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Platform fixes, documentation updates and other small stuff #405

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Feb 26, 2024
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4dab6b7
Use and configure license-maven-plugin (org.honton.chas)
jan-at-the-hyve Jul 10, 2023
5229d73
First setup of distribution verification integration test
jan-at-the-hyve Jul 14, 2023
c0f85fb
Merge branch 'master' into add-integration-test
jan-at-the-hyve Jul 14, 2023
1fd513c
Merge branch 'master' into license-compliance
janblom Sep 25, 2023
7c68c3a
Use Java 17 for compilation, updates of test dependencies, update lic…
janblom Sep 26, 2023
9914a7d
Update comment on CacioTest annotation
janblom Sep 27, 2023
bcea118
Cleanup
janblom Sep 27, 2023
f539336
Merge branch 'master' into add-integration-test
janblom Sep 27, 2023
0bc3762
Add generating fat jars for WhiteRabbit and RabbitInAHat; lock hsqldb…
janblom Sep 28, 2023
1430457
Merge branch 'master' into license-compliance
janblom Sep 28, 2023
90d9fe1
Enforce Java 1.8 for distributed dependencies
janblom Sep 29, 2023
de73c44
Merge branch 'master' into license-compliance
janblom Sep 29, 2023
4e530f1
Merge branch 'master' into add-integration-test
janblom Oct 2, 2023
c5a78bd
Merge branch 'master' into distribution-integration-test
janblom Oct 2, 2023
56cdb66
Update main.yml
janblom Oct 23, 2023
d6d56b4
Merge pull request #32 from thehyve/license-compliance
janblom Oct 24, 2023
0888764
Bump org.apache.avro:avro from 1.11.2 to 1.11.3 in /rabbit-core
dependabot[bot] Oct 24, 2023
290f9f2
Merge pull request #33 from thehyve/dependabot/maven/rabbit-core/org.…
janblom Oct 24, 2023
0ed7a93
Use jdk8 classifier for hsqldb 2.7.x
janblom Oct 26, 2023
d591898
Exclude older version of hsqldb
janblom Oct 26, 2023
b9f9344
Merge branch 'master' into distribution-integration-test
janblom Oct 26, 2023
f26d572
Merge pull request #34 from thehyve/distribution-integration-test
janblom Oct 26, 2023
4f43f5b
Fix image crop when using stem table
Spayralbe Nov 22, 2023
20697d5
Update stem table image
Spayralbe Dec 4, 2023
5c34665
Decrease size of table panel when using stem table.
Spayralbe Dec 4, 2023
7baa4ed
Add snowflake support (#37)
janblom Jan 10, 2024
e6ba99e
Merge pull request #36 from thehyve/riah-stem-docs
Spayralbe Jan 11, 2024
cbca299
Merge pull request #35 from thehyve/stem-table-image-size
Spayralbe Jan 11, 2024
7dd23d8
Merge branch 'OHDSI:master' into master
janblom Jan 21, 2024
f1dada2
Add mysql test (#38)
janblom Jan 23, 2024
60726a6
Add sas test (#39)
janblom Jan 25, 2024
a2b78be
Pom updates to enable building on MacOS
jan-at-the-hyve Jan 29, 2024
93e68a0
Prepare release (#40)
janblom Jan 30, 2024
3d35075
Update whiterabbit/src/main/java/org/ohdsi/whiterabbit/WhiteRabbitMai…
janblom Feb 7, 2024
4cbc472
Merge branch 'OHDSI:master' into master
janblom Feb 7, 2024
5613707
Fixes from windows (#41)
janblom Feb 12, 2024
d234b77
Merge branch 'OHDSI:master' into master
janblom Feb 14, 2024
f73e34d
Use The Hyve fork of the caciocavello project (#42)
janblom Feb 14, 2024
1a35c0f
Merge branch 'OHDSI:master' into master
janblom Feb 15, 2024
f862492
Update docs (#44)
janblom Feb 15, 2024
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16 changes: 12 additions & 4 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

White Rabbit and Rabbit in a Hat are structured as a Maven package. Contributions are welcome.

While the software in the project can be executed with Java 8 (1.8), for development Java 17 is needed.
While the software in the project can be executed with Java 8 (1.8), for development Java 17 (or higher, currently tested upto version 21) is needed.
This has to do with test and verification dependencies that are not available in a version compatible with Java 8 .

