Description: adapting code to use Debian package libjson-java instead of the non-free org.json. - Beware, in libjson-java, JSONObject.put returns the added object, not the JSONObject. Calls to put thus cannot be chained. - In JSONArray there is no put method, using add instead. - Error messages are not exactly the same in org.json and libjson-java. - Ignoring default excludes when parsing json string to avoid skipping a field named "class". Author: Pierre Gruet Forwarded: not-needed Last-Update: 2024-12-26 --- a/src/main/java/htsjdk/beta/io/bundle/BundleJSON.java +++ b/src/main/java/htsjdk/beta/io/bundle/BundleJSON.java @@ -4,9 +4,9 @@ import htsjdk.io.IOPath; import htsjdk.samtools.util.Log; import htsjdk.utils.ValidationUtils; -import org.json.JSONArray; -import org.json.JSONException; -import org.json.JSONObject; +import org.kordamp.json.JSONArray; +import org.kordamp.json.JSONException; +import org.kordamp.json.JSONObject; import java.util.ArrayList; import java.util.Collection; @@ -49,12 +49,12 @@ ValidationUtils.validateArg( !bundle.getPrimaryContentType().equals(JSON_PROPERTY_PRIMARY), "Primary content type cannot be named 'primary'"); - final JSONObject schemaMap = new JSONObject() - .put(JSON_PROPERTY_SCHEMA_NAME, JSON_SCHEMA_NAME) - .put(JSON_PROPERTY_SCHEMA_VERSION, JSON_SCHEMA_VERSION); - final JSONObject outerJSON = new JSONObject() - .put(JSON_PROPERTY_SCHEMA, schemaMap) - .put(JSON_PROPERTY_PRIMARY, bundle.getPrimaryContentType()); + JSONObject schemaMap = new JSONObject(); + schemaMap.put(JSON_PROPERTY_SCHEMA_NAME, JSON_SCHEMA_NAME); + schemaMap.put(JSON_PROPERTY_SCHEMA_VERSION, JSON_SCHEMA_VERSION); + JSONObject outerJSON = new JSONObject(); + outerJSON.put(JSON_PROPERTY_SCHEMA, schemaMap); + outerJSON.put(JSON_PROPERTY_PRIMARY, bundle.getPrimaryContentType()); bundle.forEach(bundleResource -> { final Optional resourcePath = bundleResource.getIOPath(); @@ -63,7 +63,8 @@ } // generate JSON for each bundle resource - final JSONObject resourceJSON = new JSONObject().put(JSON_PROPERTY_PATH, resourcePath.get().getURIString()); + JSONObject resourceJSON = new JSONObject(); + resourceJSON.put(JSON_PROPERTY_PATH, resourcePath.get().getURIString()); if (bundleResource.getFileFormat().isPresent()) { resourceJSON.put(JSON_PROPERTY_FORMAT, bundleResource.getFileFormat().get()); } @@ -114,7 +115,7 @@ ValidationUtils.nonEmpty(jsonString, "JSON string"); ValidationUtils.nonNull(ioPathConstructor, "IOPath-derived class constructor"); try { - return toBundle(new JSONObject(jsonString), ioPathConstructor); + return toBundle(JSONObject.fromObject(jsonString), ioPathConstructor); } catch (JSONException | UnsupportedOperationException e) { // see if the user provided a collection instead of a single bundle, and if so, present it as // a Bundle as long as it only contains one BundleResource @@ -152,7 +153,7 @@ final List bundles = new ArrayList<>(); try { - final JSONArray jsonArray = new JSONArray(jsonString); + final JSONArray jsonArray = JSONArray.fromObject(jsonString); jsonArray.forEach(element -> { if (! (element instanceof JSONObject jsonObject)) { throw new IllegalArgumentException( @@ -164,7 +165,7 @@ } catch (JSONException | UnsupportedOperationException e) { // see if the user provided a single bundle instead of a collection, if so, wrap it up as a collection try { - bundles.add(toBundle(new JSONObject(jsonString), ioPathConstructor)); + bundles.add(toBundle(JSONObject.fromObject(jsonString), ioPathConstructor)); } catch (JSONException | UnsupportedOperationException e2) { throw new IllegalArgumentException( String.format("JSON can be interpreted neither as an individual bundle (%s) nor as a bundle collection (%s)", @@ -234,7 +235,7 @@ jsonResources.keySet().forEach(key -> { if (!TOP_LEVEL_PROPERTIES.contains(key)) { if (jsonResources.get(key) instanceof JSONObject