed using an XSLT template.

Databrowse, being a web based platform, wants to build web pages utilizing the data being provided.

HTML, the language with which web pages are built, is a type of XML. As a result, our XSLT transform

is able to take our data ﬁle and build a web page dynamically in real time. Databrowse then handles the

process of serving that web page to a user in their web browser.

1.3 Databrowse Plugins

Databrowse plugins are responsible for providing the following: 1) registering the ﬁle types with which they

should be able to operate on, 2) providing an XML representation of the ﬁle, and 3) providing an XSLT

transform that converts the XML representation to the desired HTML view that is displayed in the web

browser. Plugins are also able to provide additional features that can be triggered or accessed from the web

view. Such features might include the automatic generation of animations, data conversions, or running of

processing scripts.

Since every ﬁle can be represented as XML, Databrowse provides an interface for recursively obtaining

an XML representation of entire directories and sub-directories. Thus, a single representation of multiple

ﬁles can be obtained. In addition to providing a set of plugins for some common ﬁle types, Databrowse

</voltages>

</measurement>

</voltages>

</measurement>

</voltages>

</measurement>

</experiment>

<xsl:stylesheet xmlns="http://www.w3.org/1999/xhtml"

xmlns:xsl="http://www.w3.org/1999/XSL/Transform">

<xsl:template match="experiment">

<html>

<head/>

<body>

<table>

<tr>

<th>#</th><th>Sample</th><th>Result</th>

</tr>

<xsl:apply-templates />

</table>

</body>

</html>

</xsl:template>

<xsl:template match="measurement">

<tr>

</tr>

</xsl:template>

</xsl:stylesheet>

XML File XSL Stylesheet

<html>

<head/>

<body>

<table>

<tr><th>#</th><th>Sample</th><th>Result</th></tr>

</table>

</body>

</html>

HTML Representation

HTML Source Code Web Browser View

Figure 2: Sample XML Data being Transformed with XSLT

includes some plugins designed to provide a simple interface for building such combined representations.

XSLT transformation stylesheets can also be provided on a per-directory basis if additional control is needed

for speciﬁc use cases.

2 Installing Databrowse

2.1 Databrowse Platforms

Databrowse comes in two ﬂavors, both of which contain the same functionality and provide nearly identical

feature sets. Databrowse Server utilizes a WSGI compliant web server which is hosted the end users data

storage system. The server version of Databrowse allows the end user to access their ﬁle system remotely

from any other device connected to the internet following a onetime installation process. Alternatively, CEF-

Databrowse has been implemented which utilizes CEFpython (Chromium Embedded Framework - Python)

to provide the entirety of the Databrowse library on a single client. This self contained client can be in-

stalled directly through PIP and will seclude the Databrowse session to the host machine. This version of

Databrowse can be especially eﬀective in environments where data cannot be accessed via the internet or be

even exposed to a network.

2.2 Databrowse Server

2.2.1 Software Requirements and Dependencies

Databrowse requires the use of a WSGI compliant web server. Databrowse has been tested extensively with

mod wsgi on Apache 2.2.15 on Red Hat Enterprise Linux 6.6 and Apache 2.4.10 on Ubuntu 15.04. The

usage of mod wsgi, Apache, and a Unix-based operating system are strongly recommended. Using Apache

on Windows has been preliminarily tested; however, its use is strongly discouraged at this time due to ﬁle

path issues that will be resolved in a later version of Databrowse.

Modern versions of Mozilla Firefox and Google Chrome are recommended for accessing Databrowse.

Usage of Microsoft Internet Explorer is strongly discouraged. Microsoft Edge has not yet been tested.

Databrowse is dependent upon Python 2 (2.6 or later, Python 3 is not supported at this time). Databrowse

also requires the following Python modules (available from PIP or the package management systems on Red

Hat and Ubuntu):

•python-lxml version 3.2 or greater

•python-magic version 0.2 or greater (python-magic-bin if platform is Windows)

•python-numpy version 1.8 or greater

•python-pillow version 2.3 or greater

Several Databrowse plugins packaged with the distribution also require the use of the following Python

modules:

•python-qrcode version 4.0 or greater

•Dataguzzler Python Bindings (http://thermal.cnde.iastate.edu/dataguzzler)

•Dataguzzler Units Support (http://thermal.cnde.iastate.edu/dataguzzler)

Databrowse also requires the use of mod rewrite for URL rewriting. Databrowse can be ran without this

support enabled; however, its use has not been tested extensively.

2.2.1.1 Experimental Windows Use A set of binary packages providing the necessary prerequisites

have been compiled and are available upon request for usage with Apache on Windows. These packages

require the usage of Apache compiled against the Microsoft Visual C++ 9 Runtime. This is a limitation

imposed by Python 2. WampServer 2.2d is one such binary distribution of Apache that meets these require-

ments. Please contact the author for additional information.

2.2.2 Installation on Unix-based Platforms

The necessary minimum prerequisites can be installed using the following commands on Debian-based plat-

forms:

sudo apt-get install python2.7 python-lxml python-magic (python-magic-bin if platform \

is Windows) python-numpy python-pip libjpeg libjpeg-dev libfreetype6 \

libfreetype6-dev zlib1g-dev apache2 libapache2-mod-wsgi libapache2-mod-rewrite \

python-dev python-setuptools libtiff5-dev libjpeg8-dev zlib1g-dev liblcms2-dev \

libwebp-dev tcl8.5-dev tk8.5-dev python-tk \

sudo pip install pillow

And for Fedora-based platforms:

sudo yum install python python-lxml python-magic python2-numpy python-pip libjpeg-turbo \

libjpeg-turbo-devel freetype freetype-devel zlib zlib-devel httpd mod_wsgi \

python-devel redhat-rpm-config libtiff-devel libjpeg-devel zlib-devel freetype-devel \

lcms2-devel libwebp-devel tcl-devel tk-devel

sudo pip install pillow

The package redhat-rpm-config is only required on Fedora 23 or later. The command dnf may also

be exchanged for yum on newer Fedora-based platforms as well. Obtain the Databrowse source from the

Databrowse website or from the GitHub repository (coming soon). From within the root directory, run the

following command:

sudo python setup.py install

This will install the Databrowse library components into the the Python site-packages directory. Ensure

that the necessary Apache modules are running and available by running the following command for Debian

platforms:

sudo a2enmod wsgi

sudo a2enmod rewrite

And for Fedora platforms, both modules should be enabled by default. Verify the presence of the

following lines in the ﬁle /etc/httpd/conf/httpd.conf or in any ﬁles contained in /etc/httpd/conf.d/

or /etc/httpd/conf.modules.d:

LoadModule rewrite_module modules/mod_rewrite.so

LoadModule wsgi_module modules/mod_wsgi.so

From the Databrowse source folder, copy the contents of the databrowse wsgi folder to an appropriate

location. For example, to install the server components in /var/www/databrowse, use the following command

from within the Databrowse source folder:

sudo mkdir /var/www/databrowse

sudo cp -a databrowse_wsgi/* /var/www/databrowse/

sudo chmod -R 755 /var/www/databrowse

Apache must now be conﬁgured. If working on a Debian-based system with a newer version of Apache,

create the ﬁle /etc/apache2/sites-available/databrowse.conf with the following example contents and

adjust as necessary for your system. On Fedora-based systems, the ﬁle name should be /etc/httpd/conf.

d/databrowse.conf with the contents below adjusted as necessary:

WSGIScriptAlias /databrowse /var/www/databrowse/databrowse.wsgi

Alias /dbres /var/www/databrowse/resources

# Implementation of proper user controls is strongly encouraged!

# Require SSL is also Strongly Encouraged But Must Be Appropriately Configured

# Also be sure to modify databrowse_wsgi.conf to reflect ‘‘https’’

# instead of ‘‘http’’ on all URLs

# SSLRequireSSL

# Suggest the following items to restrict to localhost

# Only disable if you know what you’re doing and have Apache properly configured

# AND have authentication enabled on Databrowse

Order deny,allow

Deny from all

Allow from 127.0.0.1

Options FollowSymLinks

# Rewrite Rules - No Modification Should Be Needed Unless You Change Location Above

RewriteEngine on

RedirectMatch ^databrowse$ /databrowse/

RewriteCond %{QUERY_STRING} path=

RewriteRule ^(.*)/databrowse\.wsgi(.*)$ $1/databrowse.wsgi [QSA]

RedirectMatch ^databrowse$ /databrowse/

RewriteCond %{QUERY_STRING} !path=

RewriteRule ^(.*)/databrowse\.wsgi(.*)$ $1/databrowse.wsgi?path=/$2 [QSA,L]

</Location>

WARNING! Improper conﬁguration of a web server can leave your computer and data at risk of

exposure. Databrowse does not provide any built-in authentication mechanism nor should it be relied on to

prevent access to ﬁles outside of the conﬁgured data root. Accordingly, usage of Databrowse on computer

systems in which web server access is available from the Internet is strongly discouraged without the usage

of SSL and an appropriate Apache authorization module. It is strongly encouraged that anyone deploying

Databrowse for use over the Internet be comfortable with securely conﬁguring and using Apache. The

authors provide no warranty and are not responsible for loss or damages. Please see the Databrowse license

for additional information.

