Merge pull request #137 from phenopackets/release-0.4.7

Release 0.4.7
phenopackets · Nov 13, 2022 · 43824f6 · 43824f6
2 parents aab1605 + 144aa94
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,23 @@
+=========
+Changelog
+=========
+
+0.4.7
+-----
+
+* Add more predefined constants into the builder module, update the code for generating constants
+* Write a tutorial with examples for validation and conversion functionalities
+* Add I/O module, implement YAML parser and printer
+* Add organ system validator
+* Finalize VRS-like validation
+* Let the user choose the CLI verbosity
+
+v0.4.6
+------
+
+* Validate metadata
+* Convert v1 variants
+* Extend phenopacket examples
+* Update documentation
+* Improve CLI and extend CLI documentation
+
diff --git a/README.md b/README.md
@@ -14,8 +14,7 @@ The cli application works in a standard UNIX-like manner.
 ```shell
 cd phenopacket-tools
 ./mvnw package
-PXF_VERSION="0.4.6"
-alias pfx-tools="java -jar $(pwd)/phenopacket-tools-cli/target/phenopacket-tools-cli-${PXF_VERSION}.jar"
+alias pfx-tools="java -jar $(pwd)/phenopacket-tools-cli/target/[email protected]@.jar"
 pfx-tools --help
 ```
 
