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 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.
"""
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
try:
newWikiPage = syn.getWiki(newOwn, destinationSubPageId)
except SynapseHTTPError as e:
if e.response.status_code == 404:
pass
else:
raise e
if entitySubPageId is not None:
oldWikiHeaders = _getSubWikiHeaders(oldWikiHeaders, entitySubPageId)
for wikiHeader in oldWikiHeaders:
wiki = syn.getWiki(oldOwn, wikiHeader.id)
print('Got wiki %s' % wikiHeader.id)
if wiki['attachmentFileHandleIds'] == []:
new_file_handles = []
elif wiki['attachmentFileHandleIds'] != []:
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 attach['fileHandle']['concreteType'] !=
"org.sagebionetworks.repo.model.file.PreviewFileHandle"
]
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['copyResults']:
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['copyResults']
]
#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)
newWh = syn.getWikiHeaders(newOwn)
return (newWh)
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")
