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Add maven plugin to update OBO context #608

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Feb 7, 2020
Merged

Add maven plugin to update OBO context #608

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6525c1e
Add plugin to update OBO context
Jan 20, 2020
86882e6
Remove extra parts of pom
Jan 20, 2020
1ee50d9
Add some Javadocs
Jan 21, 2020
e4b7e44
Fix WBls prefix
Feb 3, 2020
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6 changes: 6 additions & 0 deletions pom.xml
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Expand Up @@ -68,6 +68,7 @@
<modules>
<module>robot-core</module>
<module>robot-command</module>
<module>robot-maven-plugin</module>
</modules>

<profiles>
Expand Down Expand Up @@ -210,6 +211,11 @@
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<groupId>org.obolibrary.robot</groupId>
<artifactId>robot-maven-plugin</artifactId>
<version>1.6.0-SNAPSHOT</version>
</plugin>
</plugins>
</build>

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117 changes: 105 additions & 12 deletions robot-core/src/main/resources/obo_context.jsonld
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Expand Up @@ -19,83 +19,137 @@
"cc": "http://creativecommons.org/ns#",
"schema": "http://schema.org/",

"AAO": "http://purl.obolibrary.org/obo/AAO_",
"ADW": "http://purl.obolibrary.org/obo/ADW_",
"AEO": "http://purl.obolibrary.org/obo/AEO_",
"AERO": "http://purl.obolibrary.org/obo/AERO_",
"AGRO": "http://purl.obolibrary.org/obo/AGRO_",
"APO": "http://purl.obolibrary.org/obo/APO_",
"APOLLO_SV": "http://purl.obolibrary.org/obo/APOLLO_SV_",
"ARO": "http://purl.obolibrary.org/obo/ARO_",
"ATO": "http://purl.obolibrary.org/obo/ATO_",
"BCGO": "http://purl.obolibrary.org/obo/BCGO_",
"BCO": "http://purl.obolibrary.org/obo/BCO_",
"BFO": "http://purl.obolibrary.org/obo/BFO_",
"BILA": "http://purl.obolibrary.org/obo/BILA_",
"BOOTSTREP": "http://purl.obolibrary.org/obo/BOOTSTREP_",
"BSPO": "http://purl.obolibrary.org/obo/BSPO_",
"BTO": "http://purl.obolibrary.org/obo/BTO_",
"CARO": "http://purl.obolibrary.org/obo/CARO_",
"CDAO": "http://purl.obolibrary.org/obo/CDAO_",
"CEPH": "http://purl.obolibrary.org/obo/CEPH_",
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
"CHEMINF": "http://purl.obolibrary.org/obo/CHEMINF_",
"CHIRO": "http://purl.obolibrary.org/obo/CHIRO_",
"CHMO": "http://purl.obolibrary.org/obo/CHMO_",
"CIO": "http://purl.obolibrary.org/obo/CIO_",
"CL": "http://purl.obolibrary.org/obo/CL_",
"CLO": "http://purl.obolibrary.org/obo/CLO_",
"CMF": "http://purl.obolibrary.org/obo/CMF_",
"CMO": "http://purl.obolibrary.org/obo/CMO_",
"CRO": "http://purl.obolibrary.org/obo/CRO_",
"CTENO": "http://purl.obolibrary.org/obo/CTENO_",
"CVDO": "http://purl.obolibrary.org/obo/CVDO_",
"DC_CL": "http://purl.obolibrary.org/obo/DC_CL_",
"DDANAT": "http://purl.obolibrary.org/obo/DDANAT_",
"DDPHENO": "http://purl.obolibrary.org/obo/DDPHENO_",
"DIDEO": "http://purl.obolibrary.org/obo/DIDEO_",
"DINTO": "http://purl.obolibrary.org/obo/DINTO_",
"DOID": "http://purl.obolibrary.org/obo/DOID_",
"DRON": "http://purl.obolibrary.org/obo/DRON_",
"DUO": "http://purl.obolibrary.org/obo/DUO_",