@@ -51,6 +50,5 @@ pfx-tools validate family ~/phenopacket-examples/families/*.json
 pfx-tools convert phenopacket.json
 ```
 
-
-see this for VRS -- https://github.com/ga4gh/vrs/blob/76542a903b913110e67811885a8958625bbc3aae/schema/vrs.json
-import it like vrsatile
+### API
+A Javadoc description of the API of phenopacket-tools is available [here](https://javadoc.io/doc/org.phenopackets.phenopackettools).
diff --git a/constants/AdministrationRoute.tsv b/constants/AdministrationRoute.tsv
@@ -0,0 +1,10 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C38276	Intravenous Route of Administration	INTRAVENOUS_ROUTE	intravenous
+NCIT:C38222	Intraarterial Route of Administration	INTRAARTERIAL_ROUTE	intraarterial
+NCIT:C183503	Administration via Wound Irrigation	WOUND_IRRIGATION_ROUTE	woundIrrigation
+NCIT:C149695	Nebulizer Route of Administration	NEBULIZER_ROUTE	nebulizer
+NCIT:C38288	Oral Route of Administration	ORAL_ROUTE	oral
+NCIT:C38267	Intrathecal Route of Administration	INTRATHECAL_ROUTE	intrathecal
+NCIT:C38677	Peridural Route of Administration	PERIDURAL_ROUTE	peridural
+NCIT:C38304	Topical Route of Administration	TOPICAL_ROUTE	topical
+NCIT:C38305	Transdermal Route of Administration	TRANSDERMAL	transdermal
diff --git a/constants/Assays.tsv b/constants/Assays.tsv
diff --git a/constants/BiospecimenType.tsv b/constants/BiospecimenType.tsv
@@ -0,0 +1,10 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C133261	Bone Marrow Aspirate	BONE_MARROW_ASPIRATE	boneMarrowAspirate
+NCIT:C158416	Blood DNA	BLOOD_DNA	bloodDNA
+NCIT:C185194	Cerebrospinal Fluid Sample	CSF_SAMPLE	cerebrospinalFluidSample
+NCIT:C156435	Formalin-Fixed Paraffin-Embedded DNA	FORMALIN_FIXED_PARAFIN_DNA	formalinFixedParaffinEmbeddedDNA
+NCIT:C13195	Bronchoalveolar Lavage Fluid	BAL_FLUID	bronchoalveolarLavageFluid
+NCIT:C187062	Pericardial Fluid Specimen	PERICARDIAL_FLUID_SAMPLE	pericardialFluidSpecimen
+NCIT:C185197	Peritoneal Fluid Sample	PERTONIAL_FLUID_SAMPLE	peritonealFluidSample
+NCIT:C163995	Total RNA	TOTAL_RNA	totalRNA
+NCIT:C18009	Tumor Tissue	TUMOR_TISSUE	tumorTissue
diff --git a/constants/DiseaseGrade.tsv b/constants/DiseaseGrade.tsv
@@ -0,0 +1,7 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C28077	Grade 1	GRADE_1	grade1
+NCIT:C28078	Grade 2	GRADE_2	grade2
+NCIT:C28079	Grade 3	GRADE_3	grade3
+NCIT:C28080	Grade 3a	GRADE_3A	grade3a
+NCIT:C28081	Grade 3b	GRADE_3B	grade3b
+NCIT:C28082	Grade 4	GRADE_4	grade4
diff --git a/constants/DiseaseStage.tsv b/constants/DiseaseStage.tsv
@@ -0,0 +1,11 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C28051	Stage 0	STAGE_0	stage0
+NCIT:C27966	Stage I	STAGE_I	stageI
+NCIT:C28054	Stage II	STAGE_II	stageII
+NCIT:C27970	Stage III	STAGE_III	stageIII
+NCIT:C27971	Stage IV	STAGE_IV	stageIV
+NCIT:C66904	New York Heart Association Class I	NYHA_I	nyhaClassI
+NCIT:C66905	New York Heart Association Class II	NYHA_II	nyhaClassII
+NCIT:C66907	New York Heart Association Class III	NYHA_III	nyhaClassIII
+NCIT:C7922	New York Heart Association Class III/IV	NYHA_III_IV	nyhaClassIII_or_IV
+NCIT:C66908	New York Heart Association Class IV	NYHA_IV	nyhaClassIV
diff --git a/constants/Evidence.tsv b/constants/Evidence.tsv
@@ -0,0 +1,6 @@
+ontology.id	ontology.label	variable.name	function.name
+ECO:0006016	author statement from published clinical study	AUTHOR_STATEMENT_FROM_PCS	authorStatementFromPublishedClinicalStudy
+ECO:0007539	author statement from published clinical study used in automatic assertion	AUTHOR_STATEMENT_FROM_PCS_AUTOMATIC	authorStatementFromPublishedClinicalStudyAutomaticAssertion
+ECO:0006017	author statement from published clinical study used in manual assertion	AUTHOR_STATEMENT_FROM_PCS_MANUAL	authorStatementFromPublishedClinicalStudyManualAssertion
+ECO:0000033	author statement supported by traceable reference	AUTHOR_STATEMENT_TRACEABLE_REFERENCE	authorStatementSupportedByTraceableReference
+ECO:0006154	self-reported patient statement evidence	SELF_REPORTED_PATIENT_STATEMENT_EVIDENCE	selfReportedPatientStatementEvidence
diff --git a/constants/MaterialSample.tsv b/constants/MaterialSample.tsv
@@ -0,0 +1,3 @@
