def create_wiki(evaluation, challenge_home_entity, team, leaderboard_columns):
"""
Create landing page for challenge and a sub-page for a leaderboard.
Note that, while this code demonstrates programmatic generation of wiki markdown
including leader board table widget, the typical method for creating and editing
such content is via the Synapse web portal (www.synapse.org).
"""
wiki = Wiki(owner=challenge_home_entity,
markdown=CHALLENGE_PROJECT_WIKI.format(
title=CHALLENGE_PROJECT_NAME,
teamId=team['id'],
evalId=evaluation.id))
wiki = syn.store(wiki)
supertable = create_supertable_leaderboard(evaluation, leaderboard_columns)
lb_wiki = Wiki(title="Leaderboard",
owner=challenge_home_entity,
parentWikiId=wiki.id,
markdown=LEADERBOARD_MARKDOWN.format(
evaluation_name=evaluation.name, supertable=supertable))
lb_wiki = syn.store(lb_wiki)
return (wiki, lb_wiki)
def test_create_or_update_wiki():
# create wiki once
wiki = syn.store(Wiki(title='This is the title', owner=project, markdown="#Wikis are OK\n\nBlabber jabber blah blah blither blather bonk!"))
# for now, creating it again raises an exception, see SYNR-631
assert_raises(SynapseHTTPError,
syn.store,
Wiki(title='This is a different title', owner=project, markdown="#Wikis are awesome\n\nNew babble boo flabble gibber wiggle sproing!"),
createOrUpdate=True)
def setup(self):
# Create a Project
self.project_entity = syn.store(Project(name=str(uuid.uuid4())))
filename = utils.make_bogus_data_file()
attachname = utils.make_bogus_data_file()
file_entity = syn.store(File(filename, parent=self.project_entity))
schedule_for_cleanup(self.project_entity.id)
schedule_for_cleanup(filename)
schedule_for_cleanup(file_entity.id)
# Create mock wiki
md = """
This is a test wiki
=======================
Blabber jabber blah blah boo.
syn123
syn456
"""
wiki = Wiki(owner=self.project_entity,
title='A Test Wiki',
markdown=md,
attachments=[attachname])
wiki = syn.store(wiki)
# Create a Wiki sub-page
subwiki = Wiki(owner=self.project_entity,
title='A sub-wiki',
markdown='%s' % file_entity.id,
parentWikiId=wiki.id)
self.subwiki = syn.store(subwiki)
second_md = """
Testing internal links
======================
[test](#!Synapse:%s/wiki/%s)
%s)
""" % (self.project_entity.id, self.subwiki.id, file_entity.id)
sub_subwiki = Wiki(owner=self.project_entity,
title='A sub-sub-wiki',
markdown=second_md,
parentWikiId=self.subwiki.id,
attachments=[attachname])
self.sub_subwiki = syn.store(sub_subwiki)
# Set up the second project
self.second_project = syn.store(Project(name=str(uuid.uuid4())))
schedule_for_cleanup(self.second_project.id)
self.fileMapping = {'syn123': 'syn12345', 'syn456': 'syn45678'}
self.first_headers = syn.getWikiHeaders(self.project_entity)
def test_dispose(syn_client, syn_test_helper, temp_file):
project = syn_client.store(Project(name=syn_test_helper.uniq_name()))
folder = syn_client.store(
Folder(name=syn_test_helper.uniq_name(prefix='Folder '),
parent=project))
file = syn_client.store(
File(name=syn_test_helper.uniq_name(prefix='File '),
path=temp_file,
parent=folder))
team = syn_client.store(
Team(name=syn_test_helper.uniq_name(prefix='Team ')))
wiki = syn_client.store(
Wiki(title=syn_test_helper.uniq_name(prefix='Wiki '), owner=project))
wikiChild = syn_client.store(
Wiki(title=syn_test_helper.uniq_name(prefix='Wiki Child '),
owner=project,
parentWikiId=wiki.id))
syn_objects = [project, folder, file, team, wiki, wikiChild]
for syn_obj in syn_objects:
syn_test_helper.dispose_of(syn_obj)
assert syn_obj in syn_test_helper._trash
syn_test_helper.dispose()
assert len(syn_test_helper._trash) == 0
for syn_obj in syn_objects:
with pytest.raises(
synapseclient.core.exceptions.SynapseHTTPError) as ex:
if isinstance(syn_obj, Wiki):
syn_client.getWiki(syn_obj)
elif isinstance(syn_obj, Team):
syn_client.getTeam(syn_obj.id)
else:
syn_client.get(syn_obj, downloadFile=False)
err_str = str(ex.value)
assert "Not Found" in err_str or "cannot be found" in err_str or "is in trash can" in err_str or "does not exist" in err_str
try:
os.remove(temp_file)
except:
pass
def test_Wiki__markdown_defined_markdownFile_is_None():
markdown = "Somebody once told me the OS was gonna delete me. I'm not the largest file on the disk."
