How to use synapseclient - 10 common examples

def test_copyFileHandleAndchangeFileMetadata():
    project_entity = syn.store(Project(name=str(uuid.uuid4())))
    schedule_for_cleanup(project_entity.id)
    filename = utils.make_bogus_data_file()
    attachname = utils.make_bogus_data_file()
    schedule_for_cleanup(filename)
    schedule_for_cleanup(attachname)
    file_entity = syn.store(File(filename, parent=project_entity))
    schedule_for_cleanup(file_entity.id)
    wiki = Wiki(owner=project_entity, title='A Test Wiki', markdown="testing", 
                attachments=[attachname])
    wiki = syn.store(wiki)
    wikiattachments = syn._getFileHandle(wiki.attachmentFileHandleIds[0])
    # CHECK: Can batch copy two file handles (wiki attachments and file entity)
    copiedFileHandles = synapseutils.copyFileHandles(syn, [file_entity.dataFileHandleId,
                                                           wiki.attachmentFileHandleIds[0]],
                                                     [file_entity.concreteType.split(".")[-1], "WikiAttachment"],
                                                     [file_entity.id, wiki.id],

def test_store_isRestricted_flag():
    # Store a file with access requirements
    path = utils.make_bogus_binary_file()
    schedule_for_cleanup(path)
    entity = File(path, name='Secret human data', parent=project)
    
    # We don't want to spam ACT with test emails
    with patch('synapseclient.client.Synapse._createAccessRequirementIfNone') as intercepted:
        entity = syn.store(entity, isRestricted=True)
        assert_true(intercepted.called)

assert_raises(SynapseHTTPError, syn.getProvenance, output[file_entity.id])
    schedule_for_cleanup(output[file_entity.id])

    # Test: setProvenance = Existing
    output_URL = synapseutils.copy(syn, externalURL_entity.id, destinationId=second_folder.id, setProvenance="existing")
    output_prov = syn.getProvenance(output_URL[externalURL_entity.id])
    schedule_for_cleanup(output_URL[externalURL_entity.id])
    assert_equals(output_prov['name'], prov['name'])
    assert_equals(output_prov['used'], prov['used'])

    # ------------------------------------
    # TEST COPY LINKS
    # ------------------------------------
    second_file = utils.make_bogus_data_file()
    # schedule_for_cleanup(filename)
    second_file_entity = syn.store(File(second_file, parent=project_entity))
    link_entity = Link(second_file_entity.id, parent=folder_entity.id)
    link_entity = syn.store(link_entity)

    copied_link = synapseutils.copy(syn, link_entity.id, destinationId=second_folder.id)
    old = syn.get(link_entity.id, followLink=False)
    new = syn.get(copied_link[link_entity.id], followLink=False)
    assert_equals(old.linksTo['targetId'], new.linksTo['targetId'])

    schedule_for_cleanup(second_file_entity.id)
    schedule_for_cleanup(link_entity.id)
    schedule_for_cleanup(copied_link[link_entity.id])

    time.sleep(3)

    assert_raises(ValueError, synapseutils.copy, syn, link_entity.id, destinationId=second_folder.id)

"Oaxaca", "Cancún", "Curaçao", "जोधपुर",
              "অসম", "ལྷ་ས།", "ཐིམ་ཕུ་", "دبي", "አዲስ አበባ",
              "São Paulo", "Buenos Aires", "Cartagena",
              "Amsterdam", "Venice", "Rome", "Dubrovnik",
              "Sarajevo", "Madrid", "Barcelona", "Paris",
              "Αθήνα", "Ρόδος", "København", "Zürich",
              "金沢市", "서울", "แม่ฮ่องสอน", "Москва"]

    text = "Places I wanna go:\n"
    while len(text.encode('utf-8')) < multipart_upload_module.MIN_PART_SIZE:
        text += ", ".join(random.choice(cities) for i in range(5000)) + "\n"

    fhid = multipart_upload_string(syn, text)

    # Download the file and compare it with the original
    junk = File(parent=project, dataFileHandleId=fhid)
    junk.properties.update(syn._createEntity(junk.properties))
    (tmp_f, tmp_path) = tempfile.mkstemp()
    schedule_for_cleanup(tmp_path)

    junk['path'] = syn._downloadFileHandle(fhid, junk['id'], "FileEntity", tmp_path)

    with open(junk.path, encoding='utf-8') as f:
        retrieved_text = f.read()

    assert_equals(retrieved_text, text)

def test_syncFromSynapse__project_contains_empty_folder():
    project = Project(name="the project", parent="whatever", id="syn123")
    file = File(name="a file", parent=project, id="syn456")
    folder = Folder(name="a folder", parent=project, id="syn789")
    with patch.object(syn, "getChildren", side_effect=[[folder, file], []]) as patch_syn_get_children,\
         patch.object(syn, "get", side_effect=[folder, file]) as patch_syn_get:
        assert_equals([file], synapseutils.syncFromSynapse(syn, project))
        expected_get_children_agrs = [call(project['id']), call(folder['id'])]
        assert_list_equal(expected_get_children_agrs, patch_syn_get_children.call_args_list)
        expected_get_args = [
            call(folder['id'], downloadLocation=None, ifcollision='overwrite.local', followLink=False),
            call(file['id'], downloadLocation=None, ifcollision='overwrite.local', followLink=False)]
        assert_list_equal(expected_get_args, patch_syn_get.call_args_list)