+ontology.id	ontology.label	variable.name	function.name
+EFO:0009655	abnormal sample	ABNORMAL_SAMPLE	abnormalSample
+EFO:0009654	reference sample	REFERENCE_SAMPLE	referenceSample
diff --git a/constants/MedicalActions.tsv b/constants/MedicalActions.tsv
@@ -1,10 +1,10 @@
 ontology.id	ontology.label	variable.name	function.name
 NCIT:C41331	Adverse Event	ADVERSE_EVENT	adverseEvent
-NCIT:C64530	Four Times Daily	FOUR_TIMES_DAILY	fourtimesDaily
+NCIT:C64530	Four Times Daily	FOUR_TIMES_DAILY	fourTimesDaily
 NCIT:C38222	Intraarterial Route of Administration	INTRA_ARTERIAL	intraArterialAdministration
 NCIT:C38276	Intravenous Route of Administration	IV_ADMINISTRATION	intravenousAdministration
 NCIT:C38288	Oral Route of Administration	ORAL_ADMINISTRATION	oralAdministration
 NCIT:C64576	Once	ONCE	once
 NCIT:C125004	Once Daily	ONCE_DAILY	onceDaily
-NCIT:C64527	Three Times Daily	THREE_TIMES_DAILY	threetimesDaily
+NCIT:C64527	Three Times Daily	THREE_TIMES_DAILY	threeTimesDaily
 NCIT:C64496	Twice Daily	TWICE_DAILY	twiceDaily
diff --git a/constants/PathologicalTnm.tsv b/constants/PathologicalTnm.tsv
@@ -0,0 +1,37 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C48740	pM0 Stage Finding	PM0_STAGE_FINDING	pM0StageFinding
+NCIT:C48741	pM1 Stage Finding	PM1_STAGE_FINDING	pM1StageFinding
+NCIT:C48742	pM1a Stage Finding	PM1A_STAGE_FINDING	pM1aStageFinding
+NCIT:C48743	pM1b Stage Finding	PM1B_STAGE_FINDING	pM1bStageFinding
+NCIT:C48744	pM1c Stage Finding	PM1C_STAGE_FINDING	pM1cStageFinding
+NCIT:C48745	pN0 Stage Finding	PN0_STAGE_FINDING	pN0StageFinding
+NCIT:C48746	pN1 Stage Finding	PN1_STAGE_FINDING	pN1StageFinding
+NCIT:C48747	pN1a Stage Finding	PN1A_STAGE_FINDING	pN1aStageFinding
+NCIT:C48748	pN1b Stage Finding	PN1B_STAGE_FINDING	pN1bStageFinding
+NCIT:C48749	pN1c Stage Finding	PN1C_STAGE_FINDING	pN1cStageFinding
+NCIT:C48750	pN2 Stage Finding	PN2_STAGE_FINDING	pN2StageFinding
+NCIT:C48751	pN2a Stage Finding	PN2A_STAGE_FINDING	pN2aStageFinding
+NCIT:C48752	pN2b Stage Finding	PN2B_STAGE_FINDING	pN2bStageFinding
+NCIT:C48753	pN2c Stage Finding	PN2C_STAGE_FINDING	pN2cStageFinding
+NCIT:C48754	pN3 Stage Finding	PN3_STAGE_FINDING	pN3StageFinding
+NCIT:C48755	pN3a Stage Finding	PN3A_STAGE_FINDING	pN3aStageFinding
+NCIT:C48756	pN3b Stage Finding	PN3B_STAGE_FINDING	pN3bStageFinding
+NCIT:C48757	pN3c Stage Finding	PN3C_STAGE_FINDING	pN3cStageFinding
+NCIT:C48758	pT0 Stage Finding	PT0_STAGE_FINDING	pT0StageFinding
+NCIT:C48759	pT1 Stage Finding	PT1_STAGE_FINDING	pT1StageFinding
+NCIT:C48760	pT1a Stage Finding	PT1A_STAGE_FINDING	pT1aStageFinding
+NCIT:C48761	pT1b Stage Finding	PT1B_STAGE_FINDING	pT1bStageFinding
+NCIT:C48763	pT1c Stage Finding	PT1C_STAGE_FINDING	pT1cStageFinding
+NCIT:C48764	pT2 Stage Finding	PT2_STAGE_FINDING	pT2StageFinding
+NCIT:C48765	pT2a Stage Finding	PT2A_STAGE_FINDING	pT2aStageFinding
+NCIT:C48766	pT2b Stage Finding	PT2B_STAGE_FINDING	pT2bStageFinding
+NCIT:C48767	pT2c Stage Finding	PT2C_STAGE_FINDING	pT2cStageFinding
+NCIT:C48768	pT3 Stage Finding	PT3_STAGE_FINDING	pT3StageFinding
+NCIT:C48769	pT3a Stage Finding	PT3A_STAGE_FINDING	pT3aStageFinding
+NCIT:C48770	pT3b Stage Finding	PT3B_STAGE_FINDING	pT3bStageFinding
+NCIT:C48771	pT3c Stage Finding	PT3C_STAGE_FINDING	pT3cStageFinding
+NCIT:C48772	pT4 Stage Finding	PT4_STAGE_FINDING	pT4StageFinding
+NCIT:C48773	pT4a Stage Finding	PT4A_STAGE_FINDING	pT4aStageFinding
+NCIT:C48774	pT4b Stage Finding	PT4B_STAGE_FINDING	pT4bStageFinding
+NCIT:C48775	pT4c Stage Finding	PT4C_STAGE_FINDING	pT4cStageFinding
+NCIT:C48776	pT4d Stage Finding	PT4D_STAGE_FINDING	pT4dStageFinding
diff --git a/constants/Response.tsv b/constants/Response.tsv
@@ -1,3 +1,14 @@
 ontology.id	ontology.label	variable.name	function.name
-NCIT:C102560	Favorable	FAVORABLE	favorable
-NCIT:C102561	Unfavorable	UNFAVORABLE	unfavorable
+NCIT:C123584	Favorable Response	FAVORABLE_RESPONSE	favorableResponse
+NCIT:C123617	Unfavorable Response	UNFAVORABLE_RESPONSE	unfavorableResponse
+NCIT:C123600	No Response	NO_RESPONSE	noResponse
+NCIT:C123614	Stringent Complete Response	STRINGENT_COMPLETE_RESPONSE	stringentCompleteResponse
