Legacy Release Notes

v6.3.0 August 2024

• A bug has been addressed in which SMILES data in an input file following CXSMILES data caused a parsing error.

v6.3.1 September 2024

• A bug has been addressed in which SMILES data in an input file following CXSMILES data caused a parsing error.

• A bug has been addressed when exporting datasets to CSV files. All columns, or a subset thereof, can now be exported in cases when previously only Molecule and Molecule.Titled would have been exported.

v6.3.0 August 2024

• A bug has been addressed in which SMILES data in an input file following CXSMILES data caused a parsing error.

v6.2.0 June 2024

• Support for ShapeQuery (.sq) files has been added.

• Support for CXSMILES data has been added.

• Created collections have been defaulted to v1.

• A bug has been addressed by which some english language words (such as “BOTH”) could be interpreted as molecules.

v6.1.2 February 2024

• Columns can now be optionally ignored when exporting datasets.

v6.0.0 September 2023

• The version number has been synced with openeye-orionplatform.

• The Dataset to File Export ETL floes now preserve the Molecule Title when exporting to CSV files.

v2.3.0 July 2023

• This version increases the minimum versions of the requirements:

  • OpenEye-orionplatform==5.1.0

  • openeye-toolkits>=2022.2.2

v2.1.3 February 2023

• A floe for uploading large or small files from a URL has been added

v2.1.2 November 2022

• The orion-platform requirement has been updated to 4.5.2

v2.1.1 September 2022

• The orion-platform requirement has been updated to 4.4.1

• An issue where orionclient.types.Shard.download() could receive less data than expected has been fixed.

• An IOError will be raised and orionclient.types.Shard.download_to_file() will catch and retry.

v2.1.0 July 2022

• An issue with importing convert_path has been fixed.

• The etl-floe classifications has been updated to use the new PurePosixPath classifications

• The brief field has been added and the description field has been made more descriptive on all ETL floes.

• Requirement changes:

  • The Sphinx requirement has been updated to 3.5.4 and moved to requirements.txt.

  • The jinja2 requirement has been updated to 3.0.3.

  • The orion-platform requirement has been updated to 4.4.0.

  • The openeye-toolkits requirement has been updated to 2022.1.1.

  • The openeye-floe-pkg-tools requirement minimum version has been updated to 1.0.3.

• The etl-floe classifications has been updated to use the new PurePosixPath classifications.

• The “brief” field was added and the “description” field was made more descriptive on all ETL floes.

v2.0.2 February 2022

• Updated orion-platform to 4.3.0.

  • Converting datasets containing image data to csv now results in that field containing “<Image>”.

v2.0.1 December 2021

• The openeye-toolkits requirement has been updated to 2021.2.0

v2.0.0 November 2021

• The Collection Resize floe has been removed

v1.2.9 November 2021

• The orion-platform requirement has been updated to 4.2.5

v1.2.8 October 2021

• The orion-platform requirement has been updated to 4.2.4

  • A bug where the metadata of a collection was not being preserved when running the Collection Resize ETL floe has been fixed.

  • A required parameter collection_type in the ParallelCollectionResizeCube of the Collection Resize ETL floe has been promoted.

v1.2.7 October 2021

• orion-platform has been updated to 4.2.0

  • A failure caused by csv files containing no data for some columns has been fixed.

  • IUPAC names are no longer parsed, resulting in fewer column splits and ETL speedup.

  • A failure parsing lists of numbers has been fixed.

  • A bug in the naming of split columns has been fixed.

  • A failure when converting a record to OEB has been fixed. Fields with data that cannot be properly attached as generic data to a molecule are now skipped by default.

v1.2.6 June 2021

• The orion-platform requirement has been updated to 4.1.0 (mono-package)

• The OpenEye-toolkits requirement has been updated to 2021.1.1

• A regression in perceiving basic molecular properties for SMILES and CSV has been fixed.

v1.2.5 June 2021

• The orion-platform requirement has been updated to 4.0.0 (mono-package)

• Orion Platform >= 4.0.0 will not work with stacks older than 2021.1 due to usage of new APIs

• The OpenEye-toolkits requirement has been updated to 2020.2.4

• A new Converter, SmilesFileConverter, has been added.

• When converting CSV and SMILES format files to records, the original smiles are stored on output records.

• ETL floe documentation has been improved

v1.2.4 November 2020

• The orion-platform requirement has been updated to 3.1.0

  • BaseDatasetFieldAddOrReplaceCube has been added.

  • If no file extension is provided to DatasetWriterCube’s output file parameter, the file format is now OEDB.

  • OpenEye-floe==0.12.0

    • Adds support for versioning of WorkFloes.

    • Adds support for ordering of Parameters in the Orion UI.

    • An issue that resulted in Serial Cube Group initializer ports not incrementing the counts has been resolved.

  • OpenEye-drconvert==1.1.2

    • Bump OpenEye Toolkits

  • OpenEye-orionclient==3.1.0

    • Bump OpenEye Toolkits

  • OpenEye-datarecord==3.0.1

    • Bump OpenEye Toolkits

v1.2.3 August 2020

• orion-platform has been updated to 3.0.0

  • An issue with too frequent flushing in DatasetUpdaterCube has been fixed.

  • The DatasetAppenderCube now finalizes datasets.

  • OpenEye-datarecord==3.0.0

    • The implementation of datarecord has mostly moved to C++ in the toolkits.

    • A field type DesignUnit for storing OEDesignUnits has been added.

