def test_validate_url_hidden_list(self):
# Tests whether the _validate_url() sucessfully filters
# out urls as a string of a list
part_shop = sbol2.PartShop('https://initialise-partshop')
self.assertRaises(TypeError,
part_shop._validate_url,
'[1,2,3]')
def test_spoof(self):
url = 'https://example.org'
part_shop = sbol.PartShop(url)
self.assertEqual(part_shop.getSpoofedURL(), '')
spoofed_url = 'https://synbiohub.org'
part_shop.spoof(spoofed_url)
self.assertEqual(part_shop.getSpoofedURL(), spoofed_url)
def test_validate_url_type_check(self):
# Tests whether the _validate_url() sucessfully filters
# out urls of type which is not equal to string
part_shop = sbol2.PartShop('https://initialise-partshop')
self.assertRaises(TypeError,
part_shop._validate_url,
[1, 2, 3])
def test_validate_url_invalid_scheme(self):
# Tests whether the _validate_url() sucessfully filters
# out urls with schemes not equal to "http" or "https"
part_shop = sbol2.PartShop('https://initialise-partshop')
self.assertRaises(TypeError,
part_shop._validate_url,
'file://google.com')
def test_validate_url_missing_netloc(self):
# Tests whether the _validate_url() sucessfully filters
# out urls with non existent netlocs
part_shop = sbol2.PartShop('https://initialise-partshop')
self.assertRaises(TypeError,
part_shop._validate_url,
'https://')
def test_validate_url_forwardslash(self):
# Tests whether the _validate_url() sucessfully filters
# out urls containing a terminal forward slash
part_shop = sbol2.PartShop('https://initialise-partshop')
self.assertRaises(TypeError,
part_shop._validate_url,
'https://stackoverflow.com/')
def write_sbol_comp(libraries, compositions, all_parts):
"""
the function pulls the parts from their SynBioHub libraries and compiles them into an SBOL document
Parameters
----------
libraries : DICT
Dictionary containing the libraries, the keys are the library abbreviations and the
corresponding value is the url, if no abbreviation is used, the url is used for both key and value
compositions : DICT
Nested dictionary containing the collection names and the corresponding values are the names of
the composite design which are also dictionary containing the design descriptions and a
dictionary of parts
all_parts : SET
A set containing all parts that are used in the filled template
Returns
-------
doc: SBOL Document
Document containing all components and sequences
Example
-------
cwd = os.path.dirname(os.path.abspath("__file__")) #get current working directory
path_filled = os.path.join(cwd, "darpa_template.xlsx")
table = pd.read_excel (path_filled)
compositions, list_of_rows = get_data(table)
compositions, all_parts = get_parts(list_of_rows, table, compositions)
compositions = check_name(compositions)
doc = write_sbol_comp(libraries, compositions)
"""
doc = Document()
sbol2.Config.setOption('sbol_typed_uris', False)
for library in libraries:
sbol_library = sbol2.PartShop(libraries[library])
for part in all_parts:
try:
sbol_library.pull(part, doc)
except:
print(f"The part {part} was not in library {library}")
for collection in compositions:
print(collection)
coll = Collection(collection)
doc.addCollection(coll)
for design in compositions[collection]:
composite_design = doc.componentDefinitions.create(design)
composite_design.assemblePrimaryStructure(compositions[collection][design]["Parts"])
composite_design.compile()
composite_design.sequence
if type(compositions[collection][design]["Description"]) is str:
composite_design.description = compositions[collection][design]["Description"]
coll.members += [composite_design.identity]
# doc.write("Test_Collections.xml")
return(doc)
def test_submit(self):
# This test is derived from an etl-to-synbiohub_pipeline test
# case that was failing.
RESOURCE = 'https://tang.ece.utah.edu'
SPOOFED_RESOURCE = 'https://synbiohub.utah.edu'
doc = sbol.Document()
doc.version = '1'
doc.displayId = 'sbol_test'
doc.name = "SBOL Test Collection"
doc.description = "A scratch collection for automated testing of the sbol."
