Merge pull request #152 from ielis/release_1.0.0RC1

Release 1.0.0 RC1

.github/workflows/pages.yml

@@ -55,7 +55,7 @@ jobs:
         pxfcli="phenopacket-tools-cli"
         find ${pxfcli}/target \
              -regex "^${pxfcli}/target/${pxfcli}-[0-9]\.[0-9]\.[0-9]\(-SNAPSHOT\)?\.jar$" \
-             -exec java -jar {} examples --output gh-pages/examples \;
+             -exec java -jar {} examples --output-directory gh-pages/examples \;
         
         ## Build the docs
         # Generate the HTML pages and move the generated content into the target folder. 

CHANGELOG.rst

@@ -2,6 +2,14 @@
 Changelog
 =========
 
+1.0.0
+-----
+
+* Update predefined constants, convenience functions and builders
+* Improve user guide, tutorial, and documentation
+* Run `MetaDataValidator` during base validation
+* Fix example phenopackets
+
 0.4.7
 -----
 

README.md

@@ -1,6 +1,5 @@
 [![Java CI](https://github.com/phenopackets/phenopacket-tools/workflows/Java%20CI/badge.svg)](https://github.com/phenopackets/phenopacket-tools/actions/workflows/main.yml)
 [![GitHub release](https://img.shields.io/github/release/phenopackets/phenopacket-tools.svg)](https://github.com/phenopackets/phenopacket-tools/releases)
-[![Javadoc](https://javadoc.io/badge2/org.phenopackets.phenopackettools/phenopacket-tools-core/javadoc.svg)](https://javadoc.io/doc/org.phenopackets.phenopackettools)
 
 # Phenopacket-tools
 
@@ -14,17 +13,18 @@ such as anatomical organs, age of onset, biospecimen type, and clinical modifier
 The library validates the basic syntax and semantic requirements of the Phenopacket Schema as well 
 as the adherence to additional user-defined requirements. 
 
+## Availability
+
+Most users should download the latest distribution archive from the [Releases page](https://github.com/phenopackets/phenopacket-tools/releases).
+Alternatively, *phenopacket-tools* can be built from source, as described in the user guide.
+
 ## Documentation
 
 The documentation includes a [Tutorial](http://phenopackets.org/phenopacket-tools/tutorial.html) showing 
 how to use the CLI, 
 a comprehensive [CLI user guide](http://phenopackets.org/phenopacket-tools/cli.html),
 a [Library user guide](http://phenopackets.org/phenopacket-tools),
-and the [Java API documentation](https://javadoc.io/doc/org.phenopackets.phenopackettools).
-
-## Availability
-
-Most users should download the latest distribution archive from the [Releases page](https://github.com/phenopackets/phenopacket-tools/releases).
+and the [Javadoc API documentation](http://phenopackets.org/phenopacket-tools/apidocs).
 
 ## Issues
 

constants/README.md

@@ -1,8 +1,16 @@
 # README
 
 This directory contains spreadsheets with definitions of recommended constants (OntologyClass objects) that
-are useful for common data elements needed to create Phenopackets.
+are useful for common data elements needed to create phenopackets.
 
-The python script create_classes.py transforms the CSV files into the corresponding Java classes.
+The script `create_classes.py` transforms the CSV files into the corresponding Java classes:
 
-The python script create_rtd.py creates read the docs documentation files.
+```shell
+python3 create_classes.py
+```
+
+The script `create_rtd.py` creates read the docs documentation files:
+
+```shell
+python3 create_rtd.py
+```

