Release Notes

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