+NCIT:C123598	Minimal Response	MINIMAL_RESPONSE	minimalResponse
+NCIT:C4870	Complete Remission	COMPLETE_REMISSION	completeRemission
+NCIT:C18058	Partial Remission	PARTIAL_REMISSION	partialRemission
+NCIT:C70604	Primary Refractory	PRIMARY_REFRACTORY	primaryRefractory
+NCIT:C142357	iRECIST Complete Response	iRECIST_COMPLETE_RESPONSE	iRECISTCompleteResponse
+NCIT:C142356	iRECIST Confirmed Progressive Disease	iRECIST_CONFIRMED_PROGRESSIVE_DISEASE	iRECISTConfirmedProgressiveDisease
+NCIT:C142358	iRECIST Partial Response	iRECIST_PARTIAL_RESPONSE	iRECISTPartialResponse
+NCIT:C142359	iRECIST Stable Disease	iRECIST_STABLE_DISEASE	iRECISTStableDisease
+NCIT:C142360	iRECIST Unconfirmed Progressive Disease	iRECIST_UNCONFIRMED_PROGRESSIVE_DISEASE	iRECISTUnconfirmedProgressiveDisease
diff --git a/constants/Severity.tsv b/constants/Severity.tsv
@@ -0,0 +1,6 @@
+ontology.id	ontology.label	variable.name	function.name
+HP:0012827	Borderline	BORDERLINE	borderline
+HP:0012825	Mild	MILD	mild
+HP:0012826	Moderate	MODERATE	moderate
+HP:0012828	Severe	SEVERE	severe
+HP:0012829	Profound	PROFOUND	profound
diff --git a/constants/SpatialPattern.tsv b/constants/SpatialPattern.tsv
@@ -31,4 +31,4 @@ HP:0012840	Proximal	PROXIMAL	proximal
 HP:0033820	Apical	APICAL	apical
 HP:0030650	Focal	FOCAL	focal
 HP:0030651	Multifocal	MULTIFOCAL	multifocal
-HP:0032540	Jointflexorsurfacelocalization	JOINT_FLEXOR_SURFACE_LOCALIZATION	jointFlexorSurfaceLocalization
+HP:0032540	Joint flexor surface localization	JOINT_FLEXOR_SURFACE_LOCALIZATION	jointFlexorSurfaceLocalization
diff --git a/constants/TreatmentTermination.tsv b/constants/TreatmentTermination.tsv
@@ -0,0 +1,5 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C105740	Treatment Completed as Prescribed	TREATMENT_COMPLETED_AS_PRESCRIBED	treatmentCompletedAsPrescribed
+NCIT:C105741	Treatment Terminated Due to Toxicity	TREATMENT_TERMINATED_TOXICITY	treatmentTerminatedDueToToxicity
+NCIT:C106470	Treatment on Hold	TREATMENT_ON_HOLD	treatmentOnHold
+NCIT:C41331	Adverse Event	ADVERSE_EVENT	adverseEvent
diff --git a/constants/TumorProgression.tsv b/constants/TumorProgression.tsv
@@ -0,0 +1,4 @@
+ontology.id	ontology.label	variable.name	function.name
+NCIT:C8509	Primary Neoplasm	PRIMARY_NEOPLASM	primaryNeoplasm
+NCIT:C3261	Metastatic Neoplasm	METASTATIC_NEOPLASM	metastaticNeoplasm
+NCIT:C4798	Recurrent Neoplasm	RECURRENT_NEOPLASM	recurrentNeoplasm
diff --git a/constants/Unit.tsv b/constants/Unit.tsv
@@ -3,7 +3,7 @@ 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:kg	kiligram	KILIGRAM	kilogram
+UCUM:kg	kilogram	KILOGRAM	kilogram
 UCUM:L	liter	LITER	liter
 UCUM:m	meter	METER	meter
 UCUM:ug	microgram	MICROGRAM	microgram

diff --git a/constants/create_classes.py b/constants/create_classes.py
@@ -54,6 +54,9 @@ def name(self):
     def items(self):
         return self._constant_items
 
+    def __repr__(self):
+        return f"Entry name={self._name} {len(self._constant_items)} items"
+
 
 def parse_csv(fname):
     if not isfile(fname):
@@ -72,31 +75,22 @@ def parse_csv(fname):
 def create_java_class(entry):
     java_file_name = entry.name + ".java" # LATER adjust path
     java_file_path = join(JAVA_DIR_PATH, java_file_name)
-    fh = open(java_file_path, 'wt')
-    fh.write("package org.phenopackets.phenopackettools.builder.constants;\n\n")
-    fh.write("import org.phenopackets.phenopackettools.builder.builders.OntologyClassBuilder;\n")
-    fh.write("import org.phenopackets.schema.v2.core.OntologyClass;\n\n")
-    fh.write(f"public class {entry.name} {{\n\n")
-    items = entry.items
-    for item in items:
-        # e.g.,   private static final OntologyClass HETEROZYGOUS = OntologyClassBuilder.ontologyClass("GENO:0000135", "heterozygous");
-        fh.write(f"  private static final OntologyClass {item.variable_name} = OntologyClassBuilder.ontologyClass(")
-        fh.write(f"\"{item.ontology_id}\", \"{item.ontology_label}\");\n")
-    fh.write("\n\n")
-    for item in items:
-        # e.g.,  public static OntologyClass heterozygous() {return HETEROZYGOUS; }