"ECO": "http://purl.obolibrary.org/obo/ECO_",
"ECOCORE": "http://purl.obolibrary.org/obo/ECOCORE_",
"ECTO": "http://purl.obolibrary.org/obo/ECTO_",
"EHDA": "http://purl.obolibrary.org/obo/EHDA_",
"EHDAA": "http://purl.obolibrary.org/obo/EHDAA_",
"EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_",
"EMAP": "http://purl.obolibrary.org/obo/EMAP_",
"EMAPA": "http://purl.obolibrary.org/obo/EMAPA_",
"ENVO": "http://purl.obolibrary.org/obo/ENVO_",
"EO": "http://purl.obolibrary.org/obo/EO_",
"EPO": "http://purl.obolibrary.org/obo/EPO_",
"ERO": "http://purl.obolibrary.org/obo/ERO_",
"ExO": "http://purl.obolibrary.org/obo/ExO_",
"EUPATH": "http://purl.obolibrary.org/obo/EUPATH_",
"EV": "http://purl.obolibrary.org/obo/EV_",
"EXO": "http://purl.obolibrary.org/obo/EXO_",
"FAO": "http://purl.obolibrary.org/obo/FAO_",
"FBSP": "http://purl.obolibrary.org/obo/FBSP_",
"FBbi": "http://purl.obolibrary.org/obo/FBbi_",
"FBbt": "http://purl.obolibrary.org/obo/FBbt_",
"FBcv": "http://purl.obolibrary.org/obo/FBcv_",
"FBdv": "http://purl.obolibrary.org/obo/FBdv_",
"FBsp": "http://purl.obolibrary.org/obo/FBsp_",
"FIX": "http://purl.obolibrary.org/obo/FIX_",
"FLOPO": "http://purl.obolibrary.org/obo/FLOPO_",
"FLU": "http://purl.obolibrary.org/obo/FLU_",
"FMA": "http://purl.obolibrary.org/obo/FMA_",
"FOBI": "http://purl.obolibrary.org/obo/FOBI_",
"FOODON": "http://purl.obolibrary.org/obo/FOODON_",
"FYPO": "http://purl.obolibrary.org/obo/FYPO_",
"GAZ": "http://purl.obolibrary.org/obo/GAZ_",
"GENEPIO": "http://purl.obolibrary.org/obo/GENEPIO_",
"GENO": "http://purl.obolibrary.org/obo/GENO_",
"GEO": "http://purl.obolibrary.org/obo/GEO_",
"GNO": "http://purl.obolibrary.org/obo/GNO_",
"GO": "http://purl.obolibrary.org/obo/GO_",
"GRO": "http://purl.obolibrary.org/obo/GRO_",
"HABRONATTUS": "http://purl.obolibrary.org/obo/HABRONATTUS_",
"HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_",
"HAO": "http://purl.obolibrary.org/obo/HAO_",
"HOM": "http://purl.obolibrary.org/obo/HOM_",
"HP": "http://purl.obolibrary.org/obo/HP_",
"HSAPDV": "http://purl.obolibrary.org/obo/HSAPDV_",
"HTN": "http://purl.obolibrary.org/obo/HTN_",
"IAO": "http://purl.obolibrary.org/obo/IAO_",
"ICEO": "http://purl.obolibrary.org/obo/ICEO_",
"ICO": "http://purl.obolibrary.org/obo/ICO_",
"IDO": "http://purl.obolibrary.org/obo/IDO_",
"IDOMAL": "http://purl.obolibrary.org/obo/IDOMAL_",
"IEV": "http://purl.obolibrary.org/obo/IEV_",
"IMR": "http://purl.obolibrary.org/obo/IMR_",
"INO": "http://purl.obolibrary.org/obo/INO_",
"IPR": "http://purl.obolibrary.org/obo/IPR_",
"KISAO": "http://purl.obolibrary.org/obo/KISAO_",
"LiPrO": "http://purl.obolibrary.org/obo/LiPrO_",
"LABO": "http://purl.obolibrary.org/obo/LABO_",
"LIPRO": "http://purl.obolibrary.org/obo/LIPRO_",
"LOGGERHEAD": "http://purl.obolibrary.org/obo/LOGGERHEAD_",
"MA": "http://purl.obolibrary.org/obo/MA_",
"MAMO": "http://purl.obolibrary.org/obo/MAMO_",
"MAO": "http://purl.obolibrary.org/obo/MAO_",
"MAT": "http://purl.obolibrary.org/obo/MAT_",
"MCO": "http://purl.obolibrary.org/obo/MCO_",
"MF": "http://purl.obolibrary.org/obo/MF_",
"MFMO": "http://purl.obolibrary.org/obo/MFMO_",
"MFO": "http://purl.obolibrary.org/obo/MFO_",