The above conﬁguration assumes that the Databrowse WSGI components are installed in /var/www/

databrowse and will serve Databrowse from http://localhost/databrowse and will serve Databrowse

static resources from http://localhost/dbres on a default installation of Apache on Debian-based systems.

The above conﬁguration will utilize server default access permissions, so, you may wish to add additional

conﬁguration or ensure that your web server is not accessible from the Internet. Refer to the warning above.

The following command is required for Debian-based systems only and can be used to enable Databrowse:

sudo a2ensite databrowse.conf

Prior to restarting Apache, the ﬁles databrowse wsgi.conf and databrowse style.xml (or symbolic

links to these ﬁles) must exist in the same directory as databrowse.wsgi. It should be suﬃcient to simply

rename the ﬁle databrowse style.sample.xml to databrowse style.xml until you are ready to customize

the appearance of Databrowse. The databrowse wsgi.conf ﬁle will require some additional conﬁguration.

A sample ﬁle databrowse wsgi.sample.conf is provided.

The most critical line that must be changed in databrowse wsgi.conf from the sample provided ﬁle

is self.dataroot. This should be set to the absolute path of the directory containing the data you wish

Databrowse to serve. Databrowse provides very simple checks to keep the user inside directories below this

path; however, this should not be used as a method of security! Symbolic links pointing out of this directory

will be followed and there may be other methods available for a user to escape out of the data root path.

Additionally, you may wish to set self.requireuser=False if you do not presently have authenticaion

conﬁgured on Apache. This may be okay if your Apache instance is only accessible from the local machine.

However, if it is accessible to the world, it is highly encouraged to correctly conﬁgure authentication. See

the previous warning about security.

If you have SSL properly conﬁgured on your web server and you uncommented the SSLRequireSSL line in

databrowse.conf, you should update all URLs in databrowse wsgi.conf to show https at the beginning

instead of http.

It is also worth noting that ﬁles contained within data root must be at least readable by the web server

process owner. To take advantage of the full capabilities of Databrowse, you will also want write access

available to the web server process owner as well. Again, use caution when using Databrowse, especially if

you are not familiar with securely conﬁguring Apache. Additionally, if using SELinux or similar systems,

you will need to make additional conﬁguration changes to ensure the web server process has read/write

access to all ﬁles in the data repository. On newer Fedora systems, for example, if you set your dataroot to

/home/databrowse, then you could run the following command to allow access to Apache:

sudo chcon -R -t httpd_sys_rw_content_t /home/databrowse

Within databrowse wsgi.conf, you will also want to ensure that self.siteurl and self.resurl are

correct if you have changed any Apache settings from the defaults. You should also ensure that the directory

listed in self.checklistpath has been created within the data root directory. This setting is related to

the Checklist plugin, but, Databrowse presently will not run if this directory does not exist. This will be

corrected in future versions of Databrowse.

Please see Chapter 4 for more information on these ﬁles.

Restart the web server and Databrowse should now be ready for use. On Debian-based systems:

sudo service apache2 restart

On Fedora-based systems:

sudo service httpd restart

You should now be able to access Databrowse by visiting http://localhost/databrowse in your web

browser.

2.3 CEFDatabrowse

CEFDatabrowse is a standalone client that operates nearly identically to the server version of Databrowse,

however this version does not require a connection to a network and allows local usage of Databrowe’s feature

set.

2.3.1 Software Requirements and Dependencies

CEFDatabrowse utilizes the same dependencies as the server version with a few additions and can be

seen in Section 2.2.1. The dependencies are automatically pulled in through platform speciﬁc ﬁles in the

”requirements” folder of the root source directory. The Databrowse core architecture as been extensively

tested on Linux, however the CEFDatabrowse client is being used on both Linux and Windows platforms at

this time. Your experience may be diﬀerent if you are using an untested platform.

CEFDatabrowse requires Python 2.7 and will not function with any other version of Python at this

time. The following Python modules are also required, these should be automatically installed when the

PIP package or setup.py ﬁle is ran but if a package does not install correctly, then these are the packages

that are required:

•python-lxml version 3.2 or greater

•python-magic version 0.2 or greater (python-magic-bin if platform is Windows)

•python-numpy version 1.8 or greater

•python-pillow version 2.3 or greater

•cefpython3 version 57.0 or greater

2.3.2 Installation

On either Linux or Windows the installation process should be almost identical with the exception that the

python-magic library should be used on Linux and the python-magic-bin library should be used on Windows.

To install CEFDatabrowse verify that Python 2.7 is installed on your system. If not, run:

Linux:

sudo apt-get install python2.7

Windows:

Install Anaconda package manager or a Python 2.7 binary

CEFDatabrowse can be installed via PIP or from source. The PIP binaries are veriﬁed to work in

both Linux and Windows environments, therefore to install via PIP execute the following command in your

command prompt:

pip install databrowse

This will install CEFDatabrowse along with the components that would be required to run the server

version to your sites-packages directory within your Python installation directory. Following a successful

installation, CEFDatabrowse can be utilized in the following manner:

Usage: databrowse [-h] [-s path] [-e] [-g [path]]

Databrowse: An Extensible Data Management Platform

optional arguments:

-h, --help show this help message and exit

-s path, --setdataroot path path to set new dataroot

-e, --openconfig open cefdatabrowse config file

-g [path], --go [path] open cefdatabrowse in a directory

On a fresh install a few conﬁguration values will need to be changed. These include the dataroot directory

and any third party software packages that need to be added to the Python path during operation. The

CEFDatabrowse conﬁguration ﬁle can be accessed through the settings in the GUI or by using the command:

databrowse -e

This will open the conﬁguration ﬁle in your default editor. If the EDITOR envrionment variable is not

set then you will have to set it to your prefered editor program in order for these features to work. The

conﬁguration ﬁle will contain default variables like this:

[databrowse]

width = 800

height = 600

x=0

y=0

dataroot = C:/databrowse

limatix-qautils = C:/Users/nscheirer/Documents/dev/databrowse-utils/limatix-qautils

qautils = C:/Users/nscheirer/Documents/dev/databrowse-utils/QAutils

[3rdparty]

dataguzzlerlib = C:/Users/nscheirer/Documents/dev/dataguzzler-lib/python

nditoolbox = C:/Users/nscheirer/Documents/nditoolnew/NDITool

Note: If installing on a Linux platform, the conﬁguration ﬁle’s permissions might need to be changed to

allow write access.

From here you can set which directory you would like CEFDatabrowse to have access to (dataroot). Keep

in mind that CEFDatabrowse cannot access any ﬁles outside of this directory, therefore if you would like

access to all ﬁles, setting the dataroot to C:/ is an acceptable approach. When a new dataroot is set it will be

required that a directory called SOPs be created in the dataroot directory location therefore, CEFDatabrowse

will throw an error reminding you of this if you do not have a SOPs folder. The values following dataroot

correspond to required third party packages that diﬀerent plugins utilize. If you need that functionality,

replace these paths with the correct path to your installed copies. From this point CEFDatabrowse can be

used via the deﬁned usage above.

3 Getting Started

This section will provide some information on using the directory interface within Databrowse.

3.1 Features of Interest

1. Main Menu

Contains links to jump to the data directory

root, logout, and switch views

2. Current Location

Displays the location of the current view rela-

tive to the data directory root – click a folder

name to jump to it

3. File System Path

Displays the absolute path of the current view

in the ﬁle system

4. Move Up One Directory

Click this link to move up one directory until

you reach the data directory root

5. Current View Options

Displays a list of options available to modify the

current view

6. Available Views

Displays a list of various plugins that are capa-

ble of rendering the current ﬁle or folder and

views available within those plugins

7. Folder Icon

Click this folder icon to expand the folder and

dynamically load the contents of the sub folder

8. Right Click Context Menu

Right click the name of any folder or ﬁle in this

view to display this context menu

3.2 Creating New Directories

The following steps can be used to create new directories from Databrowse:

1) Navigate to the Folder that will Contain the New Folder

Using the Databrowse interface, locate the folder that will contain the

folder you wish to create.

