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Feature 1436 storage and indexing #1695

Merged
merged 215 commits into from
Sep 28, 2023
Merged

Feature 1436 storage and indexing #1695

merged 215 commits into from
Sep 28, 2023

Commits on Mar 1, 2022

  1. Development docs for storage and indexing refactor. 

    See issue #1436 and and #1364.
    @mbjones
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Commits on May 10, 2022

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

    @mbjones
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Commits on May 11, 2022

  1. Reformat POM.xml whitespace for consistency.

    @mbjones
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  2. Upgrade plantuml to current release jar.

    @mbjones
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  3. Initial pass at PlantUML component diagram.

    @mbjones
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  4. Add plantuml jar to maven dependencies. 

    Currently unused by tooling -- need way to connect Makefile to use this jar.
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  5. Renegerated doc images with new plantuml version.

    @mbjones
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  6. Second pass at component diagram. 

    Indexing components added, along with RabbitMQ and Ceph.
    @mbjones
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  7. Indexing figure layout tweaks. First fairly complete draft.

    @mbjones
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  8. Ignore sphinx build artifacts.

    @mbjones
    mbjones committed May 11, 2022
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  9. Add indexing sequence diagrams 

    Issue #1436 Add indexing sequence diagrams to storage subsystem document.
    @gothub
    gothub committed May 11, 2022
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Commits on May 12, 2022

  1. Remove extraneous vim swp file.

    @mbjones
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  2. Add filenames to sequence diagrams so the generate in the correct loc… 

    …ation.
    @mbjones
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  3. Add two diagrams for the design document.

    @taojing2002
    taojing2002 committed May 12, 2022
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  4. Update storage-subsystem.rst

    @taojing2002
    taojing2002 authored May 12, 2022
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Commits on May 13, 2022

  1. Changed proposed seq to show async calls to workers. 

    The actual worker process itself should also be asyn but is not shown that way currently.
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  2. Add basicAck to IndexWorker in proposed sequence diagram.

    @mbjones
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Commits on May 14, 2022

  1. Rename classes, harmonize component diagram with sequence diagram.

    @mbjones
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Commits on May 18, 2022

  1. Remove hand-drawn sequence diagram that has been replaced.

    @mbjones
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Commits on Jun 10, 2022

  1. Add the RabbitMQService class.

    @taojing2002
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Commits on Jun 13, 2022

  1. Use RabbitMQ to replace hazelcast on the index queue.

    @taojing2002
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  2. Remove the list of fields from the index submit method. The list was … 

    …only for the event log indexing, which is not used anymore.
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Commits on Jun 14, 2022

  1. Rename the class of RabbitMQService to IndexGenerator.

    @taojing2002
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  2. Rename the package from rabbitmq to index.queue.

    @taojing2002
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  3. Change the log statement for "RabbitMQService" to "IndexGenerator".

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Commits on Jun 15, 2022

  1. Remove system metadata from and add priority to the signature of the … 

    …publish method.
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  2. Add the method to get the file path. 

    Add a junit class for the IndexGenerator class.
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  3. Add a log statement with the index task information such as the ident… 

    …ifier, index type and file path.
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Commits on Jun 16, 2022

  1. Declare the max priority in the queue.

    @taojing2002
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Commits on Jun 24, 2022

  1. Change the max priority to 10 for the rabbitmq.

    @taojing2002
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Commits on Jul 11, 2022

  1. Merge branch 'feature-1587-rabbitmq-index' into feature-1436-storage-… 

    …and-indexing
    @taojing2002
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  2. Merge branch 'develop' into feature-1436-storage-and-indexing

    @taojing2002
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Commits on Jul 13, 2022

  1. Fixed an error on the dependency.

    @taojing2002
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  2. In the delete index type, we don't need to get the object path since … 

    …the file was removed.
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Commits on Jul 14, 2022

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

    @taojing2002
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Commits on Jul 29, 2022

  1. Remove the code to set basicQos since this value is set only on the c… 

    …onsumer part, not the producer part.
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Commits on Aug 4, 2022