"MFOEM": "http://purl.obolibrary.org/obo/MFOEM_",
"MFOMD": "http://purl.obolibrary.org/obo/MFOMD_",
"MI": "http://purl.obolibrary.org/obo/MI_",
"MIAPA": "http://purl.obolibrary.org/obo/MIAPA_",
"miRNAO": "http://purl.obolibrary.org/obo/miRNAO_",
"MICRO": "http://purl.obolibrary.org/obo/MICRO_",
"MIRNAO": "http://purl.obolibrary.org/obo/MIRNAO_",
"MIRO": "http://purl.obolibrary.org/obo/MIRO_",
"MMO": "http://purl.obolibrary.org/obo/MMO_",
"MMUSDV": "http://purl.obolibrary.org/obo/MMUSDV_",
"MO": "http://purl.obolibrary.org/obo/MO_",
"MOD": "http://purl.obolibrary.org/obo/MOD_",
"MONDO": "http://purl.obolibrary.org/obo/MONDO_",
"MOP": "http://purl.obolibrary.org/obo/MOP_",
"MP": "http://purl.obolibrary.org/obo/MP_",
"MPATH": "http://purl.obolibrary.org/obo/MPATH_",
"MPIO": "http://purl.obolibrary.org/obo/MPIO_",
"MRO": "http://purl.obolibrary.org/obo/MRO_",
"MS": "http://purl.obolibrary.org/obo/MS_",
"NBO": "http://purl.obolibrary.org/obo/NBO_",
"NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_",
"ncithesaurus": "http://purl.obolibrary.org/obo/ncithesaurus_",
"NIF_Cell": "http://purl.obolibrary.org/obo/NIF_Cell_",
"NIF_Dysfunction": "http://purl.obolibrary.org/obo/NIF_Dysfunction_",
"NCIT": "http://purl.obolibrary.org/obo/NCIT_",
"NCRO": "http://purl.obolibrary.org/obo/NCRO_",
"NIF_CELL": "http://purl.obolibrary.org/obo/NIF_CELL_",
"NIF_DYSFUNCTION": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_",
"NIF_GROSSANATOMY": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_",
"NMR": "http://purl.obolibrary.org/obo/NMR_",
"NOMEN": "http://purl.obolibrary.org/obo/NOMEN_",
"OAE": "http://purl.obolibrary.org/obo/OAE_",
"OARCS": "http://purl.obolibrary.org/obo/OARCS_",
"OBA": "http://purl.obolibrary.org/obo/OBA_",
"OBCS": "http://purl.obolibrary.org/obo/OBCS_",
"OBI": "http://purl.obolibrary.org/obo/OBI_",
Expand All @@ -105,49 +159,88 @@
"OGI": "http://purl.obolibrary.org/obo/OGI_",
"OGMS": "http://purl.obolibrary.org/obo/OGMS_",
"OGSF": "http://purl.obolibrary.org/obo/OGSF_",
"OHD": "http://purl.obolibrary.org/obo/OHD_",
"OHMI": "http://purl.obolibrary.org/obo/OHMI_",
"OHPI": "http://purl.obolibrary.org/obo/OHPI_",
"OLATDV": "http://purl.obolibrary.org/obo/OLATDV_",
"OMIABIS": "http://purl.obolibrary.org/obo/OMIABIS_",
"OMIT": "http://purl.obolibrary.org/obo/OMIT_",
"OMP": "http://purl.obolibrary.org/obo/OMP_",
"OMRSE": "http://purl.obolibrary.org/obo/OMRSE_",
"ONTONEO": "http://purl.obolibrary.org/obo/ONTONEO_",
"OOSTT": "http://purl.obolibrary.org/obo/OOSTT_",
"OPL": "http://purl.obolibrary.org/obo/OPL_",
"OPMI": "http://purl.obolibrary.org/obo/OPMI_",
"ORNASEQ": "http://purl.obolibrary.org/obo/ORNASEQ_",
"OVAE": "http://purl.obolibrary.org/obo/OVAE_",
"PAO": "http://purl.obolibrary.org/obo/PAO_",
"PATO": "http://purl.obolibrary.org/obo/PATO_",
"PCO": "http://purl.obolibrary.org/obo/PCO_",
"PDRO": "http://purl.obolibrary.org/obo/PDRO_",
"PDUMDV": "http://purl.obolibrary.org/obo/PDUMDV_",
"PD_ST": "http://purl.obolibrary.org/obo/PD_ST_",
"PECO": "http://purl.obolibrary.org/obo/PECO_",
"PGDSO": "http://purl.obolibrary.org/obo/PGDSO_",
"PHIPO": "http://purl.obolibrary.org/obo/PHIPO_",
"PLANA": "http://purl.obolibrary.org/obo/PLANA_",