constants/Unit.tsv

@@ -2,24 +2,24 @@ ontology.id	ontology.label	variable.name	function.name
 UCUM:degree	degree (plane angle)	DEGREE	degreeOfAngle
 UCUM:[diop]	diopter	DIOPTER	diopter
 UCUM:g	gram	GRAM	gram
-UCUM:g/kg	gram per kilogram	GRAM_PER_KG	gramPerKilogram
+UCUM:g.kg-1	gram per kilogram	GRAM_PER_KG	gramPerKilogram
 UCUM:kg	kilogram	KILOGRAM	kilogram
 UCUM:L	liter	LITER	liter
 UCUM:m	meter	METER	meter
 UCUM:ug	microgram	MICROGRAM	microgram
-UCUM:ug/dL	microgram per deciliter	MICROGRAM_PER_DECILITER	microgramPerDeciliter
-UCUM:ug/L	microgram per liter	MICROGRAM_PER_LITER	microgramPerLiter
+UCUM:ug.dL-1	microgram per deciliter	MICROGRAM_PER_DECILITER	microgramPerDeciliter
+UCUM:ug.L-1	microgram per liter	MICROGRAM_PER_LITER	microgramPerLiter
 UCUM:uL	microliter	MICROLITER	microliter
 UCUM:um	micrometer	MICROMETER	micrometer
 UCUM:mg	milligram	MILLIGRAM	milligram
-UCUM:mg/dL	milligram per day	MILLIGRAM_PER_DAY	milligramPerDay
-UCUM:mg/dL	milligram per deciliter	MILLIGRAM_PER_DL	milligramPerDeciliter
+UCUM:mg.d-1	milligram per day	MILLIGRAM_PER_DAY	milligramPerDay
+UCUM:mg.dL-1	milligram per deciliter	MILLIGRAM_PER_DL	milligramPerDeciliter
 UCUM:mg.kg-1	milligram per kilogram	MILLIGRAM_PER_KG	mgPerKg
 UCUM:mL	milliliter	MILLILITER	milliliter
 UCUM:mm	millimeter	MILLIMETER	millimeter
 UCUM:mm[Hg]	millimetres of mercury	MILLIMETRES_OF_MERCURY	mmHg
 UCUM:mmol	millimole	MILLIMOLE	millimole
 UCUM:mol	mole	MOLE	mole
-UCUM:mol/L	mole per liter	MOLE_PER_LITER	molePerLiter
-UCUM:mol/mL	mole per milliliter	MOLE_PER_MILLILITER	molePerMilliliter
-UCUM:U/L	enzyme unit per liter	ENZYME_UNIT_PER_LITER	enzymeUnitPerLiter
+UCUM:mol.L-1	mole per liter	MOLE_PER_LITER	molePerLiter
+UCUM:mol.mL-1	mole per milliliter	MOLE_PER_MILLILITER	molePerMilliliter
+UCUM:U.L-1	enzyme unit per liter	ENZYME_UNIT_PER_LITER	enzymeUnitPerLiter

constants/create_rtd.py

@@ -60,12 +60,17 @@ def create_csv_table(entry, fh):
 
 RTD_HEADER = """.. _rstconstants:
 
+..
+  DO NOT EDIT MANUALLY!
+  The document is generated by the `phenopacket-tools/constants/create_rtd.py` script.
+
 =========
 Constants
 =========
 
-The phenopacket-tools library offers a selection of recommended and predefined OntologyClass objects for commonly used concepts.
-For instance, this is the code one would need to write using the native Protobuf frameworkto get an OntologyClass instance that represents the modifier ``Left``.
+The *phenopacket-tools* library offers a selection of recommended and predefined `OntologyClass` objects
+for commonly used concepts. For instance, this is the code one would need to write using the native Protobuf framework
+to get an `OntologyClass` instance that represents the modifier ``Left``:
 
 .. code-block:: java
 
@@ -75,7 +80,7 @@ def create_csv_table(entry, fh):
      .build();
 
 
-In contrast, this is the code required with phenopacket-tools (omitting import statements in both cases)
+In contrast, this is the code required with *phenopacket-tools* (omitting import statements in both cases):
 
 .. code-block:: java
 
@@ -87,6 +92,6 @@ def create_csv_table(entry, fh):
 
 """
 with open(RTD_PATH, "wt") as fh:
-	fh.write(RTD_HEADER)
-	for e in entries:
-    create_csv_table(e, fh=fh)
+    fh.write(RTD_HEADER)
+    for e in entries:
+        create_csv_table(e, fh=fh)