# method under test
wiki = Wiki(owner="doesn't matter", markdown=markdown)
assert markdown == wiki.markdown
def setup(self):
"""Setting up all variables for tests"""
self.markdown = "test\nsyn123/wiki/2222\nsyn123%2Fwiki%2F2222\nsyn123"
self.wiki_mapping = {'2222': '5555'}
self.entity = Project(name="foo", id="syn123")
self.destination = Project(name="test", id="syn555")
self.expected_markdown = (
"test\nsyn555/wiki/5555\nsyn555%2Fwiki%2F5555\nsyn555")
self.syn = mock.create_autospec(Synapse)
self.entity_wiki = Wiki(markdown=self.markdown,
id="2222",
owner="syn123",
attachmentFileHandleIds=['322', '333'])
self.filehandles = [{
'fileHandle': {
"concreteType": mirrorwiki.PREVIEW_FILE_HANDLE,
"contentType": "contenttype",
"fileName": "name"
}
}, {
'fileHandle': {
"concreteType": "not_preview",
"contentType": "testing",
"fileName": "foobar"
}
}]
self.new_filehandle = [{'newFileHandle': {"id": "12356"}}]
# wiki page mapping {'title': Wiki}
self.entity_wiki_pages = {'test': self.entity_wiki}
self.destination_wiki_pages = {'test': self.entity_wiki}
# wiki headers
self.entity_wiki_headers = [{"id": "2222", "title": "test"}]
self.destination_wiki_headers = [{"id": "5555", "title": "test"}]
def create_leaderboard_wiki(intra_cell_type_evaluation,
inter_cell_type_evaluation, regression_evaluation):
LEADERBOARD_MARKDOWN = """\
## Within Cell Type Classification
{intra_cell_type_classification_supertable}
## Between Cell Type Classification
{inter_cell_type_classification_supertable}
## Between Cell Type Regression
{inter_cell_type_regression_supertable}
"""
leaderboard_wiki_text = LEADERBOARD_MARKDOWN.format(
intra_cell_type_classification_supertable=create_supertable_leaderboard(
intra_cell_type_evaluation, classification_leaderboard_columns),
inter_cell_type_classification_supertable=create_supertable_leaderboard(
inter_cell_type_evaluation, classification_leaderboard_columns),
inter_cell_type_regression_supertable=create_supertable_leaderboard(
regression_evaluation, regression_leaderboard_columns))
lb_wiki = Wiki(title="Leaderboard",
owner=project,
parentWikiId=wiki.id,
markdown=leaderboard_wiki_text)
lb_wiki = syn.store(lb_wiki)
def test_Wiki():
"""Test the construction and accessors of Wiki objects."""
# Wiki contstuctor only takes certain values
pytest.raises(ValueError, Wiki, title='foo')
# Construct a wiki and test uri's
Wiki(title='foobar2', markdown='bar', owner={'id': '5'})
def mutate(self,
info,
name,
permissions,
annotations,
wiki,
folders,
posts):
# Build the annotations
project_annotations = {}
if annotations:
for annotation in annotations:
project_annotations[annotation['key']] = annotation['value']
# Create the Project
project = Synapse.client().store(
Project(name=name, annotations=project_annotations)
)
# Add the permissions
if permissions:
for permission in permissions:
principal_id = permission['principal_id']
access = permission['access']
access_type = getattr(Synapse, '{0}_PERMS'.format(access))
Synapse.client().setPermissions(
project,
principal_id,
accessType=access_type,
warn_if_inherits=False
)
# Add the the folders
if folders:
for folder_name in folders:
Synapse.client().store(Folder(name=folder_name, parent=project))
# Add the posts
if posts:
forum_id = Synapse.client().restGET(
'/project/{0}/forum'.format(project.id)).get('id')
for post in posts:
body = {
'forumId': forum_id,
'title': post['title'],
'messageMarkdown': post['message_markdown']
}
Synapse.client().restPOST("/thread", body=json.dumps(body))
# Add the wiki
if wiki:
Synapse.client().store(Wiki(title=wiki.title, markdown=wiki.markdown, owner=project))
new_syn_project = SynProject.from_project(project)
return CreateSynProject(syn_project=new_syn_project)
def test_Wiki__markdown_is_None_markdownFile_defined():
markdown_path = "/somewhere/over/the/rainbow.txt"
with patch("synapseclient.wiki.open", mock_open(), create=True) as mocked_open,\
patch("os.path.isfile", return_value=True):
# method under test
Wiki(owner="doesn't matter", markdownFile=markdown_path)
mocked_open.assert_called_once_with(markdown_path, 'r')
mocked_open().read.assert_called_once_with()
def test_create_or_update_wiki():
# create wiki once
wiki = syn.store(
Wiki(
title='This is the title',
owner=project,
markdown=
"#Wikis are OK\n\nBlabber jabber blah blah blither blather bonk!"))
# for now, creating it again it will be updated
new_title = 'This is a different title'
wiki = syn.store(Wiki(
title=new_title,
owner=project,
markdown=
"#Wikis are awesome\n\nNew babble boo flabble gibber wiggle sproing!"),
createOrUpdate=True)
assert_equal(new_title, syn.getWiki(wiki.ownerId)['title'])
def create_wiki(self, **kwargs):
"""Creates a new Wiki and adds it to the trash queue."""
if 'title' not in kwargs:
kwargs['title'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
if 'markdown' not in kwargs:
kwargs['markdown'] = 'My Wiki {0}'.format(kwargs['title'])
wiki = SynapseProxy.client().store(Wiki(**kwargs))
self.dispose_of(wiki)
return wiki
def test_Wiki__with_markdown_file():
markdown_data = """
MARK DOWN MARK DOWN MARK DOWN MARK DOWN
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
adkflajsl;kfjasd;lfkjsal;kfajslkfjasdlkfj
"""
markdown_path = "/somewhere/over/the/rainbow.txt"
with patch("synapseclient.wiki.open", mock_open(read_data=markdown_data), create=True) as mocked_open,\
patch("os.path.isfile", return_value=True):
# method under test
wiki = Wiki(owner="doesn't matter", markdownFile=markdown_path)
mocked_open.assert_called_once_with(markdown_path, 'r')
mocked_open().read.assert_called_once_with()
assert markdown_data == wiki.markdown
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], [file_entity.contentType, wikiattachments['contentType']], [file_entity.name, wikiattachments['fileName']])
assert all([results.get("failureCode") is None for results in copiedFileHandles['copyResults']]), "NOT FOUND and UNAUTHORIZED failure codes."