"PLANP": "http://purl.obolibrary.org/obo/PLANP_",
"PLO": "http://purl.obolibrary.org/obo/PLO_",
"PO": "http://purl.obolibrary.org/obo/PO_",
"PORO": "http://purl.obolibrary.org/obo/PORO_",
"PPO": "http://purl.obolibrary.org/obo/PPO_",
"PR": "http://purl.obolibrary.org/obo/PR_",
"PROPREO": "http://purl.obolibrary.org/obo/PROPREO_",
"PSDO": "http://purl.obolibrary.org/obo/PSDO_",
"PW": "http://purl.obolibrary.org/obo/PW_",
"RESID": "http://purl.obolibrary.org/obo/RESID_",
"REX": "http://purl.obolibrary.org/obo/REX_",
"RNAO": "http://purl.obolibrary.org/obo/RNAO_",
"RO": "http://purl.obolibrary.org/obo/RO_",
"RS": "http://purl.obolibrary.org/obo/RS_",
"RXNO": "http://purl.obolibrary.org/obo/RXNO_",
"SAO": "http://purl.obolibrary.org/obo/SAO_",
"SBO": "http://purl.obolibrary.org/obo/SBO_",
"SEP": "http://purl.obolibrary.org/obo/SEP_",
"SEPIO": "http://purl.obolibrary.org/obo/SEPIO_",
"SIBO": "http://purl.obolibrary.org/obo/SIBO_",
"SO": "http://purl.obolibrary.org/obo/SO_",
"SOPHARM": "http://purl.obolibrary.org/obo/SOPHARM_",
"SPD": "http://purl.obolibrary.org/obo/SPD_",
"STATO": "http://purl.obolibrary.org/obo/STATO_",
"SWO": "http://purl.obolibrary.org/obo/SWO_",
"SYMP": "http://purl.obolibrary.org/obo/SYMP_",
"TADS": "http://purl.obolibrary.org/obo/TADS_",
"TAHE": "http://purl.obolibrary.org/obo/TAHE_",
"TAHH": "http://purl.obolibrary.org/obo/TAHH_",
"TAO": "http://purl.obolibrary.org/obo/TAO_",
"TAXRANK": "http://purl.obolibrary.org/obo/TAXRANK_",
"TGMA": "http://purl.obolibrary.org/obo/TGMA_",
"TO": "http://purl.obolibrary.org/obo/TO_",
"TRANS": "http://purl.obolibrary.org/obo/TRANS_",
"TTO": "http://purl.obolibrary.org/obo/TTO_",
"TXPO": "http://purl.obolibrary.org/obo/TXPO_",
"UBERON": "http://purl.obolibrary.org/obo/UBERON_",
"uberon-basic": "http://purl.obolibrary.org/obo/uberon-basic_",
"UO": "http://purl.obolibrary.org/obo/UO_",
"VariO": "http://purl.obolibrary.org/obo/VariO_",
"vHOG": "http://purl.obolibrary.org/obo/vHOG_",
"UPA": "http://purl.obolibrary.org/obo/UPA_",
"UPHENO": "http://purl.obolibrary.org/obo/UPHENO_",
"VARIO": "http://purl.obolibrary.org/obo/VARIO_",
"VHOG": "http://purl.obolibrary.org/obo/VHOG_",
"VO": "http://purl.obolibrary.org/obo/VO_",
"VSAO": "http://purl.obolibrary.org/obo/VSAO_",
"VT": "http://purl.obolibrary.org/obo/VT_",
"VTO": "http://purl.obolibrary.org/obo/VTO_",
"WBbt": "http://purl.obolibrary.org/obo/WBbt_",
"WBls": "http://purl.obolibrary.org/obo/WBls_",
"WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_",
"WBbt": "http://purl.obolibrary.org/obo/WBbt_",
"XAO": "http://purl.obolibrary.org/obo/XAO_",
"XCO": "http://purl.obolibrary.org/obo/XCO_",
"XLMOD": "http://purl.obolibrary.org/obo/XLMOD_",
"XPO": "http://purl.obolibrary.org/obo/XPO_",
"YPO": "http://purl.obolibrary.org/obo/YPO_",
"ZEA": "http://purl.obolibrary.org/obo/ZEA_",
"ZECO": "http://purl.obolibrary.org/obo/ZECO_",
"ZFA": "http://purl.obolibrary.org/obo/ZFA_",
"ZFS": "http://purl.obolibrary.org/obo/ZFS_"
"ZFS": "http://purl.obolibrary.org/obo/ZFS_",
"ZP": "http://purl.obolibrary.org/obo/ZP_"
}
}
51 changes: 51 additions & 0 deletions robot-maven-plugin/README.md
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# ROBOT Maven Plugins