2) Right Click Folder Name to Open Context Menu

Using the mouse, right click on the name of the folder you wish to contain

your new folder. If the current view is the location you wish to create a

new folder within, right click on the black text at the top. This is the

shaded area shown on the ﬁgure to the right.

3) Select New Folder Here from the Context Menu

4) Type a Name and Click OK

Type a name for your new folder. Spaces are special characters that are

permitted in folder names on your operating system may be used; however,

their use is discouraged.

5) Finished!

You will be taken to the new folder automatically.

3.3 Uploading Files

The following steps can be used to upload ﬁles using Databrowse:

1) Navigate to the Folder in which you wish to Upload Files

Using the Databrowse interface, locate the folder that will contain the ﬁles

you wish to upload.

2) Right Click Folder Name to Open Context Menu

Using the mouse, right click on the name of the folder in which you wish

to upload ﬁles. If the current view is the location you wish to upload ﬁles

to, right click on the black text at the top. This is the shaded area shown

on the ﬁgure to the right.

3) Select Upload Files Here from the Context Menu

4) Click Add Files to Open the File Selection Box

Inside the ﬁle selection box, you may hold Shift or Ctrl on the key-

board to select multiple ﬁles. Select Open once you have chosen

the ﬁle(s) you wish to upload. Repeat for any additional ﬁles to

be uploaded. The options you have selected will appear in the win-

dow.

Alternatively, Drag and Drop Files into the Upload Window

Using Windows Explorer, Finder, or Nautilus, depending on your operat-

ing system, you may drag ﬁles into the open space on the upload window.

The ﬁles will appear in the window.

5) Click Start Upload

You should see progress bars indicating the length of time remaining to

upload your ﬁles. If uploading photos, you will see a preview thumbnail

of the photo.

6) Click the X or Click Outside of the Upload Window to Close

The page will automatically refresh to show your new ﬁles. Do not close

the window while uploading is still taking place or your upload will be

interrupted.

4 Databrowse Conﬁguration Options

This section provides information about the various conﬁguration options that can be used to customize the

low level functionality of Databrowse.

4.1 databrowse wsgi.conf

The ﬁle databrowse wsgi.conf (or a symbolic link to this ﬁle) must be contained inside the same folder as

databrowse.wsgi. This ﬁle is a Python script that can be used to run code during the start of a web request

to the server. It is ran within the context of the web support.py ﬁle contained within databrowse/support

in the source distribution. web support.py is actually a Python class which is instantiated with the con-

ﬁguration from databrowse wsgi.conf and the default values contained within the class at the start of a

request. This code is ran directly during the call to web support. init . Accordingly any Python code

can be included within databrowse wsgi.conf and it will be executed in this context.

The following options can be set in this ﬁle:

Site URL self.siteurl (String)

Default: http://localhost/databrowse

The full URL to Databrowse. This is used internally to build URLs. No trailing slash should be used if

search engine optimized URLs are enabled. If you disable search engine optimized URLs, you should update

this to list the full URL to databrowse.wsgi.

Resource URL self.resurl (String)

Default: http://localhost/dbres

The full URL to Databrowse static resource ﬁles. This is used internally to build URLs to static JavaScript,

images, stylesheets, etc.

Logout URL self.logouturl (String)

Default: http://localhost/logout

The URL to use in order to trigger the web server’s logout mechanism. This will need to be adjusted de-

pending on your authentication method.

Icon Conﬁguration File self.icondbpath (String)

Default: os.path.join(os.path.dirname(databrowse.support. file ), "iconmap.conf")

The path to a ﬁle containing a ConﬁgParser-compatible conﬁguration ﬁle associating ﬁle extensions with

icons. See 4.2 for more information about the contents of this ﬁle.

Hidden File Conﬁguration File self.hiddenfiledbpath (String)

Default: os.path.join(os.path.dirname(databrowse.support. file ), "hiddenfiles.conf")

The path to a ﬁle containing a ConﬁgParser-compatible conﬁguration ﬁle containing Glob syntax strings that

can be used to hide certain ﬁles from view in the Databrowse directory views. See 4.3 for more information

about the contents of this ﬁle.

Search Engine Optimization self.seo urls (Boolean)

Default: True

When set to true, Databrowse will write out URLs that have been search engine optimized. Instead of the

URL http://localhost/databrowse.wsgi?path=/SOPs, the URL would be written as http://localhost/

databrowse/SOPs. Usage of this feature requires mod rewrite to be enabled with the options as suggested

in the Installation instructions. It is strongly encouraged to keep this feature turned on.

Other options can also be set in this ﬁle using the same format, if desired, for use in Databrowse plug-

ins.

4.2 iconmap.conf

This ﬁle generally does not need to be modiﬁed, unless you wish to build or modify plugins. This ﬁle tracks

the mapping between ﬁle types and icons. These icons are used to provide a graphical representation of a

ﬁle type within Databrowse. The ﬁle uses a Python ConﬁgParser module compatible format. There are two

sections that can be used inside this ﬁle: [Content-Type] and [Extension]. Content types are deﬁned

as speciﬁed in RFC 2045 and are determined utilizing libmagic. File extensions are matched against the

potion of the ﬁlename after the ﬁnal period. The content-type or extension becomes the parameter name in

iconmap.conf and the parameter value is the name of the ﬁle containing the icon served at the URL icons/

relative to the Databrowse resources URL (e.g. http://localhost/dbres/icons/folder.png).

The following is an example of how this ﬁle is laid out:

[Content-Type]

inode/directory=folder.png

application/x-directory=folder.png

[Extension]

txt=text-x-generic.png

html=text-html.png

All ﬁles that are unable to be matched with a conﬁguration option are given the icon unknown.png.

4.3 hiddenfiles.conf

This ﬁle can be used to hide ﬁles based on their ﬁle name. Glob expressions are permitted. This ﬁle uses

a Python ConﬁgParser module compatible format. There are two sections that can be used inside this ﬁle:

[Hidden] and [Shown]. The hidden section is used to deﬁne ﬁle names or glob expressions for ﬁlenames

that should be hidden from the Databrowse directory view. The shown section can be used to override glob

expressions contained in the hidden section for explicit ﬁle names. Glob expressions are also permitted here.

The parameter name is used only for comment and will be ignored by Databrowse. The parameter value

will be used by Databrowse to ﬁlter ﬁle lists in the directory view.

The following is an example of how this ﬁle is laid out:

[Hidden]

backup_files=*~

hidden_files=.*

generic_backup_files=*.bak

[Shown]

my_special_backup_file=MyBackup*.bak

5 Databrowse Library

The core components of Databrowse that are most directly responsible for building XML representations of

ﬁles and directories are packaged into Python modules. An interface has been provided that enables Python

scripts to leverage the power of Databrowse to quickly obtain XML representations for any ﬁle. This is

particularly useful in the context of processing scripts written in Python. This is also especially useful in

contexts in which the Databrowse plugin responsible for handling a particular type of ﬁle provides additional

information or meta data that wouldn’t otherwise be easily accessible working with the ﬁle directly.

The Databrowse library can be imported in Python with the following code:

from databrowse.lib import db_lib as dbl

The library contains one function named GetXML. This function will return the XML representation of a

ﬁle, as produced by Databrowse.

function dbl.GetXML(filename, output=dbl.OUTPUT ELEMENT, **params)

Aguments

ﬁlename String containing a relative or absolute path to the ﬁle of interest

output Determines the type of output to be returned from the function

dbl.OUTPUT ELEMENT returns an LXML etree.Element

dbl.OUTPUT ETREE returns an LXML etree.ElementTree

dbl.OUTPUT STRING returns a string containing the XML

dbl.OUTPUT STDOUT prints the XML string to stdout and returns nothing

**params A variable number of optional parameters that are treated the same way as query string

values that would be POST or GET to the web server when Databrowse is being used from the

web. Used to pass in various options into plugins.

Usage

>>> from databrowse.lib import db_lib as dbl

>>> dbl.GetXML(’/tmp/emptyfile’, output=dbl.OUTPUT_STDOUT)

<default:default>

<filename>emptyfile</filename>

<contenttype>text/plain</contenttype>

</default:default>

It is also worth mentioning the presence of the function DebugGetXML which operates identically to

GetXML, however, it launches a Python debugger session, enabling the user to step through the code line by

line.

6 Databrowse Plugin Format

This section provides documentation on nature of Databrowse plugins. It is intended to provide enough

information that skilled users may be able to build or customize their own Databrowse plugins, but it is not

intended to be a tutorial. Such material will be produced for Databrowse v1.0.