files = {file_entity.name:{"contentType":file_entity['contentType'],
"md5":file_entity['md5']},
wikiattachments['fileName']:{"contentType":wikiattachments['contentType'],
"md5":wikiattachments['contentMd5']}}
for results in copiedFileHandles['copyResults']:
i = results['newFileHandle']
assert files.get(i['fileName']) is not None, "Filename has to be the same"
assert files[i['fileName']]['contentType'] == i['contentType'], "Content type has to be the same"
assert files[i['fileName']]['md5'] == i['contentMd5'], "Md5 has to be the same"
assert all([results.get("failureCode") is None for results in copiedFileHandles['copyResults']]), "There should not be NOT FOUND and UNAUTHORIZED failure codes."
if 'username' not in other_user or 'password' not in other_user:
sys.stderr.write('\nWarning: no test-authentication configured. skipping testing copy function when trying to copy file made by another user.\n')
return
syn_other = synapseclient.Synapse(skip_checks=True)
syn_other.login(other_user['username'], other_user['password'])
#CHECK: UNAUTHORIZED failure code should be returned
output = synapseutils.copyFileHandles(syn_other,[file_entity.dataFileHandleId, wiki.attachmentFileHandleIds[0]], [file_entity.concreteType.split(".")[-1], "WikiAttachment"], [file_entity.id, wiki.id], [file_entity.contentType, wikiattachments['contentType']], [file_entity.name, wikiattachments['fileName']])
assert all([results.get("failureCode") == "UNAUTHORIZED" for results in output['copyResults']]), "UNAUTHORIZED codes."
#CHECK: Changing content type and downloadAs
new_entity = synapseutils.changeFileMetaData(syn, file_entity, contentType="application/x-tar", downloadAs="newName.txt")
schedule_for_cleanup(new_entity.id)
assert file_entity.md5 == new_entity.md5, "Md5s must be equal after copying"
fileResult = syn._getFileHandleDownload(new_entity.dataFileHandleId, new_entity.id)
assert fileResult['fileHandle']['fileName'] == "newName.txt", "Set new file name to be newName.txt"
assert new_entity.contentType == "application/x-tar", "Set new content type to be application/x-tar"
def get_or_create_wiki(self, **kwargs) -> Wiki:
"""Gets an existing wiki or creates a new one. If
parentWikiId is specified, a page will always be created.
There are no restrictions on wiki titles on subwiki pages.
Get doesn't work for subwiki pages
Args:
Same arguments as synapseclient.Wiki
Returns:
Synapse wiki page
"""
wiki = Wiki(**kwargs)
wiki = self._find_by_obj_or_create(wiki)
self.logger.info('{} Wiki {}'.format(self._update_str, wiki.title))
return wiki
def test_wiki_version():
## create a new project to avoid artifacts from previous tests
project = syn.store(Project(name=str(uuid.uuid4())))
wiki = syn.store(
Wiki(title='Title version 1',
owner=project,
markdown="##A heading\n\nThis is version 1 of the wiki page!\n"))
wiki.title = "Title version 2"
wiki.markdown = "##A heading\n\nThis is version 2 of the wiki page!\n"
wiki = syn.store(wiki)
w1 = syn.getWiki(owner=wiki.ownerId, subpageId=wiki.id, version=0)
assert "version 1" in w1.title
assert "version 1" in w1.markdown
w2 = syn.getWiki(owner=wiki.ownerId, subpageId=wiki.id, version=1)
assert "version 2" in w2.title
assert "version 2" in w2.markdown
def copyWiki(syn,
entity,
destinationId,
entitySubPageId=None,
destinationSubPageId=None,
updateLinks=True,
updateSynIds=True,
entityMap=None):
"""
Copies wikis and updates internal links
:param syn: A synapse object: syn = synapseclient.login()- Must be logged into synapse
:param entity: A synapse ID of an entity whose wiki you want to copy
:param destinationId: Synapse ID of a folder/project that the wiki wants to be copied to
:param updateLinks: Update all the internal links. (e.g. syn1234/wiki/34345 becomes syn3345/wiki/49508)
Defaults to True
:param updateSynIds: Update all the synapse ID's referenced in the wikis. (e.g. syn1234 becomes syn2345)
Defaults to True but needs an entityMap
:param entityMap: An entity map {'oldSynId','newSynId'} to update the synapse IDs referenced in the
wiki.
Defaults to None
:param entitySubPageId: Can specify subPageId and copy all of its subwikis
Defaults to None, which copies the entire wiki subPageId can be found:
https://www.synapse.org/#!Synapse:syn123/wiki/1234
In this case, 1234 is the subPageId.
:param destinationSubPageId: Can specify destination subPageId to copy wikis to
Defaults to None
:returns: A list of Objects with three fields: id, title and parentId.
"""
# Validate input parameters
if entitySubPageId:
entitySubPageId = str(int(entitySubPageId))
if destinationSubPageId:
destinationSubPageId = str(int(destinationSubPageId))
oldOwn = syn.get(entity, downloadFile=False)
# getWikiHeaders fails when there is no wiki
try:
oldWikiHeaders = syn.getWikiHeaders(oldOwn)
except SynapseHTTPError as e:
if e.response.status_code == 404:
return []
else:
raise e
newOwn = syn.get(destinationId, downloadFile=False)
wikiIdMap = dict()
newWikis = dict()
# If entitySubPageId is given but not destinationSubPageId, set the pageId to "" (will get the root page)
# A entitySubPage could be copied to a project without any wiki pages, this has to be checked
newWikiPage = None
if destinationSubPageId:
try:
newWikiPage = syn.getWiki(newOwn, destinationSubPageId)
except SynapseHTTPError as e:
if e.response.status_code == 404:
pass
else:
raise e
if entitySubPageId:
oldWikiHeaders = _getSubWikiHeaders(oldWikiHeaders, entitySubPageId)
if not oldWikiHeaders:
return []
for wikiHeader in oldWikiHeaders:
wiki = syn.getWiki(oldOwn, wikiHeader['id'])
print('Got wiki %s' % wikiHeader['id'])
if not wiki.get('attachmentFileHandleIds'):
new_file_handles = []
else:
results = [
syn._getFileHandleDownload(filehandleId,
wiki.id,
objectType='WikiAttachment')
for filehandleId in wiki['attachmentFileHandleIds']
]
# Get rid of the previews
nopreviews = [
attach['fileHandle'] for attach in results
if not attach['fileHandle']['isPreview']
]
contentTypes = [attach['contentType'] for attach in nopreviews]
fileNames = [attach['fileName'] for attach in nopreviews]
copiedFileHandles = copyFileHandles(
syn, nopreviews, ["WikiAttachment"] * len(nopreviews),
[wiki.id] * len(nopreviews), contentTypes, fileNames)
# Check if failurecodes exist
for filehandle in copiedFileHandles:
if filehandle.get("failureCode") is not None:
raise ValueError("%s dataFileHandleId: %s" %
(filehandle["failureCode"],
filehandle['originalFileHandleId']))
new_file_handles = [
filehandle['newFileHandle']['id']
for filehandle in copiedFileHandles
]
