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Use canonical path for calls to ZarrService #57

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merged 4 commits into from
Jul 7, 2023
Merged

Use canonical path for calls to ZarrService #57

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d017b60
Use canonical path when calling ZarrService
dgault Jun 27, 2023
741e721
Use canonicalPath for all ZarrService calls
dgault Jun 27, 2023
5dc080c
Use canonicalPath in test
joshmoore Jul 4, 2023
ab4b060
GetUsedFiles: Use FOLLOW_LINKS option
dgault Jul 6, 2023
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42 changes: 26 additions & 16 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.FileVisitOption;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
Expand Down Expand Up @@ -156,14 +157,15 @@ protected void initFile(String id) throws FormatException, IOException {
String zarrRootPath = zarrPath.substring(0, zarrPath.indexOf(".zarr") + 5);
String name = zarrRootPath.substring(zarrRootPath.lastIndexOf(File.separator)+1, zarrRootPath.length() - 5);
Location omeMetaFile = new Location( zarrRootPath + File.separator + "OME", "METADATA.ome.xml" );
String canonicalPath = new Location(zarrRootPath).getCanonicalPath();

initializeZarrService(zarrRootPath);
initializeZarrService(canonicalPath);

if(omeMetaFile.exists()) {
parseOMEXML(omeMetaFile, store);
}
// Parse base level attributes
Map<String, Object> attr = zarrService.getGroupAttr(zarrRootPath);
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
int attrIndex = 0;
if (attr != null && !attr.isEmpty()) {
parseResolutionCount(zarrRootPath, "");
Expand All @@ -181,8 +183,8 @@ protected void initFile(String id) throws FormatException, IOException {
}

// Parse group attributes
for (String key: zarrService.getGroupKeys(zarrRootPath)) {
Map<String, Object> attributes = zarrService.getGroupAttr(zarrRootPath+File.separator+key);
for (String key: zarrService.getGroupKeys(canonicalPath)) {
Map<String, Object> attributes = zarrService.getGroupAttr(canonicalPath+File.separator+key);
if (attributes != null && !attributes.isEmpty()) {
parseResolutionCount(zarrRootPath, key);
parseLabels(zarrRootPath, key);
Expand All @@ -202,8 +204,8 @@ protected void initFile(String id) throws FormatException, IOException {
}

// Parse array attributes
for (String key: zarrService.getArrayKeys(zarrRootPath)) {
Map<String, Object> attributes = zarrService.getArrayAttr(zarrRootPath+File.separator+key);
for (String key: zarrService.getArrayKeys(canonicalPath)) {
Map<String, Object> attributes = zarrService.getArrayAttr(canonicalPath+File.separator+key);
if (attributes != null && !attributes.isEmpty()) {
attrIndex++;
String jsonAttr;
Expand All @@ -220,7 +222,7 @@ protected void initFile(String id) throws FormatException, IOException {
}

arrayPaths = new ArrayList<String>();
arrayPaths.addAll(zarrService.getArrayKeys(zarrRootPath));
arrayPaths.addAll(zarrService.getArrayKeys(canonicalPath));
orderArrayPaths(zarrRootPath);

core.clear();
Expand Down Expand Up @@ -328,7 +330,8 @@ private int[] getOriginalShape(int [] shape5D, int size) {
@Override
public void reopenFile() throws IOException {
try {
initializeZarrService(currentId);
String canonicalPath = new Location(currentId).getCanonicalPath();
initializeZarrService(canonicalPath);
}
catch (FormatException e) {
throw new IOException(e);
Expand Down Expand Up @@ -433,7 +436,8 @@ private void openZarr() {
seriesIndex += resolution;
}
newZarrPath += File.separator + arrayPaths.get(seriesIndex);
zarrService.open(newZarrPath);
String canonicalPath = new Location(newZarrPath).getCanonicalPath();
zarrService.open(canonicalPath);
}
}
} catch (IOException | FormatException e) {
Expand All @@ -454,7 +458,8 @@ private void orderArrayPaths(String root) {