  1. The relative path for the object in the message is changed to be base… 

    …d on the property application.datafilepath or application.documentpath.
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Commits on Aug 8, 2022

  1. Modify the log statement to make the error more clear.

    @taojing2002
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  2. Add the code to make sure the singleton class will initialize the ins… 

    …tance again in the getInstance method if it failed in the previous try.
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Commits on Aug 30, 2022

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

    @taojing2002
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Commits on Sep 3, 2022

  1. Merge remote-tracking branch 'origin/develop' into feature-1436-stora… 

    …ge-and-indexing
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Commits on Oct 6, 2022

  1. In the testPackage method, use new indicator to show the indexing is … 

    …done.
    @taojing2002
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  2. Add more statements for waiting.

    @taojing2002
    taojing2002 committed Oct 6, 2022
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Commits on Oct 28, 2022

  1. Moutn details for FS.

    @mbjones
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Commits on Nov 3, 2022

  1. COnsiderations on content-based storage added.

    @mbjones
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  2. Merge branch 'develop' into current

    @mbjones
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Commits on Nov 4, 2022

  1. Update the proposed hash-based physical storage layout.

    @mbjones
    mbjones committed Nov 4, 2022
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  2. Modify physical layout proposal. 

    New proposal is to use content checksums for data files, and checksums
of PID values for system metadata files.
    @mbjones
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  3. Use fenced code block for directory tree.

    @mbjones
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  4. Preformatted code block with two backticks.

    @mbjones
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  5. Change to :: for preformatted block.

    @mbjones
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  6. Code fence the shasum example.

    @mbjones
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Commits on Nov 7, 2022

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

    @mbjones
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Commits on Nov 8, 2022

  1. Updated storage description to use dedicated sysmeta directory. 

    Also added an example of the sysmeta file format and header.
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Commits on Nov 9, 2022

  1. Small editorial changes to storage docs.

    @mbjones
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Commits on Nov 16, 2022

  1. Make the index tasks priority low during the reindexall process.

    @taojing2002
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Commits on Jan 24, 2023

  1. Add Public API documentation

    @doulikecookiedough
    doulikecookiedough authored Jan 24, 2023
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  2. Update Public API method name

    @doulikecookiedough
    doulikecookiedough authored Jan 24, 2023
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  3. Update Public API table for retrieve method args

    @doulikecookiedough
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Commits on Jan 25, 2023

  1. Edited HashStore API table. 

    Based on conversation about API at the 2023-01-24 dev call.
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Commits on Jan 27, 2023

  1. Update Public API table

    @doulikecookiedough
    doulikecookiedough authored Jan 27, 2023
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  2. Fix Public API table display

    @doulikecookiedough
    doulikecookiedough authored Jan 27, 2023
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Commits on Jan 30, 2023

  1. Use the new dataone-indexer library to index tasks

    @taojing2002
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Commits on Jan 31, 2023

  1. Delete those context xml files which stay in the dataone indexer comp… 

    …onent now.
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  2. Add the properties for the dataone-indexer in the metacat.properties … 

    …file.
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Commits on Feb 6, 2023

  1. Update Public API Table

    @doulikecookiedough
    doulikecookiedough authored Feb 6, 2023
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Commits on Feb 13, 2023

  1. Update Public API table

    @doulikecookiedough
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Commits on Feb 16, 2023

  1. Add a new wrap class to replace hazelcast.

    @taojing2002
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  2. Merge branch 'feature-1436-storage-and-indexing' of https://github.co… 

    …m/nceas/metacat into feature-1436-storage-and-indexing
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Commits on Feb 21, 2023

  1. Change the method of getInstance to be static.

    @taojing2002
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Commits on Feb 22, 2023

  1. Add the lock/unlock methods.

    @taojing2002
    taojing2002 committed Feb 22, 2023
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  2. Update storage-subsystem.rst

    @doulikecookiedough
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Commits on Feb 23, 2023

  1. Replace Hazelcast by SystemMetadataManager.

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  2. Replace Hazelcast by SystemMetadataManager.