# for some reason some wikis don't have titles?
if hasattr(wikiHeader, 'parentId'):
newWikiPage = Wiki(owner=newOwn,
title=wiki.get('title', ''),
markdown=wiki.markdown,
fileHandles=new_file_handles,
parentWikiId=wikiIdMap[wiki.parentWikiId])
newWikiPage = syn.store(newWikiPage)
else:
if destinationSubPageId is not None and newWikiPage is not None:
newWikiPage["attachmentFileHandleIds"] = new_file_handles
newWikiPage["markdown"] = wiki["markdown"]
newWikiPage["title"] = wiki.get("title", "")
# Need to add logic to update titles here
newWikiPage = syn.store(newWikiPage)
else:
newWikiPage = Wiki(owner=newOwn,
title=wiki.get("title", ""),
markdown=wiki.markdown,
fileHandles=new_file_handles,
parentWikiId=destinationSubPageId)
newWikiPage = syn.store(newWikiPage)
newWikis[newWikiPage['id']] = newWikiPage
wikiIdMap[wiki['id']] = newWikiPage['id']
if updateLinks:
newWikis = _updateInternalLinks(newWikis, wikiIdMap, entity,
destinationId)
if updateSynIds and entityMap is not None:
newWikis = _updateSynIds(newWikis, wikiIdMap, entityMap)
print("Storing new Wikis\n")
for oldWikiId in wikiIdMap.keys():
newWikiId = wikiIdMap[oldWikiId]
newWikis[newWikiId] = syn.store(newWikis[newWikiId])
print("\tStored: %s\n" % newWikiId)
return syn.getWikiHeaders(newOwn)
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],
[file_entity.contentType, wikiattachments['contentType']],
[file_entity.name, wikiattachments['fileName']])
for results in copiedFileHandles['copyResults']:
assert_is_none(results.get("failureCode"),
"NOT FOUND and UNAUTHORIZED failure codes.")
files = {
file_entity.name: {
"contentType": file_entity['contentType'],
"md5": file_entity['md5']
},
wikiattachments['fileName']: {
"contentType": wikiattachments['contentType'],
"md5": wikiattachments['contentMd5']
}
}
for results in copiedFileHandles['copyResults']:
i = results['newFileHandle']
assert_is_not_none(files.get(i['fileName']),
"Filename has to be the same")
assert_equals(files[i['fileName']]['contentType'], i['contentType'],
"Content type has to be the same")
assert_equals(files[i['fileName']]['md5'], i['contentMd5'],
"Md5 has to be the same")
for results in copiedFileHandles['copyResults']:
assert_is_none(
results.get("failureCode"),
"There should not be NOT FOUND and UNAUTHORIZED failure codes.")
# CHECK: Changing content type and downloadAs
new_entity = synapseutils.changeFileMetaData(
syn,
file_entity,
contentType="application/x-tar",
downloadAs="newName.txt")
schedule_for_cleanup(new_entity.id)
assert_equals(file_entity.md5, new_entity.md5,
"Md5s must be equal after copying")
fileResult = syn._getFileHandleDownload(new_entity.dataFileHandleId,
new_entity.id)
assert_equals(fileResult['fileHandle']['fileName'], "newName.txt",
"Set new file name to be newName.txt")
assert_equals(new_entity.contentType, "application/x-tar",
"Set new content type to be application/x-tar")
def test_copyWiki():
# Create a Project
project_entity = syn.store(Project(name=str(uuid.uuid4())))
schedule_for_cleanup(project_entity.id)
folder_entity = syn.store(
Folder(name=str(uuid.uuid4()), parent=project_entity))
schedule_for_cleanup(folder_entity.id)
second_folder = syn.store(
Folder(name=str(uuid.uuid4()), parent=project_entity))
schedule_for_cleanup(second_folder.id)
third_folder = syn.store(
Folder(name=str(uuid.uuid4()), parent=project_entity))
schedule_for_cleanup(third_folder.id)
filename = utils.make_bogus_data_file()
attachname = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
file_entity = syn.store(File(filename, parent=folder_entity))
nested_folder = syn.store(
Folder(name=str(uuid.uuid4()), parent=folder_entity))
second_file = syn.store(File(filename, parent=nested_folder))
schedule_for_cleanup(file_entity.id)
schedule_for_cleanup(nested_folder.id)
schedule_for_cleanup(second_file.id)
fileWiki = Wiki(owner=second_file, title='A Test Wiki', markdown="Test")
fileWiki = syn.store(fileWiki)
# Create mock wiki
md = """
This is a test wiki
=======================
Blabber jabber blah blah boo.
