Adapt parsing Bagit Profile due to specification. #128
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -19,9 +19,10 @@ | |
| import com.fasterxml.jackson.databind.deser.std.StdDeserializer; | ||
|
|
||
| /** | ||
| * Deserialize bagit profile json to a {@link BagitProfile} | ||
| */ | ||
| public class BagitProfileDeserializer extends StdDeserializer<BagitProfile> { | ||
|
|
||
| private static final long serialVersionUID = 1L; | ||
| private static final Logger logger = LoggerFactory.getLogger(BagitProfileDeserializer.class); | ||
| private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle"); | ||
|
|
@@ -36,149 +37,176 @@ public BagitProfileDeserializer(final Class<?> vc) { | |
|
|
||
| @Override | ||
| public BagitProfile deserialize(final JsonParser p, final DeserializationContext ctxt) | ||
| throws IOException, JsonProcessingException { | ||
| final BagitProfile profile = new BagitProfile(); | ||
| final JsonNode node = p.getCodec().readTree(p); | ||
|
|
||
| parseBagitProfileInfo(node, profile); | ||
|
|
||
| profile.setBagInfoRequirements(parseBagInfo(node)); | ||
|
|
||
| profile.getManifestTypesRequired().addAll(parseManifestTypesRequired(node)); | ||
|
|
||
| profile.setFetchFileAllowed(node.get("Allow-Fetch.txt").asBoolean()); | ||
| logger.debug(messages.getString("fetch_allowed"), profile.isFetchFileAllowed()); | ||
|
|
||
| profile.setSerialization(Serialization.valueOf(node.get("Serialization").asText())); | ||
| logger.debug(messages.getString("serialization_allowed"), profile.getSerialization()); | ||
|
|
||
| profile.getAcceptableMIMESerializationTypes().addAll(parseAcceptableSerializationFormats(node)); | ||
|
|
||
| profile.getTagManifestTypesRequired().addAll(parseRequiredTagmanifestTypes(node)); | ||
|
|
||
| profile.getTagFilesRequired().addAll(parseRequiredTagFiles(node)); | ||
|
|
||
| profile.getAcceptableBagitVersions().addAll(parseAcceptableVersions(node)); | ||
|
|
||
| return profile; | ||
| } | ||
|
|
||
| private static void parseBagitProfileInfo(final JsonNode node, final BagitProfile profile) { | ||
| final JsonNode bagitProfileInfoNode = node.get("BagIt-Profile-Info"); | ||
| logger.debug(messages.getString("parsing_bagit_profile_info_section")); | ||
|
|
||
| // Read required tags first | ||
| // due to specification defined at https://github.com/bagit-profiles/bagit-profiles | ||
|
Contributor
There was a problem hiding this comment. Not really sure what this comment means. Why do you need to read required tags first?
Author
There was a problem hiding this comment. First the required tags are read and then the optional tags because they have to be handled differently. It's just to keep the code clearer.
Contributor
There was a problem hiding this comment. unless there is an error being thrown that I don't know about, how are you stopping if a required tag is missing? To put it another way, what would break if you moved those Perhaps a better way to make it cleaner would be to make another method that contained all the reads for optional tags. Something like
Author
There was a problem hiding this comment. If one of the required tags is not present, a NullPointerException is thrown.
See documentation of class BagLinter:
Therefore, no error handling is done anywhere in the code. |
||
| final String profileIdentifier = bagitProfileInfoNode.get("BagIt-Profile-Identifier").asText(); | ||
| logger.debug(messages.getString("identifier"), profileIdentifier); | ||
| profile.setBagitProfileIdentifier(profileIdentifier); | ||
|
|
||
| final String sourceOrg = bagitProfileInfoNode.get("Source-Organization").asText(); | ||
| logger.debug(messages.getString("source_organization"), sourceOrg); | ||
| profile.setSourceOrganization(sourceOrg); | ||
|
|
||
| final String extDescript = bagitProfileInfoNode.get("External-Description").asText(); | ||
| logger.debug(messages.getString("external_description"), extDescript); | ||
| profile.setExternalDescription(extDescript); | ||
|
|
||
| final String version = bagitProfileInfoNode.get("Version").asText(); | ||
| logger.debug(messages.getString("version"), version); | ||
| profile.setVersion(version); | ||
|
|
||
| final JsonNode contactNameNode = bagitProfileInfoNode.get("Contact-Name"); | ||
| if (contactNameNode != null) { | ||
| final String contactName = contactNameNode.asText(); | ||
| logger.debug(messages.getString("contact_name"), contactName); | ||
| profile.setContactName(contactName); | ||
| } | ||
|
|
||
| final JsonNode contactEmailNode = bagitProfileInfoNode.get("Contact-Email"); | ||
| if (contactEmailNode != null) { | ||
| final String contactEmail = contactEmailNode.asText(); | ||