6.1 Plugin File Structure

Individual plugins are Python packages contained within the databrowse.plugins namespace. All plugin

names should start with the preﬁx db (this is a legacy requirement and will be removed in Databrowse

v1.0). The ﬁle structure of the package should be as follows:

db_plugin_name\

__init.py__

db_plugin_name.py

dbs_stylesheet_one.xml

dbs_stylesheet_two.xml

handlers.py

6.2 File Contents

This section will detail the required contents for each ﬁle in the plugin. For the purposes of providing an

example, let’s say we wish to construct a plugin that simply displays the name of a ﬁle to the web page.

This section will display the necessary ﬁle contents needed to produce such a plugin.

6.2.1 init.py

This ﬁle does not require any contents. Its presence is a trigger to the Python interpreter to search for

modules. However, you may ﬁnd it useful to place a docstring inside this ﬁle for usage from the Python

console and for documentation purposes. The presence of a copyright statement is strongly encouraged.

This ﬁle can also be used to initialize variables, though, this usage is strongly discouraged in the context of

the WSGI server.

6.2.2 db plugin name.py

This ﬁle must be named with the same name as the folder name. The top of the ﬁle should contain a

purposes.

This ﬁle must contain a class derived from databrowse.support.renderer support.renderer class

and named identically to the ﬁle name. It must have several class variables deﬁned:

namespace uri A string containing the fully qualiﬁed URL referring to the XML namespace for the plugin.

Existing Databrowse plugins follow the format http://thermal.cnde.iastate.edu/databrowse/

plugin_name.

namespace local A string containing the local abbreviated form of the namespace. You should take care

to avoid conﬂicts with other namespace preﬁxes.

Several other class variables are automatically initialized to defaults, but may be overridden by declaring

them as class variables to your inherited class:

default content mode A string identifying the default content mode to be loaded when no content mode

is speciﬁed. The content mode full is frequently used. This serves more as an internal identiﬁer for

use within the plugin; however, the content mode raw has special meaning. This content mode will

prevent the main WSGI script from outputting any content to the user. As a result, you can use the

raw content mode to serve binary content to the web browser. You must manually set the output

headers and return content as appropriate from your plugin per PEP 3333.

default style mode A string identifying the name of the stylesheet that should be applied to the content

output by default if one is not speciﬁed by the end user. This string should not include the dbs preﬁx.

See Section 6.2.3 for more information.

default recursion depth A number indicating how deep a plugin operating on a directory should recurse

down a directory tree by default. This value is not used by plugins that do not operate on directories

but should still be set.

An additional set of class variables will be initialized to contain references to objects used by other

portions of Databrowse that may be of convenience or use here:

relpath A string initialized to the ﬁle path of the currently requested ﬁle relative to the data root with a

leading forward slash. These paths are used by Databrowse internally to represent full ﬁle paths inside

URLs.

fullpath A string initialized to the absolute ﬁle path of the currently request ﬁle. This path should be

used to access the ﬁle.

web support A reference to the instantiated web support class, which contains information about the web

server request and the current conﬁguration of Databrowse.

handler support A reference to an instantiated handler support class, which provides functionality for

determining which types of plugins are capable of operating on a particular ﬁle. It also provides support

functionality to determine the icon used to represent a ﬁle.

caller A string that identiﬁes the plugin responsible for the call to this plugin. When set to databrowse,

the call to the plugin is the result of a direct request from the Databrowse WSGI application. Otherwise,

this string will contain the name of the plugin making the recursive call to get content from the plugin.

This is most frequently the Directory plugin, which can query a plugin for information about a ﬁle.

This information can then be displayed by the Directory plugin as a preview of a ﬁle’s contents.

handlers A list of other plugins that are capable of working with this particular type of ﬁle, in order of

precedence.

The class must contain at least one function – getContent. With the exception of the scenario in which

the content mode is set to raw, this function must return via with an LXML etree.Element, None, or raise

an exception. The keyword None should only be returned when the plugin is not called by Databrowse,

but rather is being called by another plugin. This is normally the desired behavior, unless your plugin

needs to return content to a directory plugin. The example contents of db plugin name.py displayed on the

following page will produce an XML document containing the ﬁlename of the requested ﬁle. The format of

the generated XML document is

<pn:pn xmlns:pn="http://thermal.cnde.iastate.edu/databrowse/plugin_name">

</pn:pn>

if the plugin were called with the ﬁlename some_file_name.txt. This example plugin is trivial, but provides

the framework needed to produce XML representations of any type of ﬁle.

#!/usr/bin/env python

###############################################################################

## Databrowse: An Extensible Data Management Platform ##

## ##

## This program is free software: you can redistribute it and/or modify ##

## it under the terms of the GNU General Public License as published by ##

## the Free Software Foundation, either version 3 of the License, or ##

## (at your option) any later version. ##

## ##

## This program is distributed in the hope that it will be useful, ##

## but WITHOUT ANY WARRANTY; without even the implied warranty of ##

## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ##

## GNU General Public License for more details. ##

## ##

## You should have received a copy of the GNU General Public License ##

## along with this program. If not, see <http://www.gnu.org/licenses/>. ##

###############################################################################

""" plugins/db_plugin_name/db_plugin_name.py - The Plugin Name Plugin """

from lxml import etree

from databrowse.support.renderer_support import renderer_class

class db_plugin_name(renderer_class):

""" The Plugin Name Plugin - This plugin is an example """

_namespace_uri = "http://thermal.cnde.iastate.edu/databrowse/plugin_name"

_namespace_local = "pn"

_default_content_mode = "full"

_default_style_mode = "default_view"

_default_recursion_depth = 2

def getContent(self):

if self._caller != "databrowse":

return None

else:

if self._content_mode == "full":

xmlroot = etree.Element(’{%s}%s’ % (self._namespace_uri, self._namespace_local),

nsmap=self.nsmap)

xmlchild = etree.SubElement(xmlroot, "filename", nsmap=self.nsmap)

xmlchild.text = os.path.basename(self._fullpath)

return xmlroot

else:

raise self.RendererException("Invalid Content Mode")

pass

6.2.3 dbs stylesheet name.xml

Plugins can contain any number of XSLT stylesheets that are used to transform the XML content produced

by the plugin for a particular ﬁle into HTML for display on the web browser. These stylesheet ﬁles must

be named with the preﬁx dbs and end with the extension .xml. Databrowse will automatically locate all

stylesheets located within the plugin named in this format and display them as options to the user in the

Databrowse menu. Databrowse will also search for stylesheets inside the data folders placed inside of the

.databrowse/stylesheets/db_plugin_name folder, enabling the end user to write stylesheets for custom

views relevant to a particular set of data.

This ﬁle does not contain a complete XSLT stylesheet. Rather, it contains XSLT template snippets which

will be combined with other snippets from other plugins that may be producing content displayed on the

page at any given time. This is particularly important in the context of a directory plugin that is displaying

representations of many diﬀerent ﬁles contained within that directory.

This ﬁle also does not produce a complete web page. Rather, it should be written such that it writes out

HTML snippets, which will be placed in the appropriate location on the web page.

The construction of an XSLT template and the usage of HTML is outside of the scope of this document.

Please refer to one of many tutorials on the topics available on line.

The following is an example of an XSLT stylesheet that could be used to transform the content produced

by the discussed plugin into HTML.

<xsl:template xmlns="http://www.w3.org/1999/xhtml"

xmlns:pn="http://thermal.cnde.iastate.edu/databrowse/plugin_name"

xmlns:xsl="http://www.w3.org/1999/XSL/Transform" match="pn:pn" mode="full">

</xsl:template>

6.2.4 handlers.py

Plugins must contain a handlers.py ﬁle. This ﬁle should contain one function with a name starting with

the preﬁx dbh . The name of this function will be used to determine the order of precedence in ascending

order in the case in which multiple plugins can operate on a ﬁle. This function receives three parameters:

path A string containing the full path to the ﬁle that has been requested.

contenttype A string containing the RFC 2045 compliant MIME type.

extension A string the portion of the ﬁlename after the ﬁnal period or empty if there is no period in the

ﬁlename.

The return from this function should either be the name of a plugin capable of responding to a request

for the given ﬁle or False otherwise.

Returning to the previous example, a handlers.py ﬁle for our example plugin might look like the ﬁle

displayed below. The displayed code will result in this plugin being able to respond to any ﬁle with the .txt

extension.