%s
%s
""" % (file_entity.id, second_file.id)
wiki = Wiki(owner=project_entity,
title='A Test Wiki',
markdown=md,
attachments=[attachname])
wiki = syn.store(wiki)
# Create a Wiki sub-page
subwiki = Wiki(owner=project_entity,
title='A sub-wiki',
markdown='%s' % file_entity.id,
parentWikiId=wiki.id)
subwiki = syn.store(subwiki)
second_md = """
Testing internal links
======================
[test](#!Synapse:%s/wiki/%s)
%s)
""" % (project_entity.id, subwiki.id, second_file.id)
sub_subwiki = Wiki(owner=project_entity,
title='A sub-sub-wiki',
markdown=second_md,
parentWikiId=subwiki.id,
attachments=[attachname])
sub_subwiki = syn.store(sub_subwiki)
# Copy wiki to second project
second_project = syn.store(Project(name=str(uuid.uuid4())))
schedule_for_cleanup(second_project.id)
fileMapping = synapseutils.copy(syn,
project_entity,
second_project.id,
skipCopyWikiPage=True)
# Test: copyWikiPage = False
assert_raises(SynapseHTTPError, syn.getWiki, second_project.id)
first_headers = syn.getWikiHeaders(project_entity)
second_headers = synapseutils.copyWiki(syn,
project_entity.id,
second_project.id,
entityMap=fileMapping)
mapping = dict()
# Test: Check that all wikis were copied correctly with the correct mapping
for index, info in enumerate(second_headers):
mapping[first_headers[index]['id']] = info['id']
assert_equals(first_headers[index]['title'], info['title'])
if info.get('parentId', None) is not None:
# Check if parent Ids are mapping correctly in the copied Wikis
assert_equals(info['parentId'],
mapping[first_headers[index]['parentId']])
# Test: Check that all wikis have the correct attachments and have correct internal synapse link/file mapping
for index, info in enumerate(second_headers):
# Check if markdown is the correctly mapped
orig_wikiPage = syn.getWiki(project_entity, first_headers[index]['id'])
new_wikiPage = syn.getWiki(second_project, info['id'])
s = orig_wikiPage.markdown
for oldWikiId in mapping.keys():
oldProjectAndWikiId = "%s/wiki/%s" % (project_entity.id, oldWikiId)
newProjectAndWikiId = "%s/wiki/%s" % (second_project.id,
mapping[oldWikiId])
s = re.sub(oldProjectAndWikiId, newProjectAndWikiId, s)
for oldFileId in fileMapping.keys():
s = re.sub(oldFileId, fileMapping[oldFileId], s)
assert_equals(s, new_wikiPage.markdown)
orig_attach = syn.getWikiAttachments(orig_wikiPage)
new_attach = syn.getWikiAttachments(new_wikiPage)
orig_file = [
i['fileName'] for i in orig_attach if i['concreteType'] !=
"org.sagebionetworks.repo.model.file.PreviewFileHandle"
]
new_file = [
i['fileName'] for i in new_attach if i['concreteType'] !=
"org.sagebionetworks.repo.model.file.PreviewFileHandle"
]
# check that attachment file names are the same
assert_equals(orig_file, new_file)
# Test: copyWikiPage = True (Default) (Should copy all wikis including wikis on files)
third_project = syn.store(Project(name=str(uuid.uuid4())))
schedule_for_cleanup(third_project.id)
copiedFile = synapseutils.copy(syn, second_file, third_project.id)
copiedWiki = syn.getWiki(copiedFile[second_file.id])
assert_equals(copiedWiki.title, fileWiki.title)
assert_equals(copiedWiki.markdown, fileWiki.markdown)
# Test: entitySubPageId
third_header = synapseutils.copyWiki(syn,
project_entity.id,
third_project.id,
entitySubPageId=sub_subwiki.id,
destinationSubPageId=None,
updateLinks=False,
updateSynIds=False,
entityMap=fileMapping)
test_ent_subpage = syn.getWiki(third_project.id, third_header[0]['id'])
# Test: No internal links updated
assert_equals(test_ent_subpage.markdown, sub_subwiki.markdown)
assert_equals(test_ent_subpage.title, sub_subwiki.title)
# Test: destinationSubPageId
fourth_header = synapseutils.copyWiki(
syn,
project_entity.id,
third_project.id,
entitySubPageId=subwiki.id,
destinationSubPageId=test_ent_subpage.id,
updateLinks=False,
updateSynIds=False,
entityMap=fileMapping)
temp = syn.getWiki(third_project.id, fourth_header[0]['id'])
# There are issues where some title pages are blank. This is an issue that needs to be addressed
assert_equals(temp.title, subwiki.title)
assert_equals(temp.markdown, subwiki.markdown)
temp = syn.getWiki(third_project.id, fourth_header[1]['id'])
assert_equals(temp.title, sub_subwiki.title)
assert_equals(temp.markdown, sub_subwiki.markdown)
def test_wikiAttachment():
# Upload a file to be attached to a Wiki
filename = utils.make_bogus_data_file()
attachname = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
schedule_for_cleanup(attachname)
fileHandle = syn._uploadToFileHandleService(filename)
# Create and store a Wiki
# The constructor should accept both file handles and file paths
md = """
This is a test wiki
=======================
Blabber jabber blah blah boo.