This directory contains additional `mvn` plugins specific to ROBOT.

Before using these plugins, you must install the JAR:
```
mvn install
```

## ROBOT Plugins

### Update Context

This plugin updates the [`obo_context.jsonld`](https://raw.githubusercontent.com/ontodev/robot/master/robot-core/src/main/resources/obo_context.jsonld) file with the most current prefixes from the [OBO Foundry context file](https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/obo_context.jsonld). You must be connected to the internet to run this plugin.

This can be run from either this directory, or the root `robot` directory:
```
mvn robot:UpdateContext -N
```

The `-N` flag is recommended so that the plugin does not run multiple times for each child module.

---

## Creating New Plugins

Add new plugins `src/main/java/org.obolibrary.robot` directory following this filename convention: `{plugin-name}Mojo.java`.

These new Java classes must extend the `AbstractMojo` class and have an `execute()` method. A `@Mojo` annotation is also required to specify the name of the plugin.
```
@Mojo(name = "MyNewPlugin")
public class MyNewPluginMojo extends AbstractMojo {

public void execute() {
// Do stuff
}
}
```

For more information on plugin development, [see here](https://maven.apache.org/guides/plugin/guide-java-plugin-development.html).

Then, install the new JAR for this module:
```
mvn install
```

Now you can run your plugin from the command line anywhere within this repo:
```
mvn robot:MyNewPlugin -N
```

63 changes: 63 additions & 0 deletions robot-maven-plugin/pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">

<modelVersion>4.0.0</modelVersion>

<parent>
<groupId>org.obolibrary.robot</groupId>
<artifactId>robot</artifactId>
<version>1.6.0-SNAPSHOT</version>
</parent>

<artifactId>robot-maven-plugin</artifactId>
<version>1.6.0-SNAPSHOT</version>
<packaging>maven-plugin</packaging>
<name>robot-maven-plugin</name>

<dependencies>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-plugin-api</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>org.apache.maven.plugin-tools</groupId>
<artifactId>maven-plugin-annotations</artifactId>
<version>3.4</version>
<scope>provided</scope>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-plugin-plugin</artifactId>
<version>3.3</version>
</plugin>

<!-- Enforce Google Java Style -->
<plugin>
<groupId>com.coveo</groupId>
<artifactId>fmt-maven-plugin</artifactId>
<version>2.1.0</version>
<executions>
<execution>
<goals>
<goal>format</goal>
</goals>
</execution>
</executions>
</plugin>

<plugin>
<groupId>org.obolibrary.robot</groupId>
<artifactId>robot-maven-plugin</artifactId>
<version>1.6.0-SNAPSHOT</version>
</plugin>
</plugins>
</build>

</project>
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