| logger.debug(messages.getString("contact_email"), contactEmail); | ||
| profile.setContactEmail(contactEmail); | ||
| } | ||
|
|
||
| final JsonNode contactPhoneNode = bagitProfileInfoNode.get("Contact-Phone"); | ||
| if (contactPhoneNode != null) { | ||
| final String contactPhone = contactPhoneNode.asText(); | ||
| logger.debug(messages.getString("contact_phone"), contactPhone); | ||
| profile.setContactPhone(contactPhone); | ||
| } | ||
| } | ||
|
|
||
| @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops") | ||
| private static Map<String, BagInfoRequirement> parseBagInfo(final JsonNode rootNode) { | ||
| final JsonNode bagInfoNode = rootNode.get("Bag-Info"); | ||
| logger.debug(messages.getString("parsing_bag_info")); | ||
| final Map<String, BagInfoRequirement> bagInfo = new HashMap<>(); | ||
|
|
||
| final Iterator<Entry<String, JsonNode>> nodes = bagInfoNode.fields(); //stuck in java 6... | ||
|
|
||
| while (nodes.hasNext()) { | ||
| final Entry<String, JsonNode> node = nodes.next(); | ||
|
|
||
| final BagInfoRequirement entry = new BagInfoRequirement(); | ||
| // due to specification required is false by default. | ||
| final JsonNode requiredNode = node.getValue().get("required"); | ||
| if (requiredNode != null) { | ||
| entry.setRequired(requiredNode.asBoolean()); | ||
| } | ||
|
|
||
| final JsonNode valuesNode = node.getValue().get("values"); | ||
| if (valuesNode != null) { | ||
| for (final JsonNode value : valuesNode) { | ||
| entry.getAcceptableValues().add(value.asText()); | ||
| } | ||
| } | ||
|
|
||
| final JsonNode repeatableNode = node.getValue().get("repeatable"); | ||
| if (repeatableNode != null) { | ||
| entry.setRepeatable(repeatableNode.asBoolean()); | ||
| } | ||
|
|
||
| logger.debug("{}: {}", node.getKey(), entry); | ||
| bagInfo.put(node.getKey(), entry); | ||
| } | ||
|
|
||
| return bagInfo; | ||
| } | ||
|
|
||
| private static List<String> parseManifestTypesRequired(final JsonNode node) { | ||
| final JsonNode manifests = node.get("Manifests-Required"); | ||
|
|
||
| final List<String> manifestTypes = new ArrayList<>(); | ||
|
|
||
| for (final JsonNode manifestName : manifests) { | ||
| manifestTypes.add(manifestName.asText()); | ||
| } | ||
|
|
||
| logger.debug(messages.getString("required_manifest_types"), manifestTypes); | ||
|
|
||
| return manifestTypes; | ||
| } | ||
|
|
||
| private static List<String> parseAcceptableSerializationFormats(final JsonNode node) { | ||
| final JsonNode serialiationFormats = node.get("Accept-Serialization"); | ||
| final List<String> serialTypes = new ArrayList<>(); | ||
|
|
||
| for (final JsonNode serialiationFormat : serialiationFormats) { | ||
| serialTypes.add(serialiationFormat.asText()); | ||
| } | ||
| logger.debug(messages.getString("acceptable_serialization_mime_types"), serialTypes); | ||
|
|
||
| return serialTypes; | ||
| } | ||
|
|
||
| private static List<String> parseRequiredTagmanifestTypes(final JsonNode node) { | ||
| final JsonNode tagManifestsRequiredNodes = node.get("Tag-Manifests-Required"); | ||
| final List<String> requiredTagmanifestTypes = new ArrayList<>(); | ||
| if (tagManifestsRequiredNodes != null) { | ||
| for (final JsonNode tagManifestsRequiredNode : tagManifestsRequiredNodes) { | ||
| requiredTagmanifestTypes.add(tagManifestsRequiredNode.asText()); | ||
| } | ||
| } | ||
| logger.debug(messages.getString("required_tagmanifest_types"), requiredTagmanifestTypes); | ||
|
|
||
| return requiredTagmanifestTypes; | ||
| } | ||
|
|
||
| private static List<String> parseRequiredTagFiles(final JsonNode node) { | ||
| final JsonNode tagFilesRequiredNodes = node.get("Tag-Files-Required"); | ||
| final List<String> requiredTagFiles = new ArrayList<>(); | ||
|
|
||
| if (tagFilesRequiredNodes != null) { | ||
| for (final JsonNode tagFilesRequiredNode : tagFilesRequiredNodes) { | ||
| requiredTagFiles.add(tagFilesRequiredNode.asText()); | ||
| } | ||
| } | ||
| logger.debug(messages.getString("tag_files_required"), requiredTagFiles); | ||
|
|
||
| return requiredTagFiles; | ||
| } | ||
|
|
||
| private static List<String> parseAcceptableVersions(final JsonNode node) { | ||
| final JsonNode acceptableVersionsNodes = node.get("Accept-BagIt-Version"); | ||
| final List<String> acceptableVersions = new ArrayList<>(); | ||
|
|
||
| for (final JsonNode acceptableVersionsNode : acceptableVersionsNodes) { | ||
| acceptableVersions.add(acceptableVersionsNode.asText()); | ||
| } | ||
| logger.debug(messages.getString("acceptable_bagit_versions"), acceptableVersions); | ||
|
|
||
| return acceptableVersions; | ||
| } | ||
| } | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.