"""
wiki = Wiki(owner=project,
title='A Test Wiki',
markdown=md,
fileHandles=[fileHandle['id']],
attachments=[attachname])
wiki = syn.store(wiki)
# Create a Wiki sub-page
subwiki = Wiki(owner=project,
title='A sub-wiki',
markdown='nothing',
parentWikiId=wiki.id)
subwiki = syn.store(subwiki)
# Retrieve the root Wiki from Synapse
wiki2 = syn.getWiki(project)
assert wiki == wiki2
# Retrieve the sub Wiki from Synapse
wiki2 = syn.getWiki(project, subpageId=subwiki.id)
assert subwiki == wiki2
# Try making an update
wiki['title'] = 'A New Title'
wiki['markdown'] = wiki['markdown'] + "\nNew stuff here!!!\n"
wiki = syn.store(wiki)
assert wiki['title'] == 'A New Title'
assert wiki['markdown'].endswith("\nNew stuff here!!!\n")
# Check the Wiki's metadata
headers = syn.getWikiHeaders(project)
assert len(headers) == 2
assert headers[0]['title'] in (wiki['title'], subwiki['title'])
# # Retrieve the file attachment
# tmpdir = tempfile.mkdtemp()
# file_props = syn._downloadWikiAttachment(project, wiki,
# os.path.basename(filename), dest_dir=tmpdir)
# path = file_props['path']
# assert os.path.exists(path)
# assert filecmp.cmp(original_path, path)
# Clean up
# syn._deleteFileHandle(fileHandle)
syn.delete(wiki)
syn.delete(subwiki)
assert_raises(SynapseHTTPError, syn.getWiki, project)
def copyWiki(syn, entity, destinationId, entitySubPageId=None, destinationSubPageId=None, updateLinks=True, updateSynIds=True, entityMap=None):
"""
Copies wikis and updates internal links
:param syn: A synapse object: syn = synapseclient.login()- Must be logged into synapse
:param entity: A synapse ID of an entity whose wiki you want to copy
:param destinationId: Synapse ID of a folder/project that the wiki wants to be copied to
:param updateLinks: Update all the internal links
Defaults to True
:param updateSynIds: Update all the synapse ID's referenced in the wikis
Defaults to True but needs an entityMap
:param entityMap: An entity map {'oldSynId','newSynId'} to update the synapse IDs referenced in the wiki
Defaults to None
:param entitySubPageId: Can specify subPageId and copy all of its subwikis
Defaults to None, which copies the entire wiki
subPageId can be found: https://www.synapse.org/#!Synapse:syn123/wiki/1234
In this case, 1234 is the subPageId.
:param destinationSubPageId: Can specify destination subPageId to copy wikis to
Defaults to None
"""
oldOwn = syn.get(entity,downloadFile=False)
# getWikiHeaders fails when there is no wiki
try:
oldWh = syn.getWikiHeaders(oldOwn)
store = True
except SynapseHTTPError:
store = False
if store:
if entitySubPageId is not None:
oldWh = _getSubWikiHeaders(oldWh,entitySubPageId,mapping=[])
newOwn =syn.get(destinationId,downloadFile=False)
wikiIdMap =dict()
newWikis=dict()
for i in oldWh:
attDir=tempfile.NamedTemporaryFile(prefix='attdir',suffix='')
#print i['id']
wiki = syn.getWiki(oldOwn, i.id)
print('Got wiki %s' % i.id)
if wiki['attachmentFileHandleIds'] == []:
attachments = []
elif wiki['attachmentFileHandleIds'] != []:
uri = "/entity/%s/wiki/%s/attachmenthandles" % (wiki.ownerId, wiki.id)
results = syn.restGET(uri)
file_handles = {fh['id']:fh for fh in results['list']}
## need to download an re-upload wiki attachments, ug!
attachments = []
tempdir = tempfile.gettempdir()
for fhid in wiki.attachmentFileHandleIds:
file_info = syn._downloadWikiAttachment(wiki.ownerId, wiki, file_handles[fhid]['fileName'], destination=tempdir)
attachments.append(file_info['path'])
#for some reason some wikis don't have titles?
if hasattr(i, 'parentId'):
wNew = Wiki(owner=newOwn, title=wiki.get('title',''), markdown=wiki.markdown, attachments=attachments, parentWikiId=wikiIdMap[wiki.parentWikiId])
wNew = syn.store(wNew)
else:
if destinationSubPageId is not None:
wNew = syn.getWiki(newOwn, destinationSubPageId)
wNew.attachments = attachments
wNew.markdown = wiki.markdown
#Need to add logic to update titles here
wNew = syn.store(wNew)
else:
wNew = Wiki(owner=newOwn, title=wiki.get('title',''), markdown=wiki.markdown, attachments=attachments, parentWikiId=destinationSubPageId)
wNew = syn.store(wNew)
newWikis[wNew.id]=wNew
wikiIdMap[wiki.id] =wNew.id
if updateLinks:
print("Updating internal links:\n")
for oldWikiId in wikiIdMap.keys():
# go through each wiki page once more:
newWikiId=wikiIdMap[oldWikiId]
newWiki=newWikis[newWikiId]
print("\tUpdating internal links for Page: %s\n" % newWikiId)
s=newWiki.markdown
# in the markdown field, replace all occurrences of entity/wiki/abc with destinationId/wiki/xyz,
# where wikiIdMap maps abc->xyz
# replace <entity>/wiki/<oldWikiId> with <destinationId>/wiki/<newWikiId>
for oldWikiId2 in wikiIdMap.keys():
oldProjectAndWikiId = "%s/wiki/%s" % (entity, oldWikiId2)
newProjectAndWikiId = "%s/wiki/%s" % (destinationId, wikiIdMap[oldWikiId2])
s=re.sub(oldProjectAndWikiId, newProjectAndWikiId, s)
# now replace any last references to entity with destinationId
s=re.sub(entity, destinationId, s)
newWikis[newWikiId].markdown=s
if updateSynIds and entityMap is not None:
print("Updating Synapse references:\n")
for oldWikiId in wikiIdMap.keys():
# go through each wiki page once more:
newWikiId = wikiIdMap[oldWikiId]
newWiki = newWikis[newWikiId]
print('Updated Synapse references for Page: %s\n' %newWikiId)
s = newWiki.markdown
for oldSynId in entityMap.keys():
# go through each wiki page once more:
newSynId = entityMap[oldSynId]
s = re.sub(oldSynId, newSynId, s)
print("Done updating Synpase IDs.\n")
newWikis[newWikiId].markdown = s
print("Storing new Wikis\n")
for oldWikiId in wikiIdMap.keys():
newWikiId = wikiIdMap[oldWikiId]
newWikis[newWikiId] = syn.store(newWikis[newWikiId])
print("\tStored: %s\n" % newWikiId)
newWh = syn.getWikiHeaders(newOwn)
return(newWh)
else:
return("no wiki")
def test_wikiAttachment():
# Upload a file to be attached to a Wiki
filename = utils.make_bogus_data_file()
attachname = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
schedule_for_cleanup(attachname)
fileHandle = upload_synapse_s3(syn, filename)
# Create and store a Wiki
# The constructor should accept both file handles and file paths
md = """
This is a test wiki
=======================
Blabber jabber blah blah boo.