private void parseResolutionCount(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
String canonicalPath = new Location(path).getCanonicalPath();
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
ArrayList<Object> multiscales = (ArrayList<Object>) attr.get("multiscales");
if (multiscales != null) {
for (int x = 0; x < multiscales.size(); x++) {
Expand Down Expand Up @@ -521,7 +526,8 @@ else if (multiscaleAxes.get(i) instanceof HashMap) {

private void parsePlate(String root, String key, MetadataStore store) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
String canonicalPath = new Location(path).getCanonicalPath();
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
Map<Object, Object> plates = (Map<Object, Object>) attr.get("plate");
if (plates != null) {
ArrayList<Object> columns = (ArrayList<Object>)plates.get("columns");
Expand Down Expand Up @@ -608,7 +614,8 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
private void parseWells(String root, String key, MetadataStore store, int plateIndex, int wellIndex,
HashMap<Integer, Integer> acqIdsIndexMap) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
String canonicalPath = new Location(path).getCanonicalPath();
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
Map<Object, Object> wells = (Map<Object, Object>) attr.get("well");
if (wells != null) {
ArrayList<Object> images = (ArrayList<Object>)wells.get("images");
Expand Down Expand Up @@ -641,7 +648,8 @@ private void parseWells(String root, String key, MetadataStore store, int plateI

private void parseLabels(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
String canonicalPath = new Location(path).getCanonicalPath();
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
ArrayList<Object> labels = (ArrayList<Object>) attr.get("labels");
if (labels != null) {
for (int l = 0; l < labels.size(); l++) {
Expand All @@ -652,7 +660,8 @@ private void parseLabels(String root, String key) throws IOException, FormatExce

private void parseImageLabels(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
String canonicalPath = new Location(path).getCanonicalPath();
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
Map<String, Object> imageLabel = (Map<String, Object>) attr.get("image-label");
if (imageLabel != null) {
String version = (String) imageLabel.get("version");
Expand Down Expand Up @@ -691,7 +700,8 @@ private void parseImageLabels(String root, String key) throws IOException, Forma

private void parseOmeroMetadata(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
String canonicalPath = new Location(path).getCanonicalPath();
Map<String, Object> attr = zarrService.getGroupAttr(canonicalPath);
Map<String, Object> omeroMetadata = (Map<String, Object>) attr.get("omero");
if (omeroMetadata != null) {
Integer id = (Integer) omeroMetadata.get("id");
Expand Down Expand Up @@ -853,7 +863,7 @@ public String[] getUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
ArrayList<String> usedFiles = new ArrayList<String>();
try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath))) {
try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath), FileVisitOption.FOLLOW_LINKS)) {
paths.filter(Files::isRegularFile)
.forEach(path -> usedFiles.add(path.toFile().getAbsolutePath()));
} catch (IOException e) {
Expand Down
8 changes: 5 additions & 3 deletions test/loci/formats/utests/ZarrReaderTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
import org.testng.annotations.Test;

import loci.common.DataTools;
import loci.common.Location;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.in.ZarrReader;
Expand All @@ -79,7 +80,8 @@ public void setUp() throws Exception {
reader = new ZarrReaderMock(zarrService);
file = File.createTempFile("tileTest", ".zarr");
String rootPath = file.getAbsolutePath();

String canonicalPath = new Location(rootPath).getCanonicalPath();

Map<String, Object> topLevelAttributes = new HashMap<String, Object>();
ArrayList<Object> multiscales = new ArrayList<Object>();
Map<String, Object> datasets = new HashMap<String, Object>();
Expand All @@ -97,8 +99,8 @@ public void setUp() throws Exception {
datasets.put("axes", Arrays.asList("t", "c", "z", "y", "x"));
multiscales.add(datasets);
topLevelAttributes.put("multiscales", multiscales);
when(zarrService.getGroupAttr(rootPath)).thenReturn(topLevelAttributes);

when(zarrService.getGroupAttr(canonicalPath)).thenReturn(topLevelAttributes);
when(zarrService.getShape()).thenReturn(shape);
when(zarrService.getPixelType()).thenReturn(0);
reader.setId(file.getAbsolutePath());
Expand Down