  • OpenEye-drconvert==1.1.0

    • Support for OEDesignUnit has been added

  • OpenEye-orionclient==3.0.0

    • Added OEDesignUnit support for dataset upload and download

    • Support for uploading OEDU files to datarecords has been added to upload()

    • orionclient.types.Datarecord.records now yields OEMolRecord

v1.2.2 April 2020

• orion-platform has been updated to 2.4.5

  • OpenEye-orionclient==2.6.3

    • The efficiency and reliability of ShardCollection.list_shards has been improved.

v1.2.1 March 2020

• orion-platform has been updated to 2.4.4

  • A bug in RecordsToCollectionCube has been fixed.

  • Improvement made to shard retries.

v1.2.0 February 2020

• The base OS image has been upgraded to Amazon Linux 2

• The environment has been upgraded to Python 3.8.1

• Package documentation has been added

• orion-platform has been updated to 2.4.2

  Improvements since 2.1.0 include:

  • Support for the OEZ format has been added to the following cubes:

    • CollectionResizeCube

    • CollectionToRecordsCube

    • RecordsToCollectionCube

  • orionplatform.cubes.files.RecordsToRecordFileConverter now uploads its files in parts reducing the disk usage

  • New parameters, which optionally enable metric collection for cubes have been added.

  • Sets lower bound on OpenEye-toolkits>=2019.10.2

  • A duplicate of output_tags in the DatasetWriterCube Options parameter group has been removed.

  • OpenEye-Drconvert==0.7.2

    • Support added for Float and Int vectors

    • Drconvert CLI now supports going from records to mols

v1.1.1 October 2019

• orion-platform 2.1.0

  • Improves reliability of uploading shards and writing shards of records

  • Adds limit parameter to ShardReaderCube to allow streaming only some shards from a collection.

v1.1.0 August 2019

• orion-platform 2.0.0

  • Improves reliability of collection floes

  • Updated version of drconvert (0.6.20) correctly handles conformer data

v1.0.0 July 2019

• orion-platform 1.0.2

v0.1.29 April 2019

• orion-platform 0.1.16

• Collection resize floe

v0.1.28 February 2019

Bugfixes

• drconvert 0.6.16

• No longer sets OEIsomericConfTest on file formats that are not mol2 or sdf

v0.1.27 February 2019

• Add Dataset Copy floe

v0.1.26 February 2019

• Orion Platform 0.1.14

  • openeye-drconvert>=0.6.15,<0.70

    • Performance improvements

Bugfixes

• Fixes ArchiveConverterCube

v0.1.25 January 2019

• Orion Platform 0.1.13

  • openeye-drconvert>=0.6.13,<0.70

    • Calls flush() before returning records from MolFileConverter

  • openeye-datarecord>=0.12.7,<0.13.0

    • Adds flush() to OERecord to write all cached values to bytes.

  • openeye-schemagen>=0.3.3,<0.4.0

    • Minor cleanup

v0.1.24 December 2018

• orion-platform 0.1.12

  Summary of changes relevant to ETL floes:

  • openeye-drconvert>=0.6.12,<0.7.0

    • Handle whitespace in SD data

  • openeye-orionclient>=0.6.10,<0.7.0

    • Makes Orion Client more robust to handling API changes

v0.1.23 November 2018

• orion-platform 0.1.11

v0.1.22 November 2018

• orion-platform 0.1.10

  Summary of changes relevant to ETL floes:

  • openeye-schemagen>=0.3.2,<0.4.0

  • survive SD data consisting of only whitespace

  • openeye-datarecord>=0.12.5,<0.13.0

  • add more testing for metadata; Serialize/deserialize round trips. ORION-6328

  • add Meta.Flags.Predicted metadata to datarecord. Minor cleanups. ORION-6328

v0.1.21 October 2018

• orion-platform 0.1.9

  Summary of changes relevant to ETL floes:

  • openeye-schemagen>=0.3.1,<0.4.0

    • delimiters back to ordering by descending priority

  • openeye-orionclient>=0.6.9,<0.7.0

    • 0.6.9

      • Adds headers to improve debugging capabilities

    • 0.6.8

      • Adds orionclient.exceptions.OrionTimeout exception that indicates that

        a request couldn’t be made to the specified Orion within the expected time

  • openeye-floe>=0.6.15,<0.7.0

    • 0.6.15

      • Fixes issue where parallel workers would incorrectly propagate failures when run in Orion

v0.1.20 October 2018

• add package uuid

v0.1.19 October 2018

• orion-platform 0.1.8 * fix memory leaks when reading dataset * improve robustness of collection handling

v0.1.18 September 2018

• orion-platform 0.1.7 orion-client fixes: * avoid writing too many records at once * fix issue retrieving records when sizes of records are not consistent

v0.1.17 September 2018

• orion-platform 0.1.6

v0.1.16 September 2018

• sync job system tags with backend/frontend

• bump orion-platform to 0.1.5 to force min versions

• remove default tag that appears to not be used

• Added continuation char BUGZID: ORION-6089

• Allowing non-SDData formats for etl export BUGZID: ORION-6089

v0.1.15 September 2018

• Needed to rev version because of Orion failing inspection due conflict with a previous failed upload of this version:

  “Workfloe Record Collection to Dataset with version:’0.1.14’ and uuid:’934d77a2-c1a1-421f-8daf-5b8ca6325fbf’ already exists for user with ID 1”

v0.1.14 September 2018

• Add package setup, tasks, tests, and release notes invoke upload-package puts package in S3 for devops to load onto stacks

• Update orion-platform requirement to 0.1.4, which pulls in toolkit, drconvert and related packages

• Add record collection floes