    @taojing2002
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Commits on Feb 24, 2023

  1. Replace Hazelcast by SystemMetadataManager.

    @taojing2002
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Commits on Feb 25, 2023

  1. Remove Hazelcast.

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Commits on Feb 28, 2023

  1. Continue to replace hazelcast.

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Commits on Mar 1, 2023

  1. Continute to remove Hazelcast.

    @taojing2002
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  2. Remove hazelcast from the test code.

    @taojing2002
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  3. Remove the import statement of hazelcast service.

    @taojing2002
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Commits on Mar 2, 2023

  1. Remove the HazelcastService and relavant files.

    @taojing2002
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  2. Update PublicAPI table

    @doulikecookiedough
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  3. Update PublicAPI table

    @doulikecookiedough
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Commits on Mar 3, 2023

  1. Remove the hazelcast configuration file.

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Commits on Mar 7, 2023

  1. Remove the dependency on hazelcast

    @taojing2002
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  2. Delete the test classes relevant to hazelcast.

    @taojing2002
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  3. Update PublicAPI table

    @doulikecookiedough
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Commits on Mar 8, 2023

  1. Make the store method thread safe.

    @taojing2002
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  2. Use ArrayList to replace Vector for the lockedIds. Since we manually … 

    …lock the code to access the lockedIds list, it can use non-thread-safe ArrayList for better performance.
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Commits on Mar 9, 2023

  1. Put the notifyAll method in the synchronzied section.

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Commits on Mar 20, 2023

  1. Update PublicAPI table

    @doulikecookiedough
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Commits on Mar 30, 2023

  1. Refactor the IdentifierManager class to move some methods to SystemMe… 

    …tadataManager.
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Commits on Apr 3, 2023

  1. In the delete access rules method, the db connection will be reused. … 

    …So it can be rolled back.
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  2. Inserting access rules doesn't check out db connection. So it will be… 

    … rolled back.
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  3. Make some methods protected so the only method exposed to public is s… 

    …tore.
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Commits on Apr 4, 2023

  1. Remove the method of insertOrUpdateSystemmetadata.

    @taojing2002
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Commits on Apr 7, 2023

  1. Make sure that removing pids from a queue is the first step in the fi… 

    …nally section.
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Commits on Apr 12, 2023

  1. Add previous physical file layout design appendix item for reference

    @doulikecookiedough
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  2. Update storage-subsystem document for authority-based identifier file… 

    … naming approach
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Commits on Apr 14, 2023

  1. Update Public API table

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Commits on Apr 24, 2023

  1. Add hashstore store_object mermaid diagram

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  2. Removed the hazelcast test files.

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  3. Add revised Hashstore store_object mermaid diagram

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  4. Update PublicAPI table and add store_object mermaid diagram

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  5. Remove the dummy methods lock and unlock which accomondate the lock m… 

    …echanism in Hazelcast.
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Commits on Jun 21, 2023

  1. Update storage-subsystem.rst

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  2. Fix typo

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  3. Update storage-subsystem.rst

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  4. Update storage-subsystem.rst

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Commits on Jul 5, 2023

  1. Update storage-subsystem.rst

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Commits on Jul 10, 2023

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

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  2. Merge branch 'feature-1436-storage-and-indexing' into feature-1606-re… 

    …move-hazelcast
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Commits on Jul 11, 2023

  1. Add code to load the metacat site property file into the index worker.

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Commits on Jul 12, 2023

  1. Fixed a typo.

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  2. Merge branch 'feature-1436-storage-and-indexing' into feature-1606-re… 

    …move-hazelcast
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  3. Add the class to validate system metadata objects.

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Commits on Jul 13, 2023

  1. Add a junit test for the SystemMetadataValidator class.

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  2. Use the getSystemMetadata method to get the current modification date.

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Commits on Jul 17, 2023

  1. Add code to change the modification date.

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  2. Don't change modification time when store the system metadata.

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Commits on Jul 18, 2023

  1. Merge remote-tracking branch 'origin/develop' into feature-1436-stora… 

    …ge-and-indexing
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  2. Merge branch 'feature-1436-storage-and-indexing' into feature-1606-re… 

    …move-hazelcast
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  3. Add the validation check during the store process.

