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Preserve catalog path in metadata for multi-ontology-input commands #1285

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Preserve catalog path in metadata for multi-ontology-input commands #1285

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174 changes: 151 additions & 23 deletions robot-command/src/main/java/org/obolibrary/robot/CommandLineHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -528,6 +528,44 @@ public static List<OWLOntology> getInputOntologies(
return inputOntologies;
}

/**
* Given an IOHelper, a state object, and a command line, return the input ontology list for
* commands whose output state ontology is the existing state ontology or the first provided input
* ontology. If the state already contains an ontology, it is prepended and state metadata is
* preserved. Otherwise, metadata for the first local input is recorded for downstream commands
* that may need to reload imports.
*
* @param ioHelper the IOHelper to load the ontology with
* @param state the command state to read and update
* @param line the command line to use
* @return the list of input ontologies, beginning with the state ontology when present
* @throws IllegalArgumentException if required options are missing
* @throws IOException if an ontology cannot be loaded
*/
public static List<OWLOntology> getPrimaryInputOntologies(
IOHelper ioHelper, CommandState state, CommandLine line)
throws IllegalArgumentException, IOException {
List<OWLOntology> inputOntologies = new ArrayList<>();
boolean hasStateOntology = state.getOntology() != null;
if (hasStateOntology) {
inputOntologies.add(state.getOntology());
inputOntologies.addAll(getInputOntologies(ioHelper, line, true));
} else {
InputOntologies loadedOntologies = getInputOntologiesWithMetadata(ioHelper, line);
inputOntologies.addAll(loadedOntologies.getOntologies());
if (loadedOntologies.getPrimaryOntologyPath() != null) {
state.setOntologyPath(loadedOntologies.getPrimaryOntologyPath());
}
if (loadedOntologies.getCatalogPath() != null) {
state.setCatalogPath(loadedOntologies.getCatalogPath());
}
if (inputOntologies.isEmpty()) {
throw new IllegalArgumentException(missingInputsError);
}
}
return inputOntologies;
}

/**
* Given an IOHelper, a state object, and a command line, update the state with the ontology.
*
Expand Down Expand Up @@ -1080,23 +1118,73 @@ private static File[] getFilesByPattern(String pattern) throws IllegalArgumentEx
*/
public static List<OWLOntology> getInputOntologies(IOHelper ioHelper, CommandLine line)
throws IllegalArgumentException, IOException {
List<OWLOntology> inputOntologies = new ArrayList<>();
return getInputOntologiesWithMetadata(ioHelper, line).getOntologies();
}

/**
* Given an IOHelper and a command line, check input options and return loaded input ontologies
* plus metadata for the first ontology.
*
* @param ioHelper the IOHelper to load the ontology with
* @param line the command line to use
* @return loaded ontologies and primary input metadata
* @throws IllegalArgumentException on bad pattern
* @throws IOException if the ontology cannot be loaded
*/
private static InputOntologies getInputOntologiesWithMetadata(IOHelper ioHelper, CommandLine line)
throws IllegalArgumentException, IOException {
String catalogPath = getOptionalValue(line, "catalog");
return getInputOntologiesWithMetadata(ioHelper, line, catalogPath);
}

/**
* Given an IOHelper, a command line, and a catalog path, check input options and return loaded
* input ontologies plus metadata for the first ontology.
*
* @param ioHelper the IOHelper to load the ontology with
* @param line the command line to use
* @param catalogPath the catalog file to use, or null to guess local catalogs
* @return loaded ontologies and primary input metadata
* @throws IllegalArgumentException on bad pattern
* @throws IOException if the ontology cannot be loaded
*/
private static InputOntologies getInputOntologiesWithMetadata(
IOHelper ioHelper, CommandLine line, String catalogPath)
throws IllegalArgumentException, IOException {
InputOntologies inputOntologies = new InputOntologies(catalogPath);
String inputFormat = getOptionalValue(line, "input-format");
// Check for input files
List<String> inputOntologyPaths = getOptionalValues(line, "input");
for (String inputOntologyPath : inputOntologyPaths) {
inputOntologies.add(ioHelper.loadOntology(inputOntologyPath, true, inputFormat));
OWLOntology ontology;
if (catalogPath != null) {
ontology = ioHelper.loadOntology(inputOntologyPath, catalogPath, inputFormat);
} else {
ontology = ioHelper.loadOntology(inputOntologyPath, true, inputFormat);
}
inputOntologies.add(ontology, inputOntologyPath);
}
// Check for input IRIs
List<String> inputOntologyIRIs = getOptionalValues(line, "input-iri");
for (String inputOntologyIRI : inputOntologyIRIs) {
inputOntologies.add(ioHelper.loadOntology(IRI.create(inputOntologyIRI), null, inputFormat));
inputOntologies.add(
ioHelper.loadOntology(IRI.create(inputOntologyIRI), catalogPath, inputFormat), null);
}
// Check for input patterns (wildcard)
String pattern = getOptionalValue(line, "inputs");
if (pattern != null) {
File catalogFile = null;
if (catalogPath != null) {
catalogFile = new File(catalogPath);
}
for (File inputOntologyFile : getFilesByPattern(pattern)) {
inputOntologies.add(ioHelper.loadOntology(inputOntologyFile, true, inputFormat));
OWLOntology ontology;
if (catalogFile != null) {
ontology = ioHelper.loadOntology(inputOntologyFile, catalogFile, inputFormat);
} else {
ontology = ioHelper.loadOntology(inputOntologyFile, true, inputFormat);
}
inputOntologies.add(ontology, inputOntologyFile.getPath());
}
}
return inputOntologies;
Expand All @@ -1114,28 +1202,68 @@ public static List<OWLOntology> getInputOntologies(IOHelper ioHelper, CommandLin
*/
public static List<OWLOntology> getInputOntologies(
IOHelper ioHelper, CommandLine line, String catalogPath) throws IOException {
List<OWLOntology> inputOntologies = new ArrayList<>();
String inputFormat = getOptionalValue(line, "input-format");
// Check for input files
List<String> inputOntologyPaths = getOptionalValues(line, "input");
for (String inputOntologyPath : inputOntologyPaths) {
inputOntologies.add(ioHelper.loadOntology(inputOntologyPath, catalogPath, inputFormat));
}
// Check for input IRIs
List<String> inputOntologyIRIs = getOptionalValues(line, "input-iri");
for (String inputOntologyIRI : inputOntologyIRIs) {
inputOntologies.add(
ioHelper.loadOntology(IRI.create(inputOntologyIRI), catalogPath, inputFormat));
return getInputOntologiesWithMetadata(ioHelper, line, catalogPath).getOntologies();
}