"""
wiki = Wiki(owner=project,
title='A Test Wiki',
markdown=md,
fileHandles=[fileHandle['id']],
attachments=[attachname])
wiki = syn.store(wiki)
# Create a Wiki sub-page
subwiki = Wiki(owner=project,
title='A sub-wiki',
markdown='nothing',
parentWikiId=wiki.id)
subwiki = syn.store(subwiki)
# Retrieve the root Wiki from Synapse
wiki2 = syn.getWiki(project)
## due to the new wiki api, we'll get back some new properties,
## namely markdownFileHandleId and markdown_path, so only compare
## properties that are in the first object
for property_name in wiki:
assert_equal(wiki[property_name], wiki2[property_name])
# Retrieve the sub Wiki from Synapse
wiki2 = syn.getWiki(project, subpageId=subwiki.id)
for property_name in wiki:
assert_equal(subwiki[property_name], wiki2[property_name])
# Try making an update
wiki['title'] = 'A New Title'
wiki['markdown'] = wiki['markdown'] + "\nNew stuff here!!!\n"
wiki = syn.store(wiki)
wiki = syn.getWiki(project)
assert wiki['title'] == 'A New Title'
assert wiki['markdown'].endswith("\nNew stuff here!!!\n")
# Check the Wiki's metadata
headers = syn.getWikiHeaders(project)
assert len(headers) == 2
assert headers[0]['title'] in (wiki['title'], subwiki['title'])
file_handles = syn.getWikiAttachments(wiki)
file_names = [fh['fileName'] for fh in file_handles]
assert all(
os.path.basename(fn) in file_names for fn in [filename, attachname])
syn.delete(subwiki)
syn.delete(wiki)
assert_raises(SynapseHTTPError, syn.getWiki, project)
def mutate(self, info, name, **kwargs):
errors = []
permissions = kwargs.get('permissions', None)
annotations = kwargs.get('annotations', None)
wiki = kwargs.get('wiki', None)
folders = kwargs.get('folders', None)
posts = kwargs.get('posts', None)
# Check if a project with the same name already exists.
project_name_taken = Synapse.client().findEntityId(name) is not None
if project_name_taken:
raise ValueError(
'Another Synapse project with the name: {0} already exists.'.
format(name))
# Build the annotations
project_annotations = {}
if annotations:
for annotation in annotations:
project_annotations[annotation['key']] = annotation['value']
# Create the Project
project = Synapse.client().store(
Project(name=name, annotations=project_annotations))
# Add the permissions
if permissions:
for permission in permissions:
try:
principal_id = permission.get('principal_id')
access = permission.get('access')
access_type = getattr(Synapse, '{0}_PERMS'.format(access))
try:
Synapse.client().setPermissions(project,
principal_id,
accessType=access_type,
warn_if_inherits=False)
except Exception as syn_ex:
logger.exception(
'Error setting permission: {0} - {1}'.format(
permission, syn_ex))
if 'a foreign key constraint fails' in str(syn_ex):
errors.append(
'User or Team ID: {0} does not exist.'.format(
principal_id))
else:
errors.append(
'Error setting permission for User or Team ID: {0}'
.format(principal_id))
except Exception as ex:
logger.exception(
'Error creating project permissions: {0} - {1}'.format(
permission, ex))
errors.append('Error creating project permissions.')
# Add the the folders
if folders:
for folder_path in folders:
folder_path_parts = list(filter(None, folder_path.split('/')))
parent = project
for folder_name in folder_path_parts:
try:
parent = Synapse.client().store(
Folder(name=folder_name, parent=parent))
except Exception as syn_ex:
logger.exception(
'Error creating project folder: {0} - {1}'.format(
folder_name, syn_ex))
errors.append(
'Error creating project folder: {0}.'.format(
folder_name))
# Add the posts
if posts:
try:
forum_id = Synapse.client().restGET(
'/project/{0}/forum'.format(project.id)).get('id')
for post in posts:
try:
body = {
'forumId': forum_id,
'title': post.get('title'),
'messageMarkdown': post.get('message_markdown')
}
Synapse.client().restPOST('/thread',
body=json.dumps(body))
except Exception as syn_ex:
logger.exception(
'Error creating project post: {0} - {1}'.format(
post, syn_ex))
errors.append(
'Error creating project post: {0}.'.format(
post.get('title', None)))
except Exception as ex:
logger.exception(
'Error creating project posts: {1} - {0}'.format(
posts, ex))
errors.append('Error creating projects posts.')
# Add the wiki
if wiki:
try:
Synapse.client().store(
Wiki(title=wiki.title,
markdown=wiki.markdown,
owner=project))
except Exception as syn_ex:
logger.exception(
'Error creating project wiki: {0} - {1}'.format(
wiki, syn_ex))
errors.append('Error creating project wiki.')
new_syn_project = SynProject.from_project(project)
return CreateSynProject(syn_project=new_syn_project,
errors=(errors if errors else None))
def copyWiki(syn, entity, destinationId, entitySubPageId=None, destinationSubPageId=None, updateLinks=True, updateSynIds=True, entityMap=None):
"""
Copies wikis and updates internal links
:param syn: A synapse object: syn = synapseclient.login()- Must be logged into synapse
:param entity: A synapse ID of an entity whose wiki you want to copy
:param destinationId: Synapse ID of a folder/project that the wiki wants to be copied to
:param updateLinks: Update all the internal links. (e.g. syn1234/wiki/34345 becomes syn3345/wiki/49508)
Defaults to True
:param updateSynIds: Update all the synapse ID's referenced in the wikis. (e.g. syn1234 becomes syn2345)
Defaults to True but needs an entityMap
:param entityMap: An entity map {'oldSynId','newSynId'} to update the synapse IDs referenced in the wiki
Defaults to None
:param entitySubPageId: Can specify subPageId and copy all of its subwikis
Defaults to None, which copies the entire wiki
subPageId can be found: https://www.synapse.org/#!Synapse:syn123/wiki/1234
In this case, 1234 is the subPageId.