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Commits on Jul 19, 2023

  1. Remove the code to modify the modification date in the system metadata.

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  2. Don't change the modification date in the archive method.

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  3. Remove the code to change modifiedDate in system metadata.

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Commits on Jul 20, 2023

  1. Add the new parameter to determine if we should modify the modificati… 

    …on date in the create method.
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Commits on Jul 21, 2023

  1. Add a test that the modification date wouldn't be changed in the cn.c… 

    …reate method.
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  2. We don't update the modification date of the system metadata since th… 

    …e change is centerized.
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  3. Check the setReplicateStatus method doesn't change the modification d… 

    …ate.
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Commits on Jul 22, 2023

  1. Check the system metadata read from the store.

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Commits on Jul 24, 2023

  1. Remove the duplicated code to modify the system metadata changed time.

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  2. Adjust the serial version in the system metadata to make it work.

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Commits on Jul 25, 2023

  1. Remove some code to set the modfication date of system metadata since… 

    … we centerize it.
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Commits on Jul 27, 2023

  1. Merge remote-tracking branch 'origin/develop' into feature-1436-stora… 

    …ge-and-indexing
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  2. Merge branch 'feature-1436-storage-and-indexing' into feature-1606-re… 

    …move-hazelcast
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Commits on Aug 7, 2023

  1. Add a new store method which has a db connection parameter.

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  2. Merge branch 'feature-1606-remove-hazelcast' of https://github.com/nc… 

    …eas/metacat into feature-1606-remove-hazelcast
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Commits on Aug 9, 2023

  1. Add the waiting time for finishing index in the getOREPackage method.

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  2. Merge remote-tracking branch 'origin/develop' into feature-1436-stora… 

    …ge-and-indexing
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  3. Merge branch 'feature-1436-storage-and-indexing' into feature-1606-re… 

    …move-hazelcast
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Commits on Aug 14, 2023

  1. Add a timer task to re-submit the index tasks.

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Commits on Aug 15, 2023

  1. Add a class to handle save/retrieve the last reindex date.

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  2. Use the new class to record the last re-index date.

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Commits on Aug 18, 2023

  1. Add a method to get list of pids in a time frame.

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Commits on Aug 21, 2023

  1. In the method of getGUIDsInTimeRange, we sorted the result.

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  2. Add code to get object id by a method in the IdentifierManager class.

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Commits on Aug 23, 2023

  1. Add code to add the class to re-generate the index tasks.

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Commits on Aug 24, 2023

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

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  2. Merge branch 'feature-1436-storage-and-indexing' into feature-1606-re… 

    …move-hazelcast
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Commits on Aug 28, 2023

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

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Commits on Sep 6, 2023

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

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  2. Rough pass at hash-tree based data package layout.

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  3. move CID document up one level.

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  4. Add HashStore annotation initial flow chart

    @doulikecookiedough
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  5. Trim white space from image flow chart

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  6. Add annotation section to storage-subsystem.rst based on current disc… 

    …ussions
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Commits on Sep 8, 2023

  1. Merge branch 'develop' into feature-1436-storage-and-indexing

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Commits on Sep 13, 2023

  1. Updated the DIP oackage layout image, and added link to dip-noodling. 

     Please enter the commit message for your changes. Lines starting
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Commits on Sep 18, 2023

  1. Use dataone-indexer to replace old d1-cn-index-processor.

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Commits on Sep 19, 2023

  1. Removed an extra variable assignment.

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Commits on Sep 20, 2023

  1. Merge remote-tracking branch 'origin/develop' into feature-1436-stora… 

    …ge-and-indexing
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  2. Add the solr configure files from dataone-indexer.

