This repository demonstrates the Transparent Research Object Vocabulary (TROV) for describing Transparent Research Objects (TROs) and the Transparent Research Systems (TRS's) that produce them.
This repository is itself structured as a Reproducible Every-Place Research Object (REPRO). It is associated with a public Docker image that aims to enable the the products of the demonstration to be reproduced at a Unix-like shell prompt on any computer that has Git, GNU Make, and Docker installed.
Make commands issued in the top-level directory are used to obtain the Docker image and run the demos.
Use the make pull-image command to pull the Docker image from Docker hub:
trace-model$ make pull-image
docker pull cirss/trace-model:latest
latest: Pulling from cirss/trace-model
d19f32bd9e41: Pull complete
f9e098bd9304: Pull complete
bd67e18a393a: Pull complete
a999842c6b8b: Pull complete
5879f0773d6f: Pull complete
d735389eb5d9: Pull complete
de60b39ca69a: Pull complete
ac79dbfddb45: Pull complete
633a376f999c: Pull complete
4c1f583c231d: Pull complete
40499f468cf6: Pull complete
438476b07eca: Pull complete
66c6f2f0117d: Pull complete
Digest: sha256:013dc3261b141fc79d7bbc5e9cede4376951917f29fa282feebe68b23eaa6666
Status: Downloaded newer image for cirss/trace-model:latest
docker.io/cirss/trace-model:latest
Alternatively, build the image locally using the make build-image command:
/trace-model$ make build-image
docker build -t cirss/trace-model:latest .
Sending build context to Docker daemon 292.1MB
Step 1/12 : FROM cirss/repro-parent:latest
latest: Pulling from cirss/repro-parent
Digest: sha256:9b589a67c0e43ebaa6a99b7a64fc9ceaf3935ae99550366d323701425dbc2418
Status: Downloaded newer image for cirss/repro-parent:latest
---> 7fe3395196d6
Step 2/12 : COPY exports /repro/exports
---> 5493da08ada1
Step 3/12 : ADD ${REPRO_DIST}/boot-setup /repro/dist/
Downloading 1.315kB
---> a84c9e2d5371
Step 4/12 : RUN bash /repro/dist/boot-setup
---> Running in 6b41b98cbc46
Get:1 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Hit:2 http://archive.ubuntu.com/ubuntu jammy InRelease
Get:3 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [114 kB]
.
.
.
Step 12/12 : CMD /bin/bash -il
---> Running in 0253e7b96eae
Removing intermediate container 0253e7b96eae
---> d183e074b43e
Successfully built d183e074b43e
Successfully tagged cirss/trace-model:latest
The demonstration and its products are stored in the demo directory tree:
trace-model$ tree demo
demo
├── 01-minimal
│ ├── Makefile
│ ├── run.sh
│ └── run.txt
├── 02-type-a
│ ├── Makefile
│ ├── run.sh
│ └── run.txt
├── common
│ ├── trace-vocab.jsonld
│ ├── tro
│ │ ├── tro-01-from-minimal-trs.jsonld
│ │ └── tro-02-from-type-a-trs.jsonld
│ ├── trs
│ │ ├── trs-01-minimal.jsonld
│ │ └── trs-02-type-a.jsonld
│ └── trs-queries.sh
└── Makefile
To establish that the demonstrations can be reproduced, first use the make clean-demo command to delete the files produced by the demo:
trace-model$ make clean-demo
20221008.054458.104 A MESG Connect to Blazegraph at http://localhost:9999.
------- Cleaning example 01-minimal/ ----------------
removed './run.txt'
------- Cleaning example 02-type-a/ ----------------
removed './run.txt'
Confirm with git status that version-controlled files have been deleted locally:
trace-model$ git status
On branch master
Your branch is up to date with 'origin/master'.
Changes not staged for commit:
(use "git add/rm <file>..." to update what will be committed)
(use "git checkout -- <file>..." to discard changes in working directory)
deleted: demo/01-minimal/run.txt
deleted: demo/02-type-a/run.txt
no changes added to commit (use "git add" and/or "git commit -a")
Now run the demonstration with the make run-demo command:
trace-model$ make run-demo
20221008.051511.921 A MESG Connect to Blazegraph at http://localhost:9999.
---------- Running example 01-minimal/ -------------
---------- Running example 02-type-a/ -------------
Finally, use git status to confirm that the demostration products have been restored:
trace-model$ git status
On branch master
Your branch is up to date with 'origin/master'.
no changes added to commit (use "git add" and/or "git commit -a")
An individual example within the demonstration can be run by starting an interactive REPRO session.
First start the REPRO in interactive mode using the make start-repro command (or the shorthand make start).
trace-model$ make start-repro
20221010.074008.007 A MESG Connect to Blazegraph at http://localhost:9999.
repro@a6c7a4e443a8:/mnt/trace-model$
Set the working directory to a particular example directory:
repro@a6c7a4e443a8:/mnt/trace-model$ cd demo/02-type-a/
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ pwd
/mnt/trace-model/demo/02-type-a
Type make to run the example:
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ make
bash run.sh > run.txt
Use the tree command to list the files associated with the example, including the temporary files in the tmp subdirectory:
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ tree
.
|-- Makefile
|-- products
|-- run.sh
|-- run.txt
`-- tmp
|-- export_tro_ntriples.sh
|-- export_tro_ntriples.txt
|-- import_tro_jsonld.sh
|-- import_tro_jsonld.txt
|-- query_policies.sh
|-- query_policies.txt
|-- query_tro_policies.sh
|-- query_tro_policies.txt
|-- query_trs_policies.sh
`-- query_trs_policies.txt
2 directories, 13 files
repro@a6c7a4e443a8:/mnt
The make clean command deletes the temporary files and the example output file, run.txt:
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ make clean
if [[ -f ./"run.txt" ]] ; then \
rm -v ./"run.txt" ; \
fi
removed './run.txt'
if [[ -d ./"tmp" ]] ; then \
rm -vf ./"tmp"/* ; \
rmdir -v ./"tmp" ; \
fi
removed './tmp/export_tro_ntriples.sh'
removed './tmp/export_tro_ntriples.txt'
removed './tmp/import_tro_jsonld.sh'
removed './tmp/import_tro_jsonld.txt'
removed './tmp/query_policies.sh'
removed './tmp/query_policies.txt'
removed './tmp/query_tro_policies.sh'
removed './tmp/query_tro_policies.txt'
removed './tmp/query_trs_policies.sh'
removed './tmp/query_trs_policies.txt'
rmdir: removing directory, './tmp'
if [[ -d ./"products" ]] ; then \
rm -vf ./"products"/* ; \
rmdir -v ./"products" ; \
fi
rmdir: removing directory, './products'
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ tree
.
|-- Makefile
`-- run.sh
Confirm that run.txt is the only version-controlled file associated with this example that has been deleted:
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ git status .
On branch master
Your branch is up to date with 'origin/master'.
Changes not staged for commit:
(use "git add/rm <file>..." to update what will be committed)
(use "git restore <file>..." to discard changes in working directory)
deleted: run.txt
no changes added to commit (use "git add" and/or "git commit -a")
Re-run the and confirm the run.txt file was restored:
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ make
bash run.sh > run.txt
repro@a6c7a4e443a8:/mnt/trace-model/demo/02-type-a$ git status .
On branch master
Your branch is up to date with 'origin/master'.
nothing to commit, working tree clean