/** Loaded input ontologies with metadata for the first loaded ontology. */
private static class InputOntologies {
/** Loaded ontologies. */
private List<OWLOntology> ontologies = new ArrayList<>();

/** Path to the explicit catalog, if one was provided. */
private String catalogPath;

/** Path to the first local input ontology, if the first input was local. */
private String primaryOntologyPath;

/**
* Create a result container.
*
* @param catalogPath path to the explicit catalog, or null
*/
InputOntologies(String catalogPath) {
this.catalogPath = catalogPath;
}
// Check for input patterns (wildcard)
String pattern = getOptionalValue(line, "inputs");
if (pattern != null) {
File catalogFile = new File(catalogPath);
for (File inputOntologyFile : getFilesByPattern(pattern)) {
inputOntologies.add(ioHelper.loadOntology(inputOntologyFile, catalogFile, inputFormat));

/**
* Add a loaded ontology and the local path that loaded it, if any.
*
* @param ontology loaded ontology
* @param ontologyPath local ontology path, or null for IRI inputs
*/
void add(OWLOntology ontology, String ontologyPath) {
if (ontologies.isEmpty()) {
primaryOntologyPath = ontologyPath;
}
ontologies.add(ontology);
}

/**
* Return the loaded ontologies.
*
* @return loaded ontologies
*/
List<OWLOntology> getOntologies() {
return ontologies;
}

/**
* Return the explicit catalog path.
*
* @return explicit catalog path, or null
*/
String getCatalogPath() {
return catalogPath;
}

/**
* Return the first local input path.
*
* @return first local input path, or null
*/
String getPrimaryOntologyPath() {
return primaryOntologyPath;
}
return inputOntologies;
}

/**
Expand Down
11 changes: 2 additions & 9 deletions robot-command/src/main/java/org/obolibrary/robot/MergeCommand.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package org.obolibrary.robot;

import java.util.ArrayList;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
Expand Down Expand Up @@ -114,14 +113,8 @@ public CommandState execute(CommandState state, String[] args) throws Exception
state = new CommandState();
}

List<OWLOntology> inputOntologies = new ArrayList<>();
// inputOntologies should not be empty
boolean notEmpty = false;
if (state.getOntology() != null) {
notEmpty = true;
inputOntologies.add(state.getOntology());
}
inputOntologies.addAll(CommandLineHelper.getInputOntologies(ioHelper, line, notEmpty));
List<OWLOntology> inputOntologies =
CommandLineHelper.getPrimaryInputOntologies(ioHelper, state, line);

boolean collapseImportClosure =
CommandLineHelper.getBooleanValue(line, "collapse-import-closure", true);
Expand Down
10 changes: 2 additions & 8 deletions robot-command/src/main/java/org/obolibrary/robot/UnmergeCommand.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package org.obolibrary.robot;

import java.util.ArrayList;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
Expand Down Expand Up @@ -101,13 +100,8 @@ public CommandState execute(CommandState state, String[] args) throws Exception
state = new CommandState();
}

List<OWLOntology> inputOntologies = new ArrayList<>();
boolean notEmpty = false;
if (state.getOntology() != null) {
notEmpty = true;
inputOntologies.add(state.getOntology());
}
inputOntologies.addAll(CommandLineHelper.getInputOntologies(ioHelper, line, notEmpty));
List<OWLOntology> inputOntologies =
CommandLineHelper.getPrimaryInputOntologies(ioHelper, state, line);

OWLOntology outputOntology = UnmergeOperation.unmerge(inputOntologies);

Expand Down
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