def test_store_with_flags():
    # -- CreateOrUpdate flag for Projects --
    # If we store a project with the same name, it should become an update
    projUpdate = Project(project.name)
    projUpdate.updatedThing = 'Yep, sho\'nuf it\'s updated!'
    projUpdate = syn.store(projUpdate, createOrUpdate=True)
    assert_equals(project.id, projUpdate.id)
    assert_equals(projUpdate.updatedThing, ['Yep, sho\'nuf it\'s updated!'])

    # Store a File
    filepath = utils.make_bogus_binary_file()
    schedule_for_cleanup(filepath)
    origBogus = File(filepath, name='Bogus Test File', parent=project)
    origBogus = syn.store(origBogus, createOrUpdate=True)
    assert_equals(origBogus.versionNumber, 1)

    # Modify existing annotations by createOrUpdate
    del projUpdate['parentId']
    del projUpdate['id']
    projUpdate.updatedThing = 'Updated again'
    projUpdate.addedThing = 'Something new'
    projUpdate = syn.store(projUpdate, createOrUpdate=True)
    assert_equals(project.id, projUpdate.id)
    assert_equals(projUpdate.updatedThing, ['Updated again'])
    
    # -- ForceVersion flag --
    # Re-store the same thing and don't up the version
    mutaBogus = syn.store(origBogus, forceVersion=False)
    assert_equals(mutaBogus.versionNumber, 1)

def test_store_activity():
    # Create a File and an Activity
    path = utils.make_bogus_binary_file()
    schedule_for_cleanup(path)
    entity = File(path, name='Hinkle horn honking holes', parent=project)
    honking = Activity(name='Hinkle horn honking', 
                       description='Nettlebed Cave is a limestone cave located on the South Island of New Zealand.')
    honking.used('http://www.flickr.com/photos/bevanbfree/3482259379/')
    honking.used('http://www.flickr.com/photos/bevanbfree/3482185673/')

    # This doesn't set the ID of the Activity
    entity = syn.store(entity, activity=honking)

    # But this does
    honking = syn.getProvenance(entity.id)

    # Verify the Activity
    assert_equals(honking['name'], 'Hinkle horn honking')
    assert_equals(len(honking['used']), 2)
    assert_equals(honking['used'][0]['concreteType'], 'org.sagebionetworks.repo.model.provenance.UsedURL')
    assert_false(honking['used'][0]['wasExecuted'])

if path[0].isalpha() and path[1] == ':':
        # A Windows file URL looks like this: file:///c:/foo/bar/bat.txt
        expected_url = 'file:///' + path.replace("\\", "/")
    else:
        expected_url = 'file://' + path

    assert_equals(bogus.externalURL, expected_url, 'URL: %s\nExpected %s' % (bogus.externalURL, expected_url))

    # A file path that doesn't exist should still work
    bogus = File('/path/to/local/file1.xyz', parentId=project.id, synapseStore=False)
    bogus = syn.store(bogus)
    assert_raises(IOError, syn.get, bogus)
    assert_false(bogus.synapseStore)

    # Try a URL
    bogus = File('http://dev-versions.synapse.sagebase.org/synapsePythonClient', parent=project, synapseStore=False)
    bogus = syn.store(bogus)
    bogus = syn.get(bogus)
    assert_false(bogus.synapseStore)

def add_file_to_cache(i, cache_root_dir):
    """
    Helper function for use in test_cache_concurrent_access
    """
    my_cache = cache.Cache(cache_root_dir=cache_root_dir)
    file_handle_ids = [1001, 1002, 1003, 1004, 1005]
    random.shuffle(file_handle_ids)
    for file_handle_id in file_handle_ids:
        cache_dir = my_cache.get_cache_dir(file_handle_id)
        file_path = os.path.join(cache_dir, "file_handle_%d_process_%02d.junk" % (file_handle_id, i))
        utils.touch(file_path)
        my_cache.add(file_handle_id, file_path)

def test_round_trip():
    fhid = None
    filepath = utils.make_bogus_binary_file(multipart_upload_module.MIN_PART_SIZE + 777771)
    try:
        fhid = multipart_upload(syn, filepath)

        # Download the file and compare it with the original
        junk = File(parent=project, dataFileHandleId=fhid)
        junk.properties.update(syn._createEntity(junk.properties))
        (tmp_f, tmp_path) = tempfile.mkstemp()
        schedule_for_cleanup(tmp_path)

        junk['path'] = syn._downloadFileHandle(fhid, junk['id'], 'FileEntity', tmp_path)
        assert_true(filecmp.cmp(filepath, junk.path))

    finally:
        try:
            if 'junk' in locals():
                syn.delete(junk)