#!/usr/bin/env python

###############################################################################

## Databrowse: An Extensible Data Management Platform ##

## ##

## This program is free software: you can redistribute it and/or modify ##

## it under the terms of the GNU General Public License as published by ##

## the Free Software Foundation, either version 3 of the License, or ##

## (at your option) any later version. ##

## ##

## This program is distributed in the hope that it will be useful, ##

## but WITHOUT ANY WARRANTY; without even the implied warranty of ##

## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ##

## GNU General Public License for more details. ##

## ##

## You should have received a copy of the GNU General Public License ##

## along with this program. If not, see <http://www.gnu.org/licenses/>. ##

###############################################################################

""" plugins/handlers/dbh_plugin_name.py - Handler for the Plugin Name plugin """

def dbh_plugin_name(path, contenttype, extension):

""" Plugin Name Handler - Responds to *.txt files"""

if extension == "txt":

return "db_plugin_name"

else:

return False

7 Included Databrowse Plugins

This section details the various plugins that are included with Databrowse for working with a variety of dif-

ferent ﬁle types. Documentation in this section is a work in progress. For the time being, simple descriptions

of each plugin have been provided.

7.1 Checklist Editor

The checklist editor plugin is one of several Databrowse

plugins that were constructed to create and modify data.

Checklists (*.chx for checklist templates and *.chf for

ﬁlled checklists) are XML ﬁles that contain the necessary

information to document laboratory procedures. The

complete details of the ﬁle format are outside of the scope

of this document. However, this plugin enables the user

to open a checklist template, ﬁll out a checklist, and save

the ﬁlled checklist to the ﬁle system.

An experimental tool for modifying a checklist is be-

ing developed as well. This tool utilizes the Axel XML

JavaScript library (http://ssire.github.io/axel/) to

provide an interface for editing the ﬁle in the web browser.

This plugin is not intended to be used from within the

Databrowse library interface.

7.2 Checklist Viewer

The checklist viewer plugin displays ﬁlled checklist ﬁles

(*.chf). Checklists (*.chx for checklist templates and *.chf

for ﬁlled checklists) are XML ﬁles that contain the nec-

essary information to document laboratory procedures.

The complete details of the ﬁle format are outside of the

scope of this document. However, this plugin will display

the status of all checklist items, along with displaying

time stamp information and notes.

7.3 Datacollect v1 Viewer

Datacollect is a tool that enables the automation of data

collection processes. Version 1 of Datacollect provides an

interface for the entry of experimental parameters and

an interface to aid in automating use of data acquisition

tools. This plugin is responsible for displaying the data

saved by Datacollect in a meaningful fashion. It can dis-

play data in both a log-style format and in a tabular form,

capable of being sorted, ﬁltered, and searched.

7.4 Datacollect v2 Viewer

Datacollect is a tool that enables the automation of data

collection processes. Version 2 of Datacollect provides an

interface for the entry of experimental parameters, an in-

terface to aid in automating use of data acquisition tools,

and an interface for managing experimental processes and

procedures. This plugin is responsible for displaying the

data saved by Datacollect in a meaningful fashion. It can

display data in both a log-style format and in a tabular

form, capable of being sorted, ﬁltered, and searched.

7.5 Dataguzzler Data File

Dataguzzler is an open source extensible data acquisition

platform – providing a high speed mechanism for data

capture, storage, and visualization. Dataguzzler also pro-

vides bindings enabling simple integration with data col-

lection automation scripts and other related programs.

The Dataguzzler data ﬁle plugin for Databrowse enables

the user to view the data contained within Dataguzzler

binary data ﬁles (*.dgs, *.dgd, *.dga, *.dgz). The plu-

gin utilizes Matplotlib for Python to produce realtime

visualizations of data, in addition to displaying all of the

associated meta data. The plugin can also export data

from Dataguzzler data ﬁles into several other common

ﬁle formats, including CSV and MAT. The plugin is also

capable of exporting videos from the appropriate types of

data.

7.6 Dataguzzler Settings File

Dataguzzler is an open source extensible data acquisition

platform – providing a high speed mechanism for data

capture, storage, and visualization. Dataguzzler also pro-

vides bindings enabling simple integration with data col-

lection automation scripts and other related programs.

The Dataguzzler set ﬁle plugin for Databrowse enables

the user to examine the contents of Dataguzzler settings

ﬁles (*.set).

7.7 Data Table

The data table plugin is a tool designed to aid in the col-

lection and compilation of large data sets from multiple

sources. This plugin operates on *.tbl ﬁles. The exact

schema of the *.tbl ﬁle is outside of the scope of this doc-

ument; however, the tbl ﬁle is an XML ﬁle which instructs

the Data Table plugin where to ﬁnd data ﬁles and how to

select data from them. The end result is a new XML doc-

ument that combines all of this data together. This XML

document can then be rendered by Databrowse in the web

browser in the form of a searchable, sortable, and ﬁlter-

able table. This table can be exported to CSV from the

web browser as well. Additionally, this plugin can prove

to be very powerful when utilized inside of a processing

script using the Databrowse library, enabling rapid de-

velopment of data processing scripts that can operate on

large sets of data in real time.

7.8 Default

The default plugin is a catch-all plugin that can operate

on any type of ﬁle. This ensures that even for ﬁles in

which Databrowse is unable to determine the appropriate

plugin to use, or a plugin does not exist that supports a

particular ﬁle type, some set of information about the ﬁle

can be returned and displayed. This plugin will extract

basic ﬁle information, such as ﬁle name, size, timestamps,

and permissions.

7.9 Directory

The generic directory plugin is capable of scanning a

folder and building an XML representation of the contents

of that folder. It is also capable of recursively building a

representation of entire directory trees. In the web in-

terface, this is displayed as the default ﬁle browser view.

The web browser interface has a number of useful features

that enable the user to perform operations on ﬁles. See

Section 3 for additional information about this interface.

7.10 File Operations

The ﬁle operations plugin is a special plugin that is nor-

mally not visible from the web or library interface. This

plugin enables other plugins to perform special operations

on ﬁles, particularly those that do not yet exist.

7.11 Generic Binary File

The generic binary ﬁle plugin is capable of reading out

data in a hex and ASCII format from a binary data ﬁle. In

the web interface, generic information is displayed about

the ﬁle, along with an interactive hex viewer tool. The

viewer will only pull in a small chunk of the ﬁle at a time,

since binary ﬁles can be rather large. AJAX requests are

made by the web browser enabling the user to browse

through the ﬁle interactively in real time.

7.12 Generic HDF5 File

The HDF5 viewer plugin is a work-in-progress plugin that

will simply display the internal structure of an HDF5 ﬁle

at this time.

7.13 Generic WSGI Application

The generic WSGI application plugin will enable a WSGI

compliant Python script to be ran inside the context of

Databrowse. This is very useful for scenarios in which

an end user wishes to quickly create an interactive web

application within the context of a particular set of data

or for a task-oriented purpose without the need to create

an infrastructure in which that application will run.

7.14 Generic XML File

The generic XML ﬁle viewer will display a textual view

of an XML ﬁle, along with basic ﬁle information.

7.15 Image Viewer

The image viewer plugin will display an image, in addition

to all internal metadata and EXIF tags associated with

an image. The plugin also supports the ability to resize

images in real time for use by other plugins as well. It will

operate on any ﬁle type supported by the Python Imaging

Library, including *.png, *.jpg, *.bmp, and many more.

7.16 Mercurial Repository

Mercurial is a version tracking tool. The Mercurial

Repository Databrowse plugin is a work-in-progress that

will display warning information to users about uncom-

mitted changes and other potential concerns associated

with a Mercurial repository. This plugin overrides the

default Directory plugin, though, all other functionality

available from the directory plugin is still available in this

context.

7.17 Movie Viewer

The movie viewer plugin is an experimental plugin that

will attempt to stream video content to the users web

browser. This requires the usage of the appropriate plu-

gins and codecs on the end user computer. This plugin is

also capable of extracting preview frames from videos. It

will operate on any video format supported by FFMPEG.

7.18 Multimedia Directory

The multimedia directory plugin will display thumbnail

previews of image, video, and other multimedia content.

It will override the default directory plugin when the ma-

jority of the content inside of a folder can be displayed

with a thumbnail preview. Clicking on a thumbnail in

the multimedia directory plugin will display a larger ver-

sion of the image without leaving the page.

7.19 Oﬃce Viewer

The oﬃce viewer plugin provides an in-browser PDF pre-

view of word processor documents, spreadsheets, presen-

tations, and other document ﬁles. This plugin operates on

any ﬁle format supported by LibreOﬃce, including *.doc,

*.ppt, *.xls, *.odt, *.odp, *.ods, and many others.

7.20 PDF Viewer

The PDF viewer plugin will display a PDF ﬁle for the

user inside the web browser.

