Merge branch 'develop'

CHANGES.md

@@ -1,3 +1,16 @@
+0.17.7 (2019-01-08)
+==================
+
+- Improvements:
+    - Fix readme rendering on PyPi
+
+0.17.6 (2019-01-08)
+==================
+
+- Improvements:
+    - Added parent and preserve_folder_structure parameters and properties to imports
+    - Updated documentation regarding cwl
+
 0.17.5 (2018-12-21)
 ==================
 

VERSION

@@ -1 +1 @@
-0.17.5
+0.17.7

docs/quickstart.rst

@@ -1003,9 +1003,9 @@ Each import has the following properties:
 
 ``id`` - Import identifier.
 
-``source`` - Source of the import, object of type ``VolumeFile``, contains info on volume and file location on the volume
+``source`` - Source of the import, object of type ``VolumeFile``, contains info on volume and file location on the volume.
 
-``destination`` - Destination of the import, object of type ``ImportDestination``, containing info on project where the file was imported to and name of the file in the project
+``destination`` - Destination of the import, object of type ``ImportDestination``, containing info on project where the file was imported to and name of the file in the project.
 
 ``state`` - State of the import. Can be *PENDING*, *RUNNING*, *COMPLETED* and *FAILED*.
 
@@ -1019,6 +1019,27 @@ Each import has the following properties:
 
 ``finished_on`` - Contains the date and time when the import was finished.
 
+``preserve_folder_structure`` - Whether to keep the exact source folder structure. The default value is true if the item being imported is a folder. Should not be used if you are importing a file.
+
+
+VolumeFile properties
+~~~~~~~~~~~~~~~~~~~~~
+
+``volume`` - Volume ID from which to import the item.
+
+``location`` - Volume-specific location pointing to the file or folder to import. This location should be recognizable to the underlying cloud service as a valid key or path to the item. If the item being imported is a folder, its path should end with a ``/``.
+
+
+ImportDestination properties
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+``project`` - The project in which to create the alias.
+
+``parent`` - The ID of the target folder to which the item should be imported. Should not be used together with project. If parent is used, the import will take place into the specified folder, within the project to which the folder belongs. If project is used, the items will be imported to the root of the project's files.
+
+``name`` - The name of the alias to create. This name should be unique to the project. If the name is already in use in the project, you should use the overwrite query parameter in this call to force any item with that name to be deleted before the alias is created. If name is omitted, the alias name will default to the last segment of the complete location (including the prefix) on the volume. Segments are considered to be separated with forward slashes ``/``.
+
+
 Import methods
 ~~~~~~~~~~~~~~
 

setup.py

@@ -27,6 +27,7 @@
     description='SBG API python client bindings',
     install_requires=install_requires,
     long_description=io.open('README.md', 'r', encoding='utf-8').read(),
+    long_description_content_type='text/markdown',
     platforms=['Windows', 'POSIX', 'MacOS'],
     maintainer='Seven Bridges Genomics Inc.',
     maintainer_email='dejan.knezevic@sbgenomics.com',

sevenbridges/__init__.py

@@ -7,7 +7,7 @@
 import ssl
 import logging
 
-__version__ = "0.17.5"
+__version__ = "0.17.7"
 
 from sevenbridges.api import Api
 from sevenbridges.config import Config

sevenbridges/models/compound/volumes/import_destination.py

@@ -10,6 +10,7 @@ class ImportDestination(Resource):
     imported on to SevenBridges platform or related product.
     """
     project = StringField(read_only=True)
+    parent = StringField(read_only=True)
     name = StringField(read_only=True)
 
     def __str__(self):

sevenbridges/models/storage_import.py

@@ -36,6 +36,7 @@ class Import(Resource):
     href = HrefField()
     id = StringField(read_only=True)
     state = StringField(read_only=True)
+    preserve_folder_structure = BooleanField(read_only=True)
     source = CompoundField(VolumeFile, read_only=True)
     destination = CompoundField(ImportDestination, read_only=True)
     started_on = DateTimeField(read_only=True)
@@ -65,9 +66,9 @@ def result(self):
             return None
 
     @classmethod
-    def submit_import(cls, volume, location, project, name=None,
-                      overwrite=False, properties=None, api=None):
-
+    def submit_import(cls, volume, location, project=None, name=None,
+                      overwrite=False, properties=None, parent=None,
+                      preserve_folder_structure=True, api=None):
         """
         Submits new import job.
         :param volume: Volume identifier.
@@ -76,26 +77,50 @@ def submit_import(cls, volume, location, project, name=None,
         :param name: Optional file name.
         :param overwrite: If true it will overwrite file if exists.
         :param properties: Properties dictionary.
+        :param parent: The ID of the target folder to which the item should be
+            imported. Should not be used together with project.
+        :param preserve_folder_structure: Whether to keep the exact source
+            folder structure. The default value is true if the item being
+            imported is a folder. Should not be used if you are importing
+            a file.
         :param api: Api instance.
         :return: Import object.
         """
         data = {}
         volume = Transform.to_volume(volume)
-        project = Transform.to_project(project)
+
+        if project and parent:
+            raise SbgError(
+                'Project and parent identifiers are mutually exclusive'
+            )
+        elif project:
+            project = Transform.to_project(project)
+            destination = {
+                'project': project
+            }
+        elif parent:
+            parent = Transform.to_file(parent)
+            destination = {
+                'parent': parent
+            }
+        else:
+            raise SbgError('Project or parent identifier is required.')
+
         source = {
             'volume': volume,
             'location': location
         }
-        destination = {
-            'project': project
-        }
+
         if name:
             destination['name'] = name
 
         data['source'] = source
         data['destination'] = destination
         data['overwrite'] = overwrite
 
+        if not preserve_folder_structure:
+            data['preserve_folder_structure'] = preserve_folder_structure
+
         if properties:
             data['properties'] = properties
 
@@ -111,12 +136,13 @@ def submit_import(cls, volume, location, project, name=None,
     @classmethod
     def query(cls, project=None, volume=None, state=None, offset=None,
               limit=None, api=None):
-
         """
         Query (List) imports.
         :param project: Optional project identifier.
         :param volume: Optional volume identifier.
         :param state: Optional import sate.
+        :param offset: Pagination offset.
+        :param limit: Pagination limit.
         :param api: Api instance.
         :return: Collection object.
         """

sevenbridges/tests/test_imports.py

@@ -1,6 +1,8 @@
 import faker
+import pytest
 
 generator = faker.Factory.create()
+pytestmark = pytest.mark.volumes
 
 
 def test_imports_query(api, given, verifier):
@@ -27,7 +29,32 @@ def test_import_submit(api, given, verifier):
     given.imports.can_be_submitted(id=id)
 
     # action
-    imports = api.imports.submit_import(volume, location, project)
+    imports = api.imports.submit_import(
+        volume=volume,
+        location=location,
+        project=project
+    )
+
+    assert imports.id == id
+    verifier.imports.submitted()
+
+
+def test_import_to_folder_submit(api, given, verifier):
+    # preconditions
+    id = generator.uuid4()
+    volume = generator.name()
+    location = generator.name()
+    parent = generator.name() + "/"
+    given.imports.can_be_submitted(id=id)
+    preserve_folder_structure = False
+
+    # action
+    imports = api.imports.submit_import(
+        volume=volume,
+        location=location,
+        parent=parent,
+        preserve_folder_structure=preserve_folder_structure
+    )
 
     assert imports.id == id
     verifier.imports.submitted()