-        fh.write(f"  public static OntologyClass {item.function_name}() {{ return {item.variable_name}; }}\n")
-    fh.write("\n}\n")
-    fh.close()
-
-
-
-
-
-
-
-
-
+    with open(java_file_path, 'wt') as fh:
+        fh.write("// Generated by phenopacket-tools/constants/create_classes.py. DO NOT EDIT!\n")
+        fh.write("package org.phenopackets.phenopackettools.builder.constants;\n\n")
+        fh.write("import org.phenopackets.phenopackettools.builder.builders.OntologyClassBuilder;\n")
+        fh.write("import org.phenopackets.schema.v2.core.OntologyClass;\n\n")
+        fh.write(f"public class {entry.name} {{\n\n")
+        items = entry.items
+        for item in items:
+            # e.g.,   private static final OntologyClass HETEROZYGOUS = OntologyClassBuilder.ontologyClass("GENO:0000135", "heterozygous");
+            fh.write(f"  private static final OntologyClass {item.variable_name} = OntologyClassBuilder.ontologyClass(")
+            fh.write(f"\"{item.ontology_id}\", \"{item.ontology_label}\");\n")
+        fh.write("\n\n")
+        for item in items:
+            # e.g.,  public static OntologyClass heterozygous() {return HETEROZYGOUS; }
+            fh.write(f"  public static OntologyClass {item.function_name}() {{ return {item.variable_name}; }}\n")
+        fh.write("\n}\n")
 
 
 entries = []

diff --git a/constants/rtd_texts.txt b/constants/rtd_texts.txt
@@ -9,4 +9,15 @@ SpatialPattern|Modifier terms from the `HPO <https://hpo.jax.org/app/>`_ are use
 Unit|With some exceptions, terms from the `The Unified Code for Units of Measure <https://units-of-measurement.org/>`_ are used to denote units.
 Response|These codes from `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ can be used to code the overall response of a patient to treatment. Favorable and Unfavorble can be used for general purposes and the remaining codes are intended to be used for oncology.
 Assays|If possible, `LOINC <https://loinc.org/>`_ codes should be used to specify laboratory test assays.
-Gender|`LOINC <https://loinc.org/>`_ codes should be used to specify self-reported gender.
+Gender|`LOINC <https://loinc.org/>`_ codes should be used to specify self-reported gender.
+PathologicalTnm|TNM staging performed as part of pathologic specimen (based on surgical specimens including sentinel lymph node biopsy specimens).
+DiseaseStage|These codes from `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ can be used to denote that clinical stage of cancer or heart failure. Other codes should be used for specific diseases with their own clinical stage systems.
+Severity|Terms from the `HPO <https://hpo.jax.org/app/>`_ are used to describe the severity, defined as the intensity or degree of a manifestation.
+Evidence|Terms from the `Evidence and Con   clusion Ontology <https://evidenceontology.org/browse/#ECO_SN>` are used to specify evidence categories.
+BiospecimenType|Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ are used to denote the source of a biospecimen.
+TumorProgression|Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ are used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence.
+TumorGrade|Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to describe microscopic appearance of tumor. Grade 1: Well differentiated (low grade); Grade 2: Moderately differentiated (intermediate grade); Grade 3: Poorly differentiated (high grade); Grade 4: Undifferentiated (high grade).
+DiseaseGrade|Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to represent the tumor grade.
+MaterialSample|Terms from the `EFO <https://www.ebi.ac.uk/ols/ontologies/efo>`_ to specify the status of the sample.
+AdministrationRoute|Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to represent the way in which a medicinal product is introduced into the body.
+TreatmentTermination|Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to represent the reason that the treatment was completed or stopped early.
diff --git a/docs/cli.rst b/docs/cli.rst
@@ -17,15 +17,18 @@ no special installation procedure if Java 17 or better is available in your envi
 Setup
 ~~~~~
 
