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Beehive Script

These are scripts to extract and parse annotations of University of Pennsylvania Ms. Codex 726, Daniel Pastorius' "Bee Hive" as a single CSV file. These annotations were generated using Glen Robson's SimpleAnnotationServer between 2016 and 2023.

For more information on this project and to see its results, visit the Digital Beehive site. For the annotation data and IIIF manifests, see the Beehive data repository on GitHub.

The CSV output by this script is used to generate the data and pages used to build the Digital Beehive Jekyll/Wax site, which is hosted on GitHub Pages. The Digital Beehive website code is also hosted on GitHub. There is a separate repository for the website generation scripts, beehive-annotation-scripts

Usage

Update data/beehive-data.nq with the latest version of Beehive SAS exported N-quads data.

Install the script and set up Fuseki with the annotations data as described below.

CSV is written to standard output:

$ bundle exec ruby bin/parse_annotations.rb > output.csv
volume,image_number,head,entry,topic,xref,see,index,item,unparsed,line,selection,full_image,annotation_uri
...
Volume 2,21,,Jesting,Jesting,buffoonry|1119 [Jest],,jesting,#item-8fd26eddf,,Entry: Jesting|Topic: Jesting|XRef: buffoonry|XRef: 1119 [Jest]|Index: jesting|#item-8fd26eddf|,"https://stacks.stanford.edu/image/iiif/fm855tg5659%2F1607_0488/360,256,3011,363/full/0/default.jpg",https://stacks.stanford.edu/image/iiif/fm855tg5659%2F1607_0488/full/full/0/default.jpg,http://dev.llgc.org.uk/annotation/1508858832957
Volume 2,21,,Jesuite,Jesuite,1292 [Jesuites],,Jesuite,#item-c421e7050,,Entry: Jesuite|Topic: Jesuite|XRef: 1292 [Jesuites]|Index: Jesuite|#item-c421e7050,"https://stacks.stanford.edu/image/iiif/fm855tg5659%2F1607_0488/350,619,3035,318/full/0/default.jpg",https://stacks.stanford.edu/image/iiif/fm855tg5659%2F1607_0488/full/full/0/default.jpg,http://dev.llgc.org.uk/annotation/1508859070768
Volume 3,25,,,,,,,,"","","https://stacks.stanford.edu/image/iiif/gw497tq8651%2F1607_0968/152,2097,448,148/full/0/default.jpg",https://stacks.stanford.edu/image/iiif/gw497tq8651%2F1607_0968/full/full/0/default.jpg,http://dev.llgc.org.uk/annotation/1508859115466
Volume 3,25,,,,,,,,"","","https://stacks.stanford.edu/image/iiif/gw497tq8651%2F1607_0968/149,2254,480,113/full/0/default.jpg",https://stacks.stanford.edu/image/iiif/gw497tq8651%2F1607_0968/full/full/0/default.jpg,http://dev.llgc.org.uk/annotation/1508859120407
Volume 2,21,,Jesus,Jesus,Christ|Saviour,,Jesus,#item-fc54ff4b7,,Entry: Jesus|Topic: Jesus|XRef: Christ|XRef: Saviour|Index: Jesus|#item-fc54ff4b7,"https://stacks.stanford.edu/image/iiif/fm855tg5659%2F1607_0488/359,929,2974,442/full/0/default.jpg",https://stacks.stanford.edu/image/iiif/fm855tg5659%2F1607_0488/full/full/0/default.jpg,http://dev.llgc.org.uk/annotation/1508859135558
...

Install

Requirements

Download this repository and install required gems

git clone https://github.com/KislakCenter/beehive-ld-parsing.git
cd beehive-ld-parsing
bundle install

Install and configure Apache Jena and Jena/Fuseki

Download and unzip/untar Apache Jena and Jena/Fuseki on your system.

Create a copy of sample.env and name it .env.

cp sample.env .env

Edit .env to match your Apache Jena and Jena/Fuseki installations

Import the latest Beehive annotations into Jena

Get the latest Beehive annotations in N-Quads format from the Beehive Data repository.

Your can use the script import_annotations.sh:

./import_annotations.sh path/to/beehive-annotations.nq

Or do it yourself manually:

source .env # configure Jena/Fuseik environment
rm -rf jena # remove existing store
# the following creates the `jena` folder
tdbloader --loc=jena path/to/beehive-annotations.nq

Setup Fuseki with the annotation data

The following runs Fuseki as a standalone server. The annotation parsing script talks to the Fuseki SPARQL endpoint to extract the annotations.

For more information on running standalone Fuseki see the Fuseki page.

Run the script start_fuseki.sh:

./start_fuseki.sh

You should see something like the following

16:10:17 INFO  Server          :: Apache Jena Fuseki 4.8.0
16:10:17 INFO  Config          :: FUSEKI_HOME=/Users/username/Java/apache-jena-fuseki-4.8.0
16:10:17 INFO  Config          :: FUSEKI_BASE=/Users/username/code/beehive-ld-parsing/run
16:10:17 INFO  Config          :: Shiro file: file:///Users/username/code/beehive-ld-parsing/run/shiro.ini
16:10:18 INFO  Server          :: Path = /beehive
16:10:18 INFO  Server          ::   Memory: 4.0 GiB
16:10:18 INFO  Server          ::   Java:   20.0.1
16:10:18 INFO  Server          ::   OS:     Mac OS X 13.4.1 aarch64
16:10:18 INFO  Server          ::   PID:    34006
16:10:18 INFO  Server          :: Started 2023/06/30 16:10:18 EDT on port 3030

If you want to do it manually, you can do this:

source .env
fuseki-server --config=fuseki_config.ttl

Annotation formats

The script parse_annotations.rb parses alphabetical, numerical, and index entry annotations.

Here are the basic formats:

Alphabetical entry*

Entry: Apples
Topic: Apples
Xref: Fruit
Index: Apfeln
#item-abcd1234

Numerical entry

Entry: 1338
Topic: To assault : besiege
Index: assault
Index: besiege
#item-xyz093442393

Both alphabetical and numerical entries may contain cross references.

Entry: Abundance
Topic: Abundance
Xref: Too much
Xref: Superfluity
Index: Abundance
#item-xyz093442393

Index entry

Index entries are distinguished by the presence of the Head: field.

Head: absurdity
Entry: a
Entry: 919 [Absurd]
Entry: 2205 [Absurd]
#item-63eec4140