resourceObject) { - bundleResources.add(toBundleResource(key, resourceObject, ioPathConstructor)); + bundleResources.add(toBundleResource((String)(key), resourceObject, ioPathConstructor)); } else { throw new IllegalArgumentException( String.format("Bundle resources may contain only BundleResource objects, found %s", key)); --- a/src/main/java/htsjdk/samtools/util/htsget/HtsgetErrorResponse.java +++ b/src/main/java/htsjdk/samtools/util/htsget/HtsgetErrorResponse.java @@ -1,7 +1,7 @@ package htsjdk.samtools.util.htsget; -import org.json.JSONObject; +import org.kordamp.json.JSONObject; /** * Class allowing deserialization from json htsget error response, as defined in https://samtools.github.io/hts-specs/htsget.html @@ -32,7 +32,7 @@ } public static HtsgetErrorResponse parse(final String s) { - final JSONObject j = new JSONObject(s); + final JSONObject j = JSONObject.fromObject(s); final JSONObject htsget = j.optJSONObject("htsget"); if (htsget == null) { throw new IllegalStateException(new HtsgetMalformedResponseException("No htsget key found in response")); --- a/src/main/java/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.java +++ b/src/main/java/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.java @@ -3,8 +3,8 @@ import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.Locatable; import htsjdk.samtools.util.RuntimeIOException; -import org.json.JSONArray; -import org.json.JSONObject; +import org.kordamp.json.JSONArray; +import org.kordamp.json.JSONObject; import java.io.IOException; import java.net.HttpURLConnection; @@ -146,19 +146,19 @@ if (!this.fields.isEmpty()) { postBody.put( "fields", - new JSONArray(this.getFields().stream() + JSONArray.fromObject(this.getFields().stream() .map(HtsgetRequestField::toString) .toArray()) ); } if (!this.tags.isEmpty()) { - postBody.put("tags", new JSONArray(this.getTags().toArray())); + postBody.put("tags", JSONArray.fromObject(this.getTags().toArray())); } if (!this.notags.isEmpty()) { - postBody.put("notags", new JSONArray(this.getNoTags().toArray())); + postBody.put("notags", JSONArray.fromObject(this.getNoTags().toArray())); } if (!this.intervals.isEmpty()) { - postBody.put("regions", new JSONArray( + postBody.put("regions", JSONArray.fromObject( this.intervals.stream() .map(interval -> { final JSONObject intervalJson = new JSONObject(); --- a/src/main/java/htsjdk/samtools/util/htsget/HtsgetResponse.java +++ b/src/main/java/htsjdk/samtools/util/htsget/HtsgetResponse.java @@ -1,8 +1,9 @@ package htsjdk.samtools.util.htsget; import htsjdk.samtools.util.RuntimeIOException; -import org.json.JSONArray; -import org.json.JSONObject; +import org.kordamp.json.JsonConfig; +import org.kordamp.json.JSONArray; +import org.kordamp.json.JSONObject; import java.io.ByteArrayInputStream; import java.io.IOException; @@ -126,9 +127,9 @@ final JSONObject headersJson = blockJson.optJSONObject("headers"); final Map headers = headersJson == null ? null - : headersJson.toMap().entrySet().stream() + : ((Set >)(headersJson.entrySet())).stream() .collect(Collectors.toMap( - Map.Entry::getKey, + Map.Entry::getKey, e -> e.getValue().toString() )); @@ -167,7 +168,9 @@ * @return parsed HtsgetResponse object */ public static HtsgetResponse parse(final String s) { - final JSONObject j = new JSONObject(s); + JsonConfig cfgJson = new JsonConfig(); + cfgJson.setIgnoreDefaultExcludes(true); //Accept "class" as a field name! + final JSONObject j = JSONObject.fromObject(s, cfgJson); final JSONObject htsget = j.optJSONObject("htsget"); if (htsget == null) { throw new HtsgetMalformedResponseException("No htsget key found in response"); @@ -181,7 +184,7 @@ throw new HtsgetMalformedResponseException("No urls field found in Htsget Response"); } - final List blocks = IntStream.range(0, blocksJson.length()) + final List blocks = IntStream.range(0, blocksJson.size()) .mapToObj(blocksJson::getJSONObject) .map(Block::parse) .collect(Collectors.toList()); --- a/src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java +++ b/src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java @@ -3,7 +3,7 @@ import htsjdk.HtsjdkTest; import htsjdk.io.HtsPath; import htsjdk.io.IOPath; -import org.json.JSONObject; +import org.kordamp.json.JSONObject; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -193,7 +193,7 @@ public void testRoundTripJSONSingle(final String jsonString, final String primaryKey, final List resources) { final Bundle bundleFromResources = new Bundle(primaryKey, resources); final String actualJSONString = BundleJSON.toJSON(bundleFromResources); - Assert.assertEquals(actualJSONString, new JSONObject(jsonString).toString(1)); + Assert.assertEquals(JSONObject.fromObject(actualJSONString), JSONObject.fromObject(jsonString)); // now recreate the bundle from JSON final Bundle bundleFromJSON = BundleJSON.toBundle(jsonString); @@ -279,7 +279,7 @@ {"", "The string is empty"}, // missing schema entirely - {"{}", "[\"schema\"] not found"}, + {"{}", "null object"}, // missing schema name { @@ -378,7 +378,7 @@ BundleJSON.JSON_SCHEMA_VERSION, BundleResourceType.CT_ALIGNED_READS, BundleResourceType.FMT_READS_BAM, BundleResourceType.CT_ALIGNED_READS), - "Expected a ':' after a key at 36 [character 19 line 3]" + "Expected a ':' after a key at" }, // missing enclosing {} -> UnsupportedOperationException (no text message) @@ -389,7 +389,7 @@ "schemaVersion":"%s", } """.formatted(BundleJSON.JSON_SCHEMA_VERSION), - "A JSONObject text must begin with '{' at 1 [character 2 line 1]", + "A JSONObject text must begin with '{' at", }, }; } --- a/src/test/java/htsjdk/samtools/util/HtsgetRequestUnitTest.java +++ b/src/test/java/htsjdk/samtools/util/HtsgetRequestUnitTest.java @@ -2,8 +2,8 @@ import htsjdk.HtsjdkTest; import htsjdk.samtools.util.htsget.*; -import org.json.JSONArray; -import org.json.JSONObject; +import org.kordamp.json.JSONArray; +import org.kordamp.json.JSONObject; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -123,27 +123,27 @@ Assert.assertEquals(postBody.getString("class"), "header"); Assert.assertEqualsNoOrder( - postBody.getJSONArray("fields").toList().stream().map(Object::toString).toArray(String[]::new), + JSONArray.toList(postBody.getJSONArray("fields")).stream().map(Object::toString).toArray(String[]::new), new String[]{"QNAME", "CIGAR"} ); Assert.assertEqualsNoOrder( - postBody.getJSONArray("tags").toList().stream().map(Object::toString).toArray(String[]::new), + JSONArray.toList(postBody.getJSONArray("tags")).stream().map(Object::toString).toArray(String[]::new), new String[]{"tag1", "tag3"} ); Assert.assertEqualsNoOrder( - postBody.getJSONArray("notags").toList().stream().map(Object::toString).toArray(String[]::new), + JSONArray.toList(postBody.getJSONArray("notags")).stream().map(Object::toString).toArray(String[]::new), new String[]{"tag2"} ); - final JSONArray expectedRegions = new JSONArray() - .put(new JSONObject("{referenceName: \"chr1\", start: 0, end: 16}")) - .put(new JSONObject("{referenceName: \"chr1\", start: 16, end: 32}")) - .put(new JSONObject("{referenceName: \"chrM\", start: 0, end: 16}")) - .put(new JSONObject("{referenceName: \"chrM\", start: 16, end: 32}")); + JSONArray expectedRegions = new JSONArray(); + expectedRegions.add(JSONObject.fromObject("{referenceName: \"chr1\", start: 0, end: 16}")); + expectedRegions.add(JSONObject.fromObject("{referenceName: \"chr1\", start: 16, end: 32}")); + expectedRegions.add(JSONObject.fromObject("{referenceName: \"chrM\", start: 0, end: 16}")); + expectedRegions.add(JSONObject.fromObject("{referenceName: \"chrM\", start: 16, end: 32}")); Assert.assertEqualsNoOrder( - postBody.getJSONArray("regions").toList(), - expectedRegions.toList() + JSONArray.toList(postBody.getJSONArray("regions")).toArray(), + JSONArray.toList(expectedRegions).toArray() ); } -} \ No newline at end of file +}