Release v1.7.3

Release 1.7.3

Release Date: 08-December-2017
Install Instructions: pip install --upgrade synapseclient or see http://docs.synapse.org/python/#installation
Documentation: http://docs.synapse.org/python/

Release 1.7.3 introduces fixes and quality of life changes to Tables and synapseutils:

• Changes to Tables:
  • You no longer have to include the etag column in your SQL query when using a tableQuery() to update File/Project Views. just SELECT the relevant columns and etags will be resolved automatically.
  • The new PartialRowSet class allows you to only have to upload changes to individual cells of a table instead of every row that had a value changed. It is recommended to use the PartialRowSet.from_mapping() classmethod instead of the PartialRowSet constructor.
• Changes to synapseutils:
  • Improved documentation
  • You can now use ~ to refer to your home directory in your manifest.tsv

We also added improved debug logging and use Python's bulitin logging module instead of printing directly to sys.stderr

Below are the full list of issues addressed by this release:

Bug

• [SYNPY-419] - support object store from client
• [SYNPY-499] - metadata manifest file name spelled wrong
• [SYNPY-504] - downloadTableFile changed return type with no change in documentation or mention in release notes
• [SYNPY-508] - syncToSynapse does not work if "the file path in "used" or "executed" of the manifest.tsv uses home directory shortcut "~"
• [SYNPY-516] - synapse sync file does not work if file is a URL
• [SYNPY-525] - Download CSV file of Synapse Table - 416 error
• [SYNPY-572] - Users should only be prompted for updates if the first or second part of the version number is changed.

New Feature

• [SYNPY-450] - Create convenience functions for synapse project settings
• [SYNPY-517] - sync command line
• [SYNPY-519] - Clean up doc string for Sync
• [SYNPY-545] - no module botocore
• [SYNPY-577] - Expose new view etags in command line clients

Task

• [SYNPY-569] - 'includeEntityEtag' should be True for Async table csv query downloads

Improvement

• [SYNPY-304] - Table objects should implement len()
• [SYNPY-511] - improve exception handling
• [SYNPY-518] - Clean up sync interface
• [SYNPY-590] - Need better logging of errors that occur in the Python client.
• [SYNPY-597] - Add ability to create PartialRowset updates

v1.7.1

Release Notes - Synapse Python Client - Version py-1.7

Release Date: 17-June-2017
Install Instructions: pip install --upgrade synapseclient or see http://docs.synapse.org/python/#installation
Documentation: http://docs.synapse.org/python/

Release 1.7 is a large bugfix release with several new features. The main ones include:

• We have expanded the syanpaseutils packages to add the abilitity to:
  • Bulk upload files to synapse (synapseutils.syncToSynapse).
  • Notify you via email on the progress of a function (useful for jobs like large file uploads that may take a long time to complete).
  • The syncFromSynapse function now creates a "manifest" which contains the metadata of downloaded files. (These can also be used to update metadata with the bulk upload function.
• File View tables can now be created from the python client using EntityViewSchema. See fileviews documentation.
• The python client is now able to upload to user owned S3 Buckets. Click here for instructions on linking your S3 bucket to synapse

We've also made vairous improvements to existing features:

• The LARGETEXT type is now supported in Tables allowing for strings up to 2Mb.
• The --description argument when creating/updating entities from the command line client will now create a Wiki for that entity. You can also use --descriptionFile to write the contents of a markdownfile as the entity's Wiki
• Two member variables of the File object, file_entity.cacheDir and file_entity.files is being DEPRECATED in favor of file_entity.path for finding the location of a downloaded File
• pandas dataframes containing datetime values can now be properly converted into csv and uploaded to Synapse.
  We also added a optional convert_to_datetime parameter to CsvFileTable.asDataFrame() that will automatically convert Synapse DATE columns into datetime objects instead of leaving them as long unix timestamps

Below are the full list of bugs and issues addressed by this release:

New Features

• [SYNPY-53] - support syn.get of external FTP links in py client
• [SYNPY-179] - Upload to user owned S3 bucket
• [SYNPY-412] - allow query-based download based on view tables from command line client
• [SYNPY-487] - Add remote monitoring of long running processes
• [SYNPY-415] - Add Docker and TableViews into Entity.py
• [SYNPY-89] - Python client: Bulk upload client/command
• [SYNPY-413] - Update table views via python client
• [SYNPY-301] - change actual file name from python client
• [SYNPY-442] - set config file path on command line

Improvements

• [SYNPY-407] - support LARGETEXT in tables
• [SYNPY-360] - Duplicate file handles are removed from BulkFileDownloadRequest
• [SYNPY-187] - Move --description in command line client to create wikis
• [SYNPY-224] - When uploading to a managed external file handle (e.g. SFTP), fill in storageLocationId
• [SYNPY-315] - Default behavior for files in cache dir should be replace
• [SYNPY-381] - Remove references to "files" and "cacheDir".
• [SYNPY-396] - Create filehandle copies in synapseutils.copy instead of downloading
• [SYNPY-403] - Use single endpoint for all downloads
• [SYNPY-435] - Convenience function for new service to get entity's children
• [SYNPY-471] - docs aren't generated for synapseutils
• [SYNPY-472] - References to wrong doc site
• [SYNPY-347] - Missing dtypes in table.DTYPE_2_TABLETYPE
• [SYNPY-463] - When copying filehandles we should add the files to the cache if we already donwloaded them
• [SYNPY-475] - Store Tables timeout error

Bug Fixes

• [SYNPY-190] - syn.login('asdfasdfasdf') should fail
• [SYNPY-344] - weird cache directories
• [SYNPY-346] - ValueError: cannot insert ROW_ID, already exists in CsvTableFile constructor
• [SYNPY-351] - Versioning broken for sftp files
• [SYNPY-366] - file URLs leads to wrong path
• [SYNPY-393] - New cacheDir causes cache to be ignored(?)
• [SYNPY-409] - Python client cannot depend on parsing Amazon pre-signed URLs
• [SYNPY-418] - Integration test failure against 167
• [SYNPY-421] - syn.getWikiHeaders has a return limit of 50 (Need to return all headers)
• [SYNPY-423] - upload rate is off or incorrect
• [SYNPY-424] - File entities don't handle local_state correctly for setting datafilehandleid
• [SYNPY-426] - multiple tests failing because of filenameOveride
• [SYNPY-427] - test dependent on config file
• [SYNPY-428] - sync function error
• [SYNPY-431] - download ending early and not restarting from previous spot
• [SYNPY-443] - tests/integration/integration_test_Entity.py:test_get_with_downloadLocation_and_ifcollision AssertionError
• [SYNPY-461] - On Windows, command line client login credential prompt fails (python 2.7)
• [SYNPY-465] - Update tests that set permissions to also include 'DOWNLOAD' permission and tests that test functions using queries
• [SYNPY-468] - Command line client incompatible with cache changes
• [SYNPY-470] - default should be read, download for setPermissions
• [SYNPY-483] - integration test fails for most users
• [SYNPY-484] - URL expires after retries
• [SYNPY-486] - Error in integration tests
• [SYNPY-488] - sync tests for command line client puts file in working directory
• [SYNPY-142] - PY: Error in login with rememberMe=True
• [SYNPY-464] - synapse get syn4988808 KeyError: u'preSignedURL'

Miscellaneous Tasks

• [SYNPY-422] - reduce default page size for GET /evaluation/{evalId}/submission/bundle/all
• [SYNPY-437] - Remove tests for access restrictions on evaluations
• [SYNPY-402] - Add release notes to Github release tag