7.21 Plain Text File

The plain text ﬁle plugin displays the contents of any

plain text ﬁle inside the web browser. It also provides

a convenient interface for editing plain text ﬁles right in

the web browser. Backups will automatically be saved by

this plugin during a save operation. It will operate on all

ﬁles with the content-type of plain/text.

7.22 SolidWorks Viewer

The SolidWorks viewer plugin provides a quick low res-

olution image preview of a SolidWorks ﬁle in the web

browser. This plugin is also capable of providing a thumb-

nail for use in the context of the multimedia directory plu-

gin and other plugins where appropriate. It operates on

ﬁles with the *.sldprt, *.sldasm, and *.slddrw extensions.

7.23 Specimen Management Plugin

The Specimen Management plugin provides an interface

for storing and tracking information about specimens.

Operating on XML ﬁles containing the *.sdb extension,

it can produce a visual display of the details of a spec-

imen, including identiﬁcation, geometry, provenance in-

formation, images, bar code labels, etc. Additionally, uti-

lizing the Axel XML JavaScript library (http://ssire.

github.io/axel/), this plugin can also provide a web-

based interface to edit the details of a specimen on an in-

teractive form. The structure of the sdb ﬁles are outside of

the context of this document. Templates that control the

display and editing of specimen ﬁles can be modiﬁed, en-

abling the introduction of new parameters. This plugin is

also capable of combining multiple sources of data about

a specimen into one uniﬁed representation, highly useful

both on the web and in the context of the Databrowse

library. This capability is presently being used to enable

specimens to be placed into specimen groups – sharing all

of the parameters from the group and thus limiting the

unnecessary repetition of data across many ﬁles.

7.24 Specimen Directory Plugin

The Specimen Directory plugin is a complementary tool

to the Specimen Management plugin, overriding the direc-

tory plugin on directories that contain *.sdb ﬁles. This

plugin displays a tabular view of specimen parameters,

enabling the quick searching, ﬁltering, and sorting of en-

tire sets of specimen data. This plugin also provides easy

access needed to create new *.sdb ﬁles in the current lo-

cation.

7.25 Specimen Group Management Plugin

The Specimen Group Management plugin is a comple-

mentary tool to the Specimen Management plugin, pro-

viding similar functionality, but acting in the context of

*.sdg ﬁles. The schema deﬁning the *.sdg ﬁle is outside

of the context of this document; however, it is similar in

structure to the *.sdb ﬁle.

7.26 SVG Viewer

The SVG viewer plugin adds the necessary support to

ensure that *.svg vector graphics image ﬁles can be dis-

played on all web browsers, producing an image thumb-

nail and preview if necessary. It also produces thumbnails

for the multimedia directory plugin and in other contexts

as needed.

7.27 Transducer Management Plugin

The Transducer Management plugin is similar in func-

tionality to the Specimen Management plugin, but de-

signed in the context of managing parameters and other

information associated with ultrasonic transducers. The

plugin operates XML ﬁles with the extension *.tdb. The

structure of these ﬁles is outside of the context of this

document.

7.28 Transducer Directory Plugin

The Transducer Directory plugin is similar in functional-

ity to the Specimen Directory plugin, overriding the di-

rectory plugin on directories that contain *.tdb ﬁles, and

providing a tabular view of the data contained within,

enabling rapid searching, sorting, and ﬁltering.

7.29 Trigger Log Plugin

The Trigger Log plugin is similar in functionality to the

Transducer Management plugin, but designed in the con-

text of tracking the usage of ultrasonic transducers. An

interface with data acquisition software ensures that an

XML ﬁle with the *.tgl extension is recorded to ensure

accurate tracking of all experimental triggers. This plu-

gin will display the data from such a ﬁle in a tabular

form, enabling rapid searching, sorting, and ﬁltering. The

structure of the *.tgl ﬁle is outside of the context of this

document.

7.30 Trigger Log Directory Plugin

The Trigger Log Directory plugin functions similarly to

the Trigger Log plugin, but enabling an entire directory of

*.tgl ﬁles to be combined into one single representation.

This representation is displayed in tabular form, enabling

rapid searching, sorting and ﬁltering. This plugin also

provides the capability of exporting this data to a CSV

ﬁle for further analysis.

7.31 Web Page Viewer

The web page viewer plugin will display the contents of

an HTML ﬁle within the Databrowse interface. Combined

with the plain text editor plugin, this plugin can provide

a convenient mechanism for documentation while being

able to pull together all of the other resources available

inside the context of Databrowse.

7.32 SDT File Viewer

The SDT ﬁle viewer operates on .sdt ﬁles generated from

third party data collection software, i.e. Inspectionware.

With the ability to generate images and gifs of the in-

cluded data sets as well as collecting the header informa-

tion all of the experimental data is located in one easy

to ﬁnd location. Integration with the NDIToolBox is also

available if that software is available.

8 License and Third-Party Components

Databrowse is distributed under the terms of the BSD-3 clause license.

Databrowse is packaged with the following third party components:

Portions of this software are adapted from gnome-icon-theme-3.7.4:

2005-2013 The GNOME Project

License: LGPL v3 or CC-BY-SA v3.0

Portions of this software are adapted from jQuery-1.9.1:

2013 jQuery Foundation and other contributors

License: MIT

Portions of this software are adapted from DataTables-1.9.4:

2008-2010 Allan Jardine

License: GPL v2 or BSD-3

Portions of this software are adapted from hurry.ﬁlesize-0.9:

2009 Martijn Faassen, Startifact

License: ZPL v2.1

Portions of this software are adapted from prettify-4-Mar-2013:

2011 Mike Samuel et al

License: Apache v2.0

Portions of this software are adapted from jQuery-File-Upload-7.4.1-jquery.ui:

2013 Sebastian Tschan

License: MIT

Portions of this software are adapted from axel-1.1.2-beta:

2008 - 2010 Staphane Sire

License: LGPL v2.1 or newer

Portions of this software are adapted from images2gif.py:

2012 Almar Klein, Ant1, Marius van Voorden

License: BSD-3

Portions of this software are adapted from exif-py-1.2.0:

2002-2007 Gene Cash

2007-2013 Ianar Svi and contributors

License: BSD-3

Portions of this software are adapted from cefpython:

2012 The CEF Python authors - see the Authors ﬁle in cefpython repository.

See project website: https://github.com/cztomczak/cefpython

License: BSD-3

8.1 BSD 3-Clause License

Redistribution and use in source and binary forms, with or without modiﬁcation, are permitted provided

that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the

following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and

the following disclaimer in the documentation and/or other materials provided with the distribution.

3. The name of the author may not be used to endorse or promote products derived from this software

without speciﬁc prior written permission.

THIS SOFTWARE IS PROVIDED BY THE AUTHOR “AS IS” AND ANY EXPRESS OR IMPLIED

WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MER-

CHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT

SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEM-

PLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT

OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS IN-

TERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CON-

TRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN

ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF

SUCH DAMAGE.

8.2 GNU General Public License v3

GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

2007 Free Software Foundation, Inc. http://fsf.org/

Everyone is permitted to copy and distribute verbatim copies of this

license document, but changing it is not allowed.

Preamble

The GNU General Public License is a free, copyleft license for software and other kinds of works.

The licenses for most software and other practical works are designed to take away your freedom to

share and change the works. By contrast, the GNU General Public License is intended to guarantee your

freedom to share and change all versions of a program–to make sure it remains free software for all its

users. We, the Free Software Foundation, use the GNU General Public License for most of our software;

it applies also to any other work released this way by its authors. You can apply it to your programs,

too.

When we speak of free software, we are referring to freedom, not price. Our General Public Licenses

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To protect your rights, we need to prevent others from denying you these rights or asking you to

surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software,

or if you modify it: responsibilities to respect the freedom of others.

For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass

on to the recipients the same freedoms that you received. You must make sure that they, too, receive or

can get the source code. And you must show them these terms so they know their rights.

Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the

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Terms and Conditions

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Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contrib-

utor’s essential patent claims, to make, use, sell, oﬀer for sale, import and otherwise run, modify and

propagate the contents of its contributor version.

In the following three paragraphs, a “patent license” is any express agreement or commitment, however

denominated, not to enforce a patent (such as an express permission to practice a patent or covenant

not to sue for patent infringement). To “grant” such a patent license to a party means to make such

an agreement or commitment not to enforce a patent against the party.