-Most users should *download* the precompiled JAR file from *phenopacket-tools* release page.
+Most users should *download* the distribution ZIP file with precompiled JAR file from *phenopacket-tools* release page.
 However, it is also possible to *build* the JAR from sources.
 
 Download
 ^^^^^^^^
 
-*phenopacket-tools* JAR is provided as part of *phenopacket-tools*' release schedule
+*phenopacket-tools* JAR is provided in the distribution ZIP file as part of *phenopacket-tools*' release schedule
 from `Releases <https://github.com/phenopackets/phenopacket-tools/releases>`_.
 
+The ZIP archive contains the executable JAR file along with README and example phenopackets required to run the setup
+and the tutorial.
+
 Build from source code
 ^^^^^^^^^^^^^^^^^^^^^^
 
@@ -44,12 +47,9 @@ Run the following commands to check out the stable source code and to build the
   $ cd phenopacket-tools
   $ ./mvnw -Prelease package
 
-After a successful build, a file ``phenopacket-tools-cli-${project.version}.jar`` will be created in
-the ``phenopacket-tools-cli/target`` directory. Use the JAR file in the same way as the JAR downloaded
-from *phenopacket-tools* releases.
-
-.. note::
-  Replace ``${project.version}`` with a given version (e.g. ``0.4.6``).
+After a successful build, a distribution ZIP file "phenopacket-tools-cli-|release|-distribution.zip"
+will be created in the ``phenopacket-tools-cli/target`` directory. Use the ZIP archive in the same way as the archive
+downloaded from *phenopacket-tools* releases.
 
 
 Commands
@@ -70,6 +70,10 @@ In the next sections, we will run *phenopacket-tools* by using the following ali
 
   $ alias pxf="java -jar phenopacket-tools-cli-${project.version}.jar"
 
+.. note::
+  The commands report warnings and errors by default. Use `-v` to increase the verbosity and see what's
+  going on under the hood. The `-v` can be specified multiple times (e.g. `-vvv`).
+
 *examples* - generate examples of the top-level elements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -172,11 +176,11 @@ Results are written into STDOUT in CSV/TSV format. The CSV output has a header,
 The header contains phenopacket-tools version, date time of validation, and list of validators that were run.
 A row with column names follows the header, and then the individual validation results.
 
-..
-  TODO - check the validation description.
+.. TODO - check the validation description.
 
 Set up autocompletion
 ~~~~~~~~~~~~~~~~~~~~~
 
-TODO - write the section
+.. TODO - write the section
 
+TODO - write
diff --git a/docs/conf.py b/docs/conf.py
@@ -23,8 +23,17 @@
 ##############
 
 project = 'phenopacket-tools'
-copyright = '2022, Peter Robinson'
-author = 'Peter Robinson'
+copyright = '2022, Daniel Danis, Peter Robinson'
+author = u'Daniel Danis, Peter Robinson'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.4'
+# The full version, including alpha/beta/rc tags.
+release = '0.4.7'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration