From 6fc12756457b8a9e598b72fb234a71ee054b29a4 Mon Sep 17 00:00:00 2001 From: KimYen Ladia Date: Thu, 17 Jan 2019 11:52:07 -0800 Subject: [PATCH] update docs --- docs/build/html/.buildinfo | 2 +- docs/build/html/Activity.html | 52 +- docs/build/html/Annotations.html | 47 +- docs/build/html/Client.html | 92 +- docs/build/html/CommandLineClient.html | 47 +- docs/build/html/Entity.html | 47 +- docs/build/html/Evaluation.html | 47 +- docs/build/html/Multipart_upload.html | 37 +- docs/build/html/Table.html | 88 +- docs/build/html/Team.html | 37 +- docs/build/html/Upload.html | 206 +++ docs/build/html/Utilities.html | 47 +- docs/build/html/Versions.html | 47 +- docs/build/html/Views.html | 214 ++++ docs/build/html/Wiki.html | 47 +- docs/build/html/_static/background_b01.png | Bin 0 -> 78 bytes docs/build/html/_static/bizstyle.css | 490 ++++++++ docs/build/html/_static/bizstyle.js | 41 + docs/build/html/_static/css3-mediaqueries.js | 1 + .../html/_static/css3-mediaqueries_src.js | 1104 +++++++++++++++++ docs/build/html/_static/custom.css | 6 +- .../html/_static/documentation_options.js | 2 +- docs/build/html/_static/favicon.png | Bin 0 -> 3863 bytes docs/build/html/_static/synapse_logo.png | Bin 8839 -> 19570 bytes docs/build/html/genindex.html | 23 +- docs/build/html/index.html | 84 +- docs/build/html/news.html | 339 +++-- docs/build/html/objects.inv | Bin 2012 -> 2028 bytes docs/build/html/py-modindex.html | 23 +- docs/build/html/search.html | 23 +- docs/build/html/searchindex.js | 2 +- docs/build/html/sftp.html | 47 +- docs/build/html/synapseutils.html | 47 +- synapseclient/synapsePythonClient | 2 +- 34 files changed, 2796 insertions(+), 495 deletions(-) create mode 100644 docs/build/html/Upload.html create mode 100644 docs/build/html/Views.html create mode 100644 docs/build/html/_static/background_b01.png create mode 100644 docs/build/html/_static/bizstyle.css create mode 100644 docs/build/html/_static/bizstyle.js create mode 100644 docs/build/html/_static/css3-mediaqueries.js create mode 100644 docs/build/html/_static/css3-mediaqueries_src.js create mode 100644 docs/build/html/_static/favicon.png diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo index e2dba95df..c03e46f94 100644 --- a/docs/build/html/.buildinfo +++ b/docs/build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: f44d763881eb2f384aa0384e43b7de52 +config: a8c6b29b14987fc58c61db8838ee4956 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/Activity.html b/docs/build/html/Activity.html index c1cfe5b20..7b452e034 100644 --- a/docs/build/html/Activity.html +++ b/docs/build/html/Activity.html @@ -1,26 +1,33 @@ - + + - Provenance — Synapse Python Client 1.9.0 documentation + Provenance — Synapse Python Client 1.9.1 documentation + + + - + + +
- Synapse + Synapse

Synapse Python Client API

@@ -39,11 +46,23 @@

Navigation

  • previous |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -168,10 +175,7 @@

    Activity -
    See also: Provenance in Synapse
    -
    and the W3C’s provenance ontology
    - +

    See also: The W3C’s provenance ontology

    executed(target=None, targetVersion=None, url=None, name=None)
    @@ -260,12 +264,12 @@

    Navigation

  • previous |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -39,11 +46,23 @@

    Navigation

  • previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -151,12 +158,12 @@

    Navigation

  • previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -37,13 +44,25 @@

    Navigation

    next |
  • - previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -291,10 +298,7 @@

    Synapse
    downloadTableFile(table, column, downloadLocation=None, rowId=None, versionNumber=None, rowIdAndVersion=None, ifcollision='keep.both')
    -
    -

    Deprecated since version 1.9.0: This will be removed in 2.0. please use downloadTableColumns() instead

    -
    -

    Downloads a file associated with a row in a Synapse table.

    +

    Downloads a file associated with a row in a Synapse table.

    @@ -322,6 +326,10 @@

    Synapseprint(file_path) +
    +

    Deprecated since version 1.9.0: This will be removed in 2.0. Please use downloadTableColumns() +instead

    +
    @@ -502,7 +510,7 @@

    Synapse

    - +
    Parameters:configPath – Path to configuration file on local file system
    Returns:a ConfigParser populated with properties from the user’s configuration file.
    Returns:a RawConfigParser populated with properties from the user’s configuration file.
    @@ -1379,10 +1387,11 @@

    SynapseParameters:

    @@ -820,12 +826,12 @@

    Navigation

  • previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -31,18 +38,11 @@

    Navigation

  • modules |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -181,12 +188,12 @@

    Navigation

  • modules |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + + + + + + + + + + + + +
    + Synapse +

    Synapse Python Client API

    +
    + + + + +
    +
    +
    +
    + +
    +

    File Upload

    +

    Files in Synapse are versionable. Please see Files and Versioning for more information about how versions in Files works.

    +
    +

    Uploading a New Version

    +

    Uploading a new version follows the same steps as uploading a file for the first time - use the same file name and store it in the same location (e.g., the same parentId). It is recommended to add a comment to the new version in order to easily track differences at a glance. The example file raw_data.txt will now have a version of 2 and a comment describing the change.

    +

    Explicit example:

    +
    import synapseclient
+
+# fetch the file in Synapse
+file_to_update = syn.get('syn2222', downloadFile=False)
+
+# save the local path to the new version of the file
+file_to_update.path = '/path/to/new/version/of/raw_data.txt'
+
+# add a version comment
+file_to_update.versionComment = 'Added 5 random normally distributed numbers.'
+
+# store the new file
+updated_file = syn.store(file_to_update)
+
    +
    +

    Implicit example:

    +
    # Assuming that there is a file created with:
+syn.store(File('path/to/old/raw_data.txt', parentId='syn123456'))
+
+# To create a new version of that file, make sure you store it with the exact same name
+new_file = syn.store(File('path/to/new_version/raw_data.txt',  parentId='syn123456'))
+
    +
    +
    +
    +

    Updating Annotations or Provenance without Changing Versions

    +

    Any change to a File will automatically update its version. If this isn’t the desired behavior, such as minor changes to the metadata, you can set forceVersion=False with the Python client. For command line, the commands set-annotations and set-provenance will update the metadata without creating a new version. Adding/updating annotations and provenance in the web client will also not cause a version change.

    +

    Important: Because Provenance is tracked by version, set `forceVersion=False` for minor changes to avoid breaking Provenance.

    +

    Setting annotations without changing version:

    +
    # Get file from Synapse, set download=False since we are only updating annotations
+file = syn.get('syn56789', download=False)
+
+# Add annotations
+file.annotations = {"fileType":"bam", "assay":"RNA-seq"}
+
+# Store the file without creating a new version
+file = syn.store(file, forceVersion=False)
+
    +
    +
    +
    +

    Setting Provenance without Changing Version

    +

    To set Provenance without changing the file version:

    +
    # Get file from Synapse, set download=False since we are only updating provenance
+file = syn.get('syn56789', download=False)
+
+# Add provenance
+file = syn.setProvenance(file, activity = Activity(used = '/path/to/example_code'))
+
+# Store the file without creating a new version
+file = syn.store(file, forceVersion=False)
+
    +
    +
    +
    +

    Downloading a Specific Version

    +

    By default, the File downloaded will always be the most recent version. However, a specific version can be downloaded by passing the version parameter:

    +
    entity = syn.get("syn3260973", version=1)
+
    +
    +
    +
    + + +
    +
    +
    +
    +
    + +
    + © Sage Bionetworks. + Last updated on Jan 17, 2019. + Created using Sphinx 1.8.1. +
    + + + \ No newline at end of file diff --git a/docs/build/html/Utilities.html b/docs/build/html/Utilities.html index e72a0088d..c8446f683 100644 --- a/docs/build/html/Utilities.html +++ b/docs/build/html/Utilities.html @@ -1,26 +1,33 @@ - + + - Utility Functions — Synapse Python Client 1.9.0 documentation + Utility Functions — Synapse Python Client 1.9.1 documentation + + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -39,11 +46,23 @@

    Navigation

  • previous |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -497,12 +504,12 @@

    Navigation

  • previous |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -39,11 +46,23 @@

    Navigation

  • previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -136,12 +143,12 @@

    Navigation

  • previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + + + + + + + + + + + + +
    + Synapse +

    Synapse Python Client API

    +
    + + + + +
    +
    +
    +
    + +
    +

    Views

    +

    A view is a view of all entities (File, Folder, Project, Table, Docker Repository, View) within one or more Projects or Folders. Views can:

    +
      +
    • Provide a way of isolating or linking data based on similarities
      • +
    • Provide the ability to link entities together by their annotations
      • +
    • Allow view/editing entities attributes in bulk
      • +
    • Allow entities to be easily searched and queried
      • +
    +

    Let’s go over some examples to demonstrate how view works. First, create a new project and add some files:

    +
    import synapseclient
+from synapseclient import Project, File, Column, Table, EntityViewSchema, EntityViewType
+syn = synapseclient.Synapse()
+syn.login()
+
+# Create a new project
+
+project = syn.store(Project("test view"))
+
+# Create some files
+
+file1 = syn.store(File(path="path/to/file1.txt", parent=project))
+file2 = syn.store(File(path="path/to/file2.txt", parent=project))
+
+# add some annotations
+
+syn.setAnnotations(file1, {"contributor":"Sage", "class":"V"})
+syn.setAnnotations(file2, {"contributor":"UW", "rank":"X"})
+
    +
    +
    +

    Creating a View

    +

    To create a view, defines its name, columns, parent, scope, and the type of the view:

    +
    view = EntityViewSchema(name="my first file view",
+                        columns=[
+                            Column(name="contributor", columnType="STRING"),
+                            Column(name="class", columnType="STRING"),
+                            Column(name="rank", columnType="STRING")),
+                        parent=project['id'],
+                        scopes=project['id'],
+                        includeEntityTypes=[EntityViewType.FILE, EntityViewType.FOLDER],
+                        add_default_columns=True)
+view = syn.store(view)
+
    +
    +

    We support the following entity type in a View:

    +
    EntityViewType.FILE
+EntityViewType.PROJECT
+EntityViewType.TABLE
+EntityViewType.FOLDER
+EntityViewType.VIEW
+EntityViewType.DOCKER
+
    +
    +

    To see the content of your newly created View, use syn.tableQuery():

    +
    query_results = syn.tableQuery("select * from %s" % view['id'])
+data = query_results.asDataFrame()
+
    +
    +
    +
    +

    Updating Annotations using View

    +

    To update class annotation for file2, simply update the view:

    +
    # Retrieve the view data using table query
+query_results = syn.tableQuery("select * from %s" % view['id'])
+data = query_results.asDataFrame()
+
+# Modify the annotations by modifying the view data and store it
+data["class"] = ["V", "VI"]
+syn.store(Table(view['id'], data))
+
    +
    +

    The change in annotations reflect in synGetAnnotations():

    +
    syn.getAnnotations(file2['id'])
+
    +
    +

    A View is a Table. Please visit Tables to see how to change schema, update content, and other operations that can be done on View.

    +
    +
    + + +
    +
    +
    +
    +
    + +
    + © Sage Bionetworks. + Last updated on Jan 17, 2019. + Created using Sphinx 1.8.1. +
    + + + \ No newline at end of file diff --git a/docs/build/html/Wiki.html b/docs/build/html/Wiki.html index 1d21841a6..89484ed3a 100644 --- a/docs/build/html/Wiki.html +++ b/docs/build/html/Wiki.html @@ -1,26 +1,33 @@ - + + - Wiki — Synapse Python Client 1.9.0 documentation + Wiki — Synapse Python Client 1.9.1 documentation + + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -39,11 +46,23 @@

    Navigation

  • previous |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -210,12 +217,12 @@

    Navigation

  • previous |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -32,7 +39,7 @@

    Navigation

  • modules |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -33,13 +40,25 @@

    Navigation

    modules |
  • - next |
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  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -347,6 +355,15 @@

    Getting Updates +

    Articles

    +
    + +
    +

    Reference

    @@ -370,15 +387,16 @@

    Release Notes @@ -401,14 +419,14 @@

    Navigation

    modules |
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    - Synapse + Synapse

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    @@ -35,64 +42,83 @@

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    • @@ -132,7 +146,102 @@

    Quick search

    Release Notes

    -

    1.9.0 (2018-09-28)

    +

    1.9.1 (2019-01-20)

    +

    In version 1.9.1, we fix various bugs and added two new features:

    +
      +
    • Python 3.7 is supported.
      • +
    • Deprecation warnings are visible by default.
      • +
    +
    +

    Features

    +
      +
    • [SYNPY-802] - +Support Python 3.7
      • +
    • [SYNPY-849] - +Add deprecation warning that isn’t filtered by Python
      • +
    +
    +
    +

    Bug Fixes

    +
      +
    • [SYNPY-454] - +Some integration tests do not clean up after themselves
      • +
    • [SYNPY-456] - +Problems with updated query system
      • +
    • [SYNPY-515] - +sphinx documentation not showing for some new classes
      • +
    • [SYNPY-526] - +deprecate downloadTableFile()
      • +
    • [SYNPY-578] - +switch away from POST /entity/#/table/deleterows
      • +
    • [SYNPY-594] - +Getting error from dev branch in integration test against staging
      • +
    • [SYNPY-796] - +fix or remove PyPI downloads badge in readme
      • +
    • [SYNPY-799] - +Unstable test: Test PartialRow updates to entity views from rowset +queries
      • +
    • [SYNPY-846] - +error if password stored in config file contains a ‘%’
      • +
    +
    +
    +

    Tasks

    +
      +
    • [SYNPY-491] - +Figure out custom release note fitlers
      • +
    • [SYNPY-840] - +Install not working on latest python
      • +
    • [SYNPY-847] - +uploadFileHandle should not be deprecated nor removed
      • +
    • [SYNPY-852] - +Check and update docs.synapse.org to reflect the change in the Python +client
      • +
    • [SYNPY-860] - +vignette for how to upload a new version of a file directly to a +synapse entity
      • +
    • [SYNPY-863] - +Update public documentation to move away from the query services
      • +
    • [SYNPY-866] - +Update Synapse logo in Python docs :)
      • +
    • [SYNPY-873] - +consolidate integration testing to platform dev account
      • +
    +
    +
    +

    Improvements

    +
      +
    • [SYNPY-473] - +Change syn.list to no longer use deprecated function chunkedQuery
      • +
    • [SYNPY-573] - +synapse list command line shouldn’t list the parent container
      • +
    • [SYNPY-581] - +<entity>.annotations return object is inconsistent with +getAnnotations()
      • +
    • [SYNPY-612] - +Rename view_type to viewType in EntityViewSchema for consistency
      • +
    • [SYNPY-777] - +Python client _list still uses chunckedQuery and result seem out of +date
      • +
    • [SYNPY-804] - +Update styling in the python docs to more closely match the Docs site +styling
      • +
    • [SYNPY-815] - +Update the build to use test user instead of migrationAdmin
      • +
    • [SYNPY-848] - +remove outdated link to confluence for command line query
      • +
    • [SYNPY-856] - +build_table example in the docs does not look right
      • +
    • [SYNPY-858] - +Write file view documentation in python client that is similar to +synapser
      • +
    • [SYNPY-870] - +Submitting to an evaluation queue can’t accept team as int
      • +
    +
    +
    +
    +

    1.9.0 (2018-09-28)

    In version 1.9.0, we deprecated and removed query() and chunkedQuery(). These functions used the old query services which does not perform well. To query for entities filter by annotations, please use EntityViewSchema.

    We also deprecated the following functions and will remove them in Synapse Python client version 2.0. In the Activity object:

    @@ -154,14 +263,14 @@

    1.9.0 (2018-09-28) -

    Features

    +
    +

    Features

    • SYNPY-806 - Support Folders and Tables in View
    -
    -

    Bug Fixes

    +
    +

    Bug Fixes

    • SYNPY-195 - Dangerous exception handling
    • SYNPY-261 - error downloading data from synapse (python client)
      • @@ -170,16 +279,16 @@

      Bug FixesSYNPY-819 - command-line clients need to be updated to replace the EntityView ‘viewType’ with ‘viewTypeMask’

    -
    -

    Tasks

    +
    +

    Tasks

    • SYNPY-759 - Look for all functions that are documented as “Deprecated” and apply the deprecation syntax
    • SYNPY-812 - Add Github issue template
    • SYNPY-824 - Remove the deprecated function query() and chunkedQuery()
    -
    -

    Improvements

    +
    +

    Improvements

    • SYNPY-583 - Better error message for create Link object
    • SYNPY-810 - simplify docs for deleting rows
      • @@ -189,8 +298,8 @@

      Improvements -

      1.8.2 (2018-08-17)

      +
      +

      1.8.2 (2018-08-17)

      In this release, we have been performed some house-keeping on the code base. The two major changes are:

        @@ -217,8 +326,8 @@

        1.8.2 (2018-08-17) -

        Bug Fixes

        +
        +

        Bug Fixes

        • SYNPY-535 - Synapse Table update: Connection Reset
        • SYNPY-603 - Python client and synapser cannot handle table column type LINK
          • @@ -232,42 +341,42 @@

          Bug FixesSYNPY-795 - Not recognizable column in query result

        -
        -

        Features

        +
        +

        Features

        • SYNPY-582 - move file or folder in the client
        • SYNPY-788 - Add option to use syn.store() without exercising multithreads
        -
        -

        Tasks

        +
        +

        Tasks

        • SYNPY-729 - Deprecate query() and chunkedQuery()
        • SYNPY-797 - Check Python client code base on using PLFM object model
        • SYNPY-798 - Using github.io to host documentation
        -
        -

        Improvements

        +
        +

        Improvements

        • SYNPY-646 - Error output of synGet is non-informative
        • SYNPY-743 - lint the entire python client code base
        -
        -

        1.8.1 (2018-05-17)

        +
        +

        1.8.1 (2018-05-17)

        This release is a hotfix for a bug. Please refer to 1.8.0 release notes for information about additional changes.

        -
        -

        Bug Fixes

        +
        +

        Bug Fixes

        • SYNPY-706 - syn.username can cause attribute not found if user not logged in
        -
        -

        1.8.0 (2018-05-07)

        +
        +

        1.8.0 (2018-05-07)

        This release has 2 major changes:

        • The client will no longer store your saved credentials in your synapse cache (~/synapseCache/.session). The python client now relies on keyring to handle credential storage of your Synapse credentials.
          • @@ -275,8 +384,8 @@

          1.8.0 (2018-05-07) -

          Bug Fixes

          +
          +

          Bug Fixes

          • SYNPY-654 - syn.getColumns does not terminate
          • SYNPY-658 - Security vunerability on clusters
            • @@ -285,28 +394,28 @@

            Bug FixesSYNPY-693 - synapseutils.sync.generateManifest() UnicodeEncodingError in python 2

          -
          -

          Tasks

          +
          +

          Tasks

          • SYNPY-617 - Remove use of deprecated service to delete table rows
          • SYNPY-673 - Fix Integration Tests being run on Appveyor
          • SYNPY-683 - Clean up print()s used in unit/integration tests
          -
          -

          Improvements

          +
          +

          Improvements

          • SYNPY-408 - Add bettter error messages when /filehandle/batch fails.
          • SYNPY-647 - Use connection pooling for Python client’s requests
          -
          -

          1.7.5 (2018-01-31)

          +
          +

          1.7.5 (2018-01-31)

          v1.7.4 release was broken for new users that installed from pip. v1.7.5 has the same changes as v1.7.4 but fixes the pip installation.

          -
          -

          1.7.4 (2018-01-29)

          +
          +

          1.7.4 (2018-01-29)

          This release mostly includes bugfixes and improvements for various Table classes:
            @@ -323,15 +432,15 @@

            1.7.4 (2018-01-29) -

            Features

            +
            +

            Features

            -
            -

            Improvements

            +
            +

            Improvements

            • SYNPY-267 - Update Synapse tables for integer types
            • SYNPY-304 - Table objects should implement len()
              • @@ -344,8 +453,8 @@

              ImprovementsSYNPY-539 - When creating table Schemas, enforce a limit on the number of columns that can be created.

            -
            -

            Bug Fixes

            +
            +

            Bug Fixes

            • SYNPY-235 - can’t print Row objects with dates in them
            • SYNPY-272 - bug syn.storing rowsets containing Python datetime objects
              • @@ -362,16 +471,16 @@

              Bug FixesSYNPY-605 - Update documentation for getUserProfile to include information about refreshing and memoization

            -
            -

            Tasks

            +
            +

            Tasks

            • SYNPY-451 - Add limit and offset for accessApproval and accessRequirement API calls and remove 0x400 flag default when calling GET /entity/{id}/bundle
            • SYNPY-546 - Change warning message when user does not DOWNLOAD permissions.
            -
            -

            1.7.3 (2017-12-08)

            +
            +

            1.7.3 (2017-12-08)

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

            • Changes to Tables:

              @@ -393,8 +502,8 @@

              1.7.3 (2017-12-08) -

              Bug Fixes

              +
              +

              Bug Fixes

              • SYNPY-419 - support object store from client
              • SYNPY-499 - metadata manifest file name spelled wrong
                • @@ -405,8 +514,8 @@

                Bug FixesSYNPY-572 - Users should only be prompted for updates if the first or second part of the version number is changed.

              -
              -

              Features

              +
              +

              Features

              • SYNPY-450 - Create convenience functions for synapse project settings
              • SYNPY-517 - sync command line
                • @@ -415,14 +524,14 @@

                FeaturesSYNPY-577 - Expose new view etags in command line clients

              -
              -

              Tasks

              +
              +

              Tasks

              • SYNPY-569 - ‘includeEntityEtag’ should be True for Async table csv query downloads
              -
              -

              Improvements

              +
              +

              Improvements

              • SYNPY-304 - Table objects should implement len()
              • SYNPY-511 - improve exception handling
                • @@ -432,8 +541,8 @@

                Improvements -

                1.7.1 (2017-11-17)

                +
                +

                1.7.1 (2017-11-17)

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

                • We have expanded the synapseutils packages to add the ability to:

                  @@ -459,8 +568,8 @@

                  1.7.1 (2017-11-17) -

                  Features

                  +
                  +

                  Features

                  • SYNPY-53 - support syn.get of external FTP links in py client
                  • SYNPY-179 - Upload to user owned S3 bucket
                    • @@ -473,8 +582,8 @@

                    FeaturesSYNPY-442 - set config file path on command line

                  -
                  -

                  Improvements

                  +
                  +

                  Improvements

                  • SYNPY-407 - support LARGETEXT in tables
                  • SYNPY-360 - Duplicate file handles are removed from BulkFileDownloadRequest
                    • @@ -492,8 +601,8 @@

                    ImprovementsSYNPY-475 - Store Tables timeout error

                  -
                  -

                  Bug Fixes

                  +
                  +

                  Bug Fixes

                  • SYNPY-190 - syn.login(‘asdfasdfasdf’) should fail
                  • SYNPY-344 - weird cache directories
                    • @@ -523,8 +632,8 @@

                    Bug FixesSYNPY-464 - synapse get syn4988808 KeyError: u’preSignedURL’

                  -
                  -

                  Tasks

                  +
                  +

                  Tasks

                  • SYNPY-422 - reduce default page size for GET /evaluation/{evalId}/submission/bundle/all
                  • SYNPY-437 - Remove tests for access restrictions on evaluations
                    • @@ -532,8 +641,8 @@

                    Tasks

                  -
                  -

                  1.6.1 (2016-11-02)

                  +
                  +

                  1.6.1 (2016-11-02)

                  What is New

                  In version 1.6 we introduce a new sub-module _synapseutils_ that @@ -547,8 +656,8 @@

                  What is NewSYNPY-371 - Support paths in syn.onweb

                -
                -

                Improvements

                +
                +

                Improvements

                We have improved download robustness and error checking, along with extensive recovery on failed operations. This includes the ability for the client to pause operation when Synapse is updated.

                • SYNPY-270 - Synapse READ ONLY mode should cause pause in execution
                  • @@ -562,8 +671,8 @@

                  ImprovementsSYNPY-390 - Move recursive download to Python client utils

                -
                -

                Bug Fixes

                +
                +

                Bug Fixes

                © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
                + + - + + +
                - Synapse + Synapse

                Synapse Python Client API

                @@ -34,7 +41,7 @@

                Navigation

              • modules |
                • -
              • Synapse Python Client 1.9.0 documentation »
                • +
              • Synapse Python Client 1.9.1 documentation »

            © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
            + + - + + +
            - Synapse + Synapse

            Synapse Python Client API

            @@ -40,7 +47,7 @@

            Navigation

          • modules |
            • -
          • Synapse Python Client 1.9.0 documentation »
            • +
          • Synapse Python Client 1.9.1 documentation »

        © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
        + + - + + +
        - Synapse + Synapse

        Synapse Python Client API

        @@ -39,11 +46,23 @@

        Navigation

      • previous |
        • -
      • Synapse Python Client 1.9.0 documentation »
        • +
      • Synapse Python Client 1.9.1 documentation »

      @@ -146,12 +153,12 @@

      Navigation

    • previous |
      • -
    • Synapse Python Client 1.9.0 documentation »
      • +
    • Synapse Python Client 1.9.1 documentation »
    © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.
    + + - + + +
    - Synapse + Synapse

    Synapse Python Client API

    @@ -31,11 +38,23 @@

    Navigation

  • modules |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • @@ -643,12 +650,12 @@

    Navigation

  • modules |
    • -
  • Synapse Python Client 1.9.0 documentation »
    • +
  • Synapse Python Client 1.9.1 documentation »
    • © Sage Bionetworks. - Last updated on Sep 28, 2018. + Last updated on Jan 17, 2019. Created using Sphinx 1.8.1.