If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of

the work is not available for anyone to copy, free of charge and under the terms of this License, through

a publicly available network server or other readily accessible means, then you must either (1) cause

the Corresponding Source to be so available, or (2) arrange to deprive yourself of the beneﬁt of the

patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of

this License, to extend the patent license to downstream recipients. “Knowingly relying” means you

have actual knowledge that, but for the patent license, your conveying the covered work in a country,

or your recipient’s use of the covered work in a country, would infringe one or more identiﬁable patents

in that country that you have reason to believe are valid.

If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by

procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving

the covered work authorizing them to use, propagate, modify or convey a speciﬁc copy of the covered

work, then the patent license you grant is automatically extended to all recipients of the covered work

and works based on it.

A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits

the exercise of, or is conditioned on the non-exercise of one or more of the rights that are speciﬁcally

granted under this License. You may not convey a covered work if you are a party to an arrangement

with a third party that is in the business of distributing software, under which you make payment to

the third party based on the extent of your activity of conveying the work, and under which the third

party grants, to any of the parties who would receive the covered work from you, a discriminatory

patent license (a) in connection with copies of the covered work conveyed by you (or copies made from

those copies), or (b) primarily for and in connection with speciﬁc products or compilations that contain

the covered work, unless you entered into that arrangement, or that patent license was granted, prior

to 28 March 2007.

Nothing in this License shall be construed as excluding or limiting any implied license or other defenses

to infringement that may otherwise be available to you under applicable patent law.

12. No Surrender of Others’ Freedom.

If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the

conditions of this License, they do not excuse you from the conditions of this License. If you cannot

convey a covered work so as to satisfy simultaneously your obligations under this License and any other

pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to

terms that obligate you to collect a royalty for further conveying from those to whom you convey the

Program, the only way you could satisfy both those terms and this License would be to refrain entirely

from conveying the Program.

13. Use with the GNU Aﬀero General Public License.

Notwithstanding any other provision of this License, you have permission to link or combine any

covered work with a work licensed under version 3 of the GNU Aﬀero General Public License into a

single combined work, and to convey the resulting work. The terms of this License will continue to

apply to the part which is the covered work, but the special requirements of the GNU Aﬀero General

Public License, section 13, concerning interaction through a network will apply to the combination as

such.

14. Revised Versions of this License.

The Free Software Foundation may publish revised and/or new versions of the GNU General Public

License from time to time. Such new versions will be similar in spirit to the present version, but may

diﬀer in detail to address new problems or concerns.

Each version is given a distinguishing version number. If the Program speciﬁes that a certain numbered

version of the GNU General Public License “or any later version” applies to it, you have the option of

following the terms and conditions either of that numbered version or of any later version published by

the Free Software Foundation. If the Program does not specify a version number of the GNU General

Public License, you may choose any version ever published by the Free Software Foundation.

If the Program speciﬁes that a proxy can decide which future versions of the GNU General Public

License can be used, that proxy’s public statement of acceptance of a version permanently authorizes

you to choose that version for the Program.

Later license versions may give you additional or diﬀerent permissions. However, no additional obli-

gations are imposed on any author or copyright holder as a result of your choosing to follow a later

version.

15. Disclaimer of Warranty.

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLI-

CABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLD-

ERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY

OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,

THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR

PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PRO-

GRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE

COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

16. Limitation of Liability.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING

WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CON-

VEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, IN-

CLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARIS-

ING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT

LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUS-

TAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE

WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN

ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

17. Interpretation of Sections 15 and 16.

If the disclaimer of warranty and limitation of liability provided above cannot be given local legal

eﬀect according to their terms, reviewing courts shall apply local law that most closely approximates

an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption

of liability accompanies a copy of the Program in return for a fee.

End of Terms and Conditions

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the

best way to achieve this is to make it free software which everyone can redistribute and change under

these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each

source ﬁle to most eﬀectively state the exclusion of warranty; and each ﬁle should have at least the

“copyright” line and a pointer to where the full notice is found.

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU General Public License for more details.

You should have received a copy of the GNU General Public License

along with this program. If not, see <http://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a short notice like this when it starts in an

interactive mode:

<program> Copyright (C) <year> <name of author>

This program comes with ABSOLUTELY NO WARRANTY; for details type ‘show w’.

This is free software, and you are welcome to redistribute it

under certain conditions; type ‘show c’ for details.

The hypothetical commands show w and show c should show the appropriate parts of the General

Public License. Of course, your program’s commands might be diﬀerent; for a GUI interface, you

would use an “about box”.

You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright

disclaimer” for the program, if necessary. For more information on this, and how to apply and follow

the GNU GPL, see http://www.gnu.org/licenses/.

The GNU General Public License does not permit incorporating your program into proprietary pro-

grams. If your program is a subroutine library, you may consider it more useful to permit linking

proprietary applications with the library. If this is what you want to do, use the GNU Lesser Gen-

eral Public License instead of this License. But ﬁrst, please read http://www.gnu.org/philosophy/

why-not-lgpl.html.

8.3 GNU Lesser General Public License v3

GNU LESSER GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

2007 Free Software Foundation, Inc. http://fsf.org/

Everyone is permitted to copy and distribute verbatim copies of this

license document, but changing it is not allowed.

This version of the GNU Lesser General Public License incorporates the terms and conditions of version

3 of the GNU General Public License, supplemented by the additional permissions listed below.

0. Additional Deﬁnitions.

As used herein, “this License” refers to version 3 of the GNU Lesser General Public License, and the

“GNU GPL” refers to version 3 of the GNU General Public License.

“The Library” refers to a covered work governed by this License, other than an Application or a

Combined Work as deﬁned below.

An “Application” is any work that makes use of an interface provided by the Library, but which is

not otherwise based on the Library. Deﬁning a subclass of a class deﬁned by the Library is deemed a

mode of using an interface provided by the Library.

A “Combined Work” is a work produced by combining or linking an Application with the Library. The

particular version of the Library with which the Combined Work was made is also called the “Linked

Version”.

The “Minimal Corresponding Source” for a Combined Work means the Corresponding Source for the

Combined Work, excluding any source code for portions of the Combined Work that, considered in

isolation, are based on the Application, and not on the Linked Version.

The “Corresponding Application Code” for a Combined Work means the object code and/or source

code for the Application, including any data and utility programs needed for reproducing the Combined

Work from the Application, but excluding the System Libraries of the Combined Work.

1. Exception to Section 3 of the GNU GPL.

You may convey a covered work under sections 3 and 4 of this License without being bound by section

3 of the GNU GPL.

2. Conveying Modiﬁed Versions.

If you modify a copy of the Library, and, in your modiﬁcations, a facility refers to a function or data

to be supplied by an Application that uses the facility (other than as an argument passed when the

facility is invoked), then you may convey a copy of the modiﬁed version:

(a) under this License, provided that you make a good faith eﬀort to ensure that, in the event an

Application does not supply the function or data, the facility still operates, and performs whatever

part of its purpose remains meaningful, or

(b) under the GNU GPL, with none of the additional permissions of this License applicable to that

copy.

3. Object Code Incorporating Material from Library Header Files.

The object code form of an Application may incorporate material from a header ﬁle that is part of

the Library. You may convey such object code under terms of your choice, provided that, if the

incorporated material is not limited to numerical parameters, data structure layouts and accessors, or

small macros, inline functions and templates (ten or fewer lines in length), you do both of the following:

(a) Give prominent notice with each copy of the object code that the Library is used in it and that

the Library and its use are covered by this License.

(b) Accompany the object code with a copy of the GNU GPL and this license document.

4. Combined Works.

You may convey a Combined Work under terms of your choice that, taken together, eﬀectively do

not restrict modiﬁcation of the portions of the Library contained in the Combined Work and reverse

engineering for debugging such modiﬁcations, if you also do each of the following:

(a) Give prominent notice with each copy of the Combined Work that the Library is used in it and

that the Library and its use are covered by this License.

(b) Accompany the Combined Work with a copy of the GNU GPL and this license document.

notice for the Library among these notices, as well as a reference directing the user to the copies

of the GNU GPL and this license document.

(d) Do one of the following:

. Convey the Minimal Corresponding Source under the terms of this License, and the Corre-

sponding Application Code in a form suitable for, and under terms that permit, the user to

recombine or relink the Application with a modiﬁed version of the Linked Version to pro-

duce a modiﬁed Combined Work, in the manner speciﬁed by section 6 of the GNU GPL for

conveying Corresponding Source.

i. Use a suitable shared library mechanism for linking with the Library. A suitable mechanism

is one that (a) uses at run time a copy of the Library already present on the user’s computer

system, and (b) will operate properly with a modiﬁed version of the Library that is interface-

compatible with the Linked Version.