Please note that when using an IDE for development, source and target release must still be Java 8 (1.8) . This is enforced
Expand All @@ -14,11 +14,13 @@ To generate the files ready for distribution, run `mvn install`.

When creating a pull request, please make sure the verification phase (`mvn verify`) does not fail.

When contributing code, please make sure that `mvn verify` runs without errors.

### Testing

A number of unit and integration tests exist. The integration tests run only in the maven verification phase,
(`mvn verify`) and depend on docker being available to the user running the verification. If docker is not available, the
integration tests will fail.
(`mvn verify`) and depend on Docker being available to the user running the verification. If Docker is not available, the
integration tests will fail.

When adding test, please follow these conventions:

Expand Down Expand Up @@ -47,6 +49,12 @@ These are used for testing of the main White Rabbit and Rabbit in a Hat features
| `riah_input` | An example mapping file used to create the Rabbit in a Hat outputs. |
| `riah_output` | All export formats created by Rabbit in a Hat: as word, html, markdown, sql skeleton and the R TestFramework.<br> These are all generated from `riah_input/riah_mapping_example.gz`. |

### Database support

If you are considering adding support for a new type of database, it is recommended to follow the pattern as used
by the SnowflakeHandler class, which extends the StorageHandler interface. This way, the brand/database specific code
is isolated into one class, instead of through the code paths that implement support for the
databases that were added earlier. This will lead to clearer code, that will also be easier to test and debug.

### Snowflake

Expand All @@ -68,4 +76,4 @@ and do not relate in any way to any production environment.
The schema should not contain any tables when the test is started.

It is possible to skip the Snowflake tests without failing the build by passing
`-Dohdsi.org.whiterabbit.skip_snowflake_tests=1` to maven.
`-Dohdsi.org.whiterabbit.skip_snowflake_tests=1` to maven.
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ Requires Java 1.8 or higher for running, and read access to the database to be s

Dependencies
============
For the distributable packages, the only requirement is Java 8. For building the package, Java 17 and Maven are needed.
For the distributable packages, the only requirement is Java 8. For building the package, Java 17+ and Maven are needed.

Getting Started
===============
Expand Down
218 changes: 40 additions & 178 deletions docs/RabbitInAHat.html

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16 changes: 3 additions & 13 deletions docs/ReadMe.html
Original file line number Diff line number Diff line change
Expand Up @@ -377,24 +377,14 @@

<div id="white-rabbit-documentation-readme" class="section level1">
<h1>White Rabbit Documentation Readme</h1>
<p>This folder contains the raw (<code>.md</code>) and rendered
(<code>.html</code>) documentation of WhiteRabbit. The documentation is
renderd with the R package <code>rmarkdown</code> and used for the <a
href="https://ohdsi.github.io/WhiteRabbit/">github.io page</a>.</p>
<p>This folder contains the raw (<code>.md</code>) and rendered (<code>.html</code>) documentation of WhiteRabbit. The documentation is renderd with the R package <code>rmarkdown</code> and used for the <a href="https://ohdsi.github.io/WhiteRabbit/">github.io page</a>.</p>
<div id="contribute" class="section level2">
<h2>Contribute</h2>
<p>Contributions to the documentation are very welcome and even a must
when new features are implemented. To update the documentation, edit one
of the following markdown files or create a new markdown file: - <a
href="/docs/WhiteRabbit.md">WhiteRabbit.md</a> - <a
href="/docs/RabbitInAHat.md">RabbitInAHat.md</a> - <a
href="/docs/riah_test_framework.md">riah_test_framework.md</a> - <a
href="/docs/best_practices.md">best_practices.md</a></p>
<p>Contributions to the documentation are very welcome and even a must when new features are implemented. To update the documentation, edit one of the following markdown files or create a new markdown file: - <a href="/docs/WhiteRabbit.md">WhiteRabbit.md</a> - <a href="/docs/RabbitInAHat.md">RabbitInAHat.md</a> - <a href="/docs/riah_test_framework.md">riah_test_framework.md</a> - <a href="/docs/best_practices.md">best_practices.md</a></p>
</div>
<div id="render-html" class="section level2">
<h2>Render html</h2>
<p>To generate the site from markdown files, run the following R code
with the <code>./docs</code> folder as working directory.</p>
<p>To generate the site from markdown files, run the following R code with the <code>./docs</code> folder as working directory.</p>
<pre class="r"><code>#devtools::install_github(&quot;ropenscilabs/icon&quot;)
library(rmarkdown)
rmarkdown::render_site()</code></pre>
Expand Down
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