:param destinationSubPageId: Can specify destination subPageId to copy wikis to
Defaults to None
:returns: A list of Objects with three fields: id, title and parentId.
"""
stagingSyn = synapseclient.login()
stagingSyn.setEndpoints(**synapseclient.client.STAGING_ENDPOINTS)
oldOwn = stagingSyn.get(entity,downloadFile=False)
# getWikiHeaders fails when there is no wiki
try:
oldWh = stagingSyn.getWikiHeaders(oldOwn)
except SynapseHTTPError as e:
if e.response.status_code == 404:
return([])
else:
raise e
if entitySubPageId is not None:
oldWh = _getSubWikiHeaders(oldWh,entitySubPageId)
newOwn =syn.get(destinationId,downloadFile=False)
wikiIdMap = dict()
newWikis = dict()
for wikiHeader in oldWh:
attDir=tempfile.NamedTemporaryFile(prefix='attdir',suffix='')
#print i['id']
wiki = stagingSyn.getWiki(oldOwn, wikiHeader.id)
print('Got wiki %s' % wikiHeader.id)
if wiki['attachmentFileHandleIds'] == []:
attachments = []
elif wiki['attachmentFileHandleIds'] != []:
attachments = []
tempdir = tempfile.gettempdir()
for filehandleId in wiki['attachmentFileHandleIds']:
result = stagingSyn._getFileHandleDownload(filehandleId, wiki.id, objectType='WikiAttachment')
file_info = stagingSyn._downloadFileHandle(result['preSignedURL'],tempdir,result['fileHandle'])
attachments.append(file_info)
#for some reason some wikis don't have titles?
if hasattr(wikiHeader, 'parentId'):
wNew = Wiki(owner=newOwn, title=wiki.get('title',''), markdown=wiki.markdown, attachments=attachments, parentWikiId=wikiIdMap[wiki.parentWikiId])
wNew = syn.store(wNew)
else:
if destinationSubPageId is not None:
wNew = syn.getWiki(newOwn, destinationSubPageId)
wNew.attachments = attachments
wNew.markdown = wiki.markdown
#Need to add logic to update titles here
wNew = syn.store(wNew)
else:
wNew = Wiki(owner=newOwn, title=wiki.get('title',''), markdown=wiki.markdown, attachments=attachments, parentWikiId=destinationSubPageId)
wNew = syn.store(wNew)
newWikis[wNew.id]=wNew
wikiIdMap[wiki.id] =wNew.id
if updateLinks:
newWikis = _updateInternalLinks(newWikis, wikiIdMap, entity, destinationId)
if updateSynIds and entityMap is not None:
newWikis = _updateSynIds(newWikis, wikiIdMap, entityMap)
print("Storing new Wikis\n")
for oldWikiId in wikiIdMap.keys():
newWikiId = wikiIdMap[oldWikiId]
newWikis[newWikiId] = syn.store(newWikis[newWikiId])
print("\tStored: %s\n" % newWikiId)
newWh = syn.getWikiHeaders(newOwn)
return(newWh)
def test_Wiki__markdown_and_markdownFile_both_defined():
with pytest.raises(ValueError):
Wiki(owner="doesn't matter",
markdown="asdf",
markdownFile="~/fakeFile.txt")
#! /usr/bin/env python
# KKD for Sage Bionetworks
# Jan. 25, 2016
# sys.argv[1] = folder ID containing bigwigs to which to add genome browser in wiki
import sys
import synapseclient
from synapseclient import Wiki
syn = synapseclient.login()
results = syn.chunkedQuery('select id,fileType,organism,versionNumber from file where parentId=="%s"' % sys.argv[1])
for result in results:
# print '%s' % result
if result['file.fileType'][0] == "bigwig":
temp = syn.get(result['file.id'], downloadFile = False)
if result['file.organism'][0] == "H**o sapiens":
browser = ''.join([' """${biodalliance13?chr=1&species=HUMAN&viewStart=3025001&viewEnd=3525001&source0=%7B"name"%3A""%2C "entityId"%3A"', result['file.id'], '"%2C "entityVersion"%3A"', str(result['file.versionNumber']), '"%2C "styleType"%3A"default"%2C "styleGlyphType"%3A"HISTOGRAM"%2C "color"%3A"%23808080"%2C "type"%3A"BIGWIG"%2C "height"%3A"120"%7D}""" ' ])
# print '%s' % browser
elif result['file.organism'][0] == "Mus musculus":
browser = ''.join([' """${biodalliance13?chr=1&species=MOUSE&viewStart=3025001&viewEnd=3525001&source0=%7B"name"%3A""%2C "entityId"%3A"', result['file.id'], '"%2C "entityVersion"%3A"', str(result['file.versionNumber']), '"%2C "styleType"%3A"default"%2C "styleGlyphType"%3A"HISTOGRAM"%2C "color"%3A"%23808080"%2C "type"%3A"BIGWIG"%2C "height"%3A"120"%7D}""" ' ])
wiki = Wiki(owner=temp, markdown=browser)
wiki = syn.store(wiki)
def test_wiki_with_none_attachments():
syn = Synapse(skip_checks=True)
with patch.object(syn, 'restPOST'):
w = Wiki(owner="syn1", markdown="markdown", attachments=None)
syn.store(w)
def test_Wiki__markdownFile_path_not_exist():
# method under test
with pytest.raises(ValueError):
Wiki(owner="doesn't matter",
markdownFile="/this/is/not/the/file/you/are/looking.for")