(e) Provide Installation Information, but only if you would otherwise be required to provide such

information under section 6 of the GNU GPL, and only to the extent that such information is

necessary to install and execute a modiﬁed version of the Combined Work produced by recombin-

ing or relinking the Application with a modiﬁed version of the Linked Version. (If you use option

4d0, the Installation Information must accompany the Minimal Corresponding Source and Corre-

sponding Application Code. If you use option 4d1, you must provide the Installation Information

in the manner speciﬁed by section 6 of the GNU GPL for conveying Corresponding Source.)

5. Combined Libraries.

You may place library facilities that are a work based on the Library side by side in a single library

together with other library facilities that are not Applications and are not covered by this License, and

convey such a combined library under terms of your choice, if you do both of the following:

(a) Accompany the combined library with a copy of the same work based on the Library, uncombined

with any other library facilities, conveyed under the terms of this License.

(b) Give prominent notice with the combined library that part of it is a work based on the Library,

and explaining where to ﬁnd the accompanying uncombined form of the same work.

6. Revised Versions of the GNU Lesser General Public License.

The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General

Public License from time to time. Such new versions will be similar in spirit to the present version,

but may diﬀer in detail to address new problems or concerns.

Each version is given a distinguishing version number. If the Library as you received it speciﬁes that

a certain numbered version of the GNU Lesser General Public License “or any later version” applies

to it, you have the option of following the terms and conditions either of that published version or of

any later version published by the Free Software Foundation. If the Library as you received it does

not specify a version number of the GNU Lesser General Public License, you may choose any version

of the GNU Lesser General Public License ever published by the Free Software Foundation.

If the Library as you received it speciﬁes that a proxy can decide whether future versions of the GNU

Lesser General Public License shall apply, that proxy’s public statement of acceptance of any version

is permanent authorization for you to choose that version for the Library.

8.4 MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated

documentation ﬁles (the ”Software”), to deal in the Software without restriction, including without limitation

the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and

to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial

portions of the Software.

THE SOFTWARE IS PROVIDED ”AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS

OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LI-

ABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

THE SOFTWARE.

8.5 Zope Public License v2.1

A copyright notice accompanies this license document that identiﬁes the copyright holders. This license

has been certiﬁed as open source. It has also been designated as GPL compatible by the Free Software

Foundation (FSF). Redistribution and use in source and binary forms, with or without modiﬁcation, are

permitted provided that the following conditions are met:

1. Redistributions in source code must retain the accompanying copyright notice, this list of conditions,

and the following disclaimer.

2. Redistributions in binary form must reproduce the accompanying copyright notice, this list of condi-

tions, and the following disclaimer in the documentation and/or other materials provided with the distribu-

tion.

3. Names of the copyright holders must not be used to endorse or promote products derived from this

software without prior written permission from the copyright holders.

4. The right to distribute this software or to use it for any purpose does not give You the right to use

Servicemarks (sm) or Trademarks (tm) of the copyright holders.

5. If You make a patent infringement claim against any entity (including a cross- claim or counterclaim in a

lawsuit) alleging that the software licensed hereunder constitutes direct or contributory patent infringement,

then any patent and any right-to-use licenses granted to You under this License for that software shall

terminate as of the date such claim is made.

If any ﬁles are modiﬁed by You then you must cause the modiﬁed ﬁles to carry prominent notices stating

that you changed the ﬁles and the date of any change.

Disclaimer

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AS IS AND ANY EXPRESSED

OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES

OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN

NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY DIRECT, INDIRECT, IN-

CIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS

OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER

CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

8.6 Apache License v2.0

Apache License

Version 2.0, January 2004

http://www.apache.org/licenses/

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Deﬁnitions.

”License” shall mean the terms and conditions for use, reproduction, and distribution as deﬁned by

Sections 1 through 9 of this document.

”Licensor” shall mean the copyright owner or entity authorized by the copyright owner that is granting

the License.

”Legal Entity” shall mean the union of the acting entity and all other entities that control, are controlled

by, or are under common control with that entity. For the purposes of this deﬁnition, ”control” means (i)

the power, direct or indirect, to cause the direction or management of such entity, whether by contract or

otherwise, or (ii) ownership of ﬁfty percent (50outstanding shares, or (iii) beneﬁcial ownership of such entity.

”You” (or ”Your”) shall mean an individual or Legal Entity exercising permissions granted by this License.

”Source” form shall mean the preferred form for making modiﬁcations, including but not limited to

software source code, documentation source, and conﬁguration ﬁles.

”Object” form shall mean any form resulting from mechanical transformation or translation of a Source

form, including but not limited to compiled object code, generated documentation, and conversions to other

media types.

”Work” shall mean the work of authorship, whether in Source or Object form, made available under

the License, as indicated by a copyright notice that is included in or attached to the work (an example is

provided in the Appendix below).

”Derivative Works” shall mean any work, whether in Source or Object form, that is based on (or derived

from) the Work and for which the editorial revisions, annotations, elaborations, or other modiﬁcations

represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works

shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of,

the Work and Derivative Works thereof.

”Contribution” shall mean any work of authorship, including the original version of the Work and any

modiﬁcations or additions to that Work or Derivative Works thereof, that is intentionally submitted to

Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to

submit on behalf of the copyright owner. For the purposes of this deﬁnition, ”submitted” means any form

of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not

limited to communication on electronic mailing lists, source code control systems, and issue tracking systems

that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but

excluding communication that is conspicuously marked or otherwise designated in writing by the copyright

owner as ”Not a Contribution.”

”Contributor” shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution

has been received by Licensor and subsequently incorporated within the Work.

2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor

hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright li-

cense to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute

the Work and such Derivative Works in Source or Object form.

3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby

grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated

in this section) patent license to make, have made, use, oﬀer to sell, sell, import, and otherwise transfer

the Work, where such license applies only to those patent claims licensable by such Contributor that are

necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work

to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including

a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the

Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under

this License for that Work shall terminate as of the date such litigation is ﬁled.

4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof

in any medium, with or without modiﬁcations, and in Source or Object form, provided that You meet the

following conditions:

(a) You must give any other recipients of the Work or Derivative Works a copy of this License; and

(b) You must cause any modiﬁed ﬁles to carry prominent notices stating that You changed the ﬁles; and

patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that

do not pertain to any part of the Derivative Works; and

(d) If the Work includes a ”NOTICE” text ﬁle as part of its distribution, then any Derivative Works

that You distribute must include a readable copy of the attribution notices contained within such NOTICE

ﬁle, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the

following places: within a NOTICE text ﬁle distributed as part of the Derivative Works; within the Source

form or documentation, if provided along with the Derivative Works; or, within a display generated by the

Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE

ﬁle are for informational purposes only and do not modify the License. You may add Your own attribution

notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from

the Work, provided that such additional attribution notices cannot be construed as modifying the License.

You may add Your own copyright statement to Your modiﬁcations and may provide additional or diﬀerent

license terms and conditions for use, reproduction, or distribution of Your modiﬁcations, or for any such

Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise

complies with the conditions stated in this License.

5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally

submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of

this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall

supersede or modify the terms of any separate license agreement you may have executed with Licensor

regarding such Contributions.

6. Trademarks. This License does not grant permission to use the trade names, trademarks, service

marks, or product names of the Licensor, except as required for reasonable and customary use in describing

the origin of the Work and reproducing the content of the NOTICE ﬁle.

7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the

Work (and each Contributor provides its Contributions) on an ”AS IS” BASIS, WITHOUT WARRANTIES

OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties

or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTIC-

ULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing

the Work and assume any risks associated with Your exercise of permissions under this License.

8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence),

contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or

agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect,

special, incidental, or consequential damages of any character arising as a result of this License or out of the

use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage,

computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor

has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works

thereof, You may choose to oﬀer, and charge a fee for, acceptance of support, warranty, indemnity, or other

liability obligations and/or rights consistent with this License. However, in accepting such obligations, You

may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor,

and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred

by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional

liability.

END OF TERMS AND CONDITIONS

APPENDIX: How to apply the Apache License to your work.

To apply the Apache License to your work, attach the following boilerplate notice, with the ﬁelds enclosed

by brackets ”[]” replaced with your own identifying information. (Don’t include the brackets!) The text

should be enclosed in the appropriate comment syntax for the ﬁle format. We also recommend that a ﬁle or

class name and description of purpose be included on the same ”printed page” as the copyright notice for

easier identiﬁcation within third-party archives.

Licensed under the Apache License, Version 2.0 (the "License");

you may not use this file except in compliance with the License.

You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software

distributed under the License is distributed on an "AS IS" BASIS,

WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and

limitations under the License.

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