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Commits on Sep 21, 2023

  1. typo fixes

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  2. reformat, del commented code, and typo fixes

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  3. reformat, del commented code, and typo fixes

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  4. reformat, del commented code, and typo fixes

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  5. reformat, del commented code, and typo fixes

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  6. more commented code

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  7. Add mermaid diagram of sdip hash tree layout

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  8. reformat, del commented code, and typo fixes

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  9. Merge branch 'feature-1436-storage-and-indexing' of github.com:NCEAS/… 

    …metacat into feature-1436-storage-and-indexing
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  10. removed old header comments

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  11. reformat, del commented code, and javadoc fixes

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  12. reformat, del commented code

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  13. reformat, del commented code

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Commits on Sep 25, 2023

  1. Revert MetacatHandler changes to avoid whitespace conflicts for Jing'… 

    …s other branch

This reverts commit 5cd64ad.
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  2. Revert DocumentImpl changes (2 of 2) to avoid whitespace conflicts fo… 

    …r Jing's other branch

This reverts commit 6a1a9e3.
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  3. Revert DocumentImpl changes (2 of 2) to avoid whitespace conflicts fo… 

    …r Jing's other branch

This reverts commit 56e6ede.
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  4. MetacatHandler NON-WHTSPC changes only

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  5. DocumentImpl NON-WHTSPC changes only

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  6. CNodeService NON-WHTSPC changes (delete commented code)

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Commits on Sep 26, 2023

  1. whitespace only

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  2. remove commented code & reformat

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  3. whitespace only

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  4. remove commented code & reformat long lines

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  5. whitespace only

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  6. delete commented code & wrap long lines

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  7. rename updateSystemMetadataWithoutLock() -> updateSystemMetadata()

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  8. Remove the properties related to hazelcast. 

    Remove the commented out rabitmq properties.
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  9. del commented code. no whtspc changes

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  10. Merge branch 'feature-1436-storage-and-indexing' of https://github.co… 

    …m/nceas/metacat into feature-1436-storage-and-indexing
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  11. whitespace only

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  12. del commented code & wrap long lines

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  13. Merge branch 'feature-1436-storage-and-indexing' of github.com:NCEAS/… 

    …metacat into feature-1436-storage-and-indexing
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  14. whitespace only

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  15. del commented code & wrap long lines

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  16. del commented code; wrap long lines; tabs to spaces

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  17. minor edits

    @artntek
    artntek committed Sep 26, 2023
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  18. whitespace only

    @artntek
    artntek committed Sep 26, 2023
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  19. del commented code; reformat; tabs -> spaces

    @artntek
    artntek committed Sep 26, 2023
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  20. reformat long lines & remove licensing

    @artntek
    artntek committed Sep 26, 2023
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  21. whitespace only

    @artntek
    artntek committed Sep 26, 2023
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  22. del commented code; reformat long lines

    @artntek
    artntek committed Sep 26, 2023
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  23. remove licensing; wrap long line

    @artntek
    artntek committed Sep 26, 2023
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  24. Add a comment to indicate the time regenerating index task use the de… 

    …fault time zone in the host.
    @taojing2002
    taojing2002 committed Sep 26, 2023
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Commits on Sep 27, 2023

  1. Reformat some long lines and correct some typos.

    @taojing2002
    taojing2002 committed Sep 27, 2023
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  2. Put + at the beginning of the lines.

    @taojing2002
    taojing2002 committed Sep 27, 2023
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  3. Fixed a typo in the name of a constant.

    @taojing2002
    taojing2002 committed Sep 27, 2023
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  4. Change the name of a constant since the definition was changed.

    @taojing2002
    taojing2002 committed Sep 27, 2023
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  5. Make a variable final and wrap long lines.

    @taojing2002
    taojing2002 committed Sep 27, 2023
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  6. Replace the thread sleeping for a long time by checking the solr quer… 

    …y result.
    @taojing2002
    taojing2002 committed Sep 27, 2023
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  7. Fixed an issue that a property was splitted into two strings. 

    Removed some commented out code.
    @taojing2002
    taojing2002 committed Sep 27, 2023
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  8. changed Angel Chen's ORCID to Jing's instead, since Angel no longer i… 

    …n correct group
    @artntek
    artntek committed Sep 27, 2023
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  9. added test-fast target

    @artntek
    artntek committed Sep 27, 2023
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