sbh = sbol.PartShop(RESOURCE, SPOOFED_RESOURCE)
try:
sbh.login(username, password)
except sbol2.SBOLError as sbol_error:
if sbol_error.error_code(
) == sbol2.SBOLErrorCode.SBOL_ERROR_BAD_HTTP_REQUEST:
if '503' in sbol_error.what():
return
raise
try:
sbh.submit(doc)
except Exception:
# What exception type should we really be expecting? The
# original test had a bare except.
uri_template = '{0}/user/{1}/{2}/{2}_collection/1'
target_collection = uri_template.format(RESOURCE, username,
doc.displayId)
sbh.submit(doc, target_collection, 1)
def test_login_bad(self):
igem = sbol.PartShop(TEST_RESOURCE_MAIN)
try:
igem.login('*****@*****.**', 'test1')
self.fail('SBOLError not raised')
except sbol.SBOLError as sbol_error:
self.assertEqual(sbol_error.error_code(),
sbol.SBOLErrorCode.SBOL_ERROR_BAD_HTTP_REQUEST)
def sbh_login(SBH_USER, SBH_PASSWORD, spoof_bool, parts_doc):
# submit to staging server
if spoof_bool:
sbh_server = sbol.PartShop('https://hub-staging.sd2e.org')
sbh_server.spoof("https://hub.sd2e.org")
sbol.setHomespace(
'https://hub-staging.sd2e.org/user/sd2e/{collection}'.format(
collection=parts_doc.displayId))
# submit to production server
else:
sbh_server = sbol.PartShop('https://hub.sd2e.org')
sbol.setHomespace('https://hub.sd2e.org/user/sd2e/{collection}'.format(
collection=parts_doc.displayId))
sbh_server.login(SBH_USER, SBH_PASSWORD)
return sbh_server
def test_search_count(self):
part_shop = sbol2.PartShop('https://synbiohub.org/public/igem')
# searchCount did not exist, see #322
self.assertTrue(hasattr(part_shop, 'searchCount'))
count = part_shop.searchCount('plasmid')
# Make sure we get an int back, not a string representation of a number
self.assertIs(type(count), int)
# Expecting at least 1 plasmid
self.assertGreater(count, 0)
def test_pull_00(self):
# Based on tutorial: https://pysbol2.readthedocs.io/en/latest/repositories.html
doc = sbol.Document()
igem = sbol.PartShop(TEST_RESOURCE_MAIN)
igem.pull('https://synbiohub.org/public/igem/BBa_R0010/1', doc)
# print(doc)
# for obj in doc:
# print(obj)
self.assertEqual(3, len(doc))
def test_search_general(self):
sbh = sbol2.PartShop(TEST_RESOURCE_MAIN)
# sbh.login(username, password)
results = sbh.search("NAND")
# The response is a list
self.assertIsInstance(results, list)
# The response items are all of type Identified
self.assertTrue(all([isinstance(x, sbol2.Identified)
for x in results]))
def test_gsoc_count_5(self):
part_shop = sbol2.PartShop(GSOC_SBH_URL)
query = sbol2.SearchQuery()
collection = 'https://synbiohub.org/public/bsu/bsu_collection/1'
query[sbol2.SBOL_COLLECTION] = collection
query[sbol2.SBOL_NAME] = 'accA'
# GSOC is always looking for DNA Region
query[sbol2.SBOL_TYPES] = sbol2.BIOPAX_DNA
count = part_shop.searchCount(query)
self.assertEqual(1, count)
def test_pull_doc_version(self):
# After a pull the document version was erroneously set to None (#281)
doc = sbol.Document()
self.assertIsNotNone(doc.version)
old_version = doc.version
igem = sbol.PartShop(TEST_RESOURCE_MAIN)
igem.pull('https://synbiohub.org/public/igem/BBa_R0010/1', doc)
self.assertEqual(3, len(doc))
self.assertIsNotNone(doc.version)
self.assertEqual(old_version, doc.version)
def test_pull_01(self):
# Based on tutorial: https://pysbol2.readthedocs.io/en/latest/repositories.html
doc = sbol.Document()
igem = sbol.PartShop('https://synbiohub.org/public/igem')
igem.pull('BBa_B0032', doc)
igem.pull('BBa_E0040', doc)
igem.pull('BBa_B0012', doc)
# print(doc)
# for obj in doc:
# print(obj)
self.assertEqual(7, len(doc))
def test_pull_02(self):
# I don't know what this adds over test_pull_01
# This is a replacement for a previous test whose part was no
# longer available at SynBioHub
doc = sbol.Document()
ps = sbol.PartShop('https://synbiohub.org/public/bsu')
ps.pull('SyBiOntKB2sbol', doc)
# print(doc)
# for obj in doc:
# print(obj)
self.assertEqual(1, len(doc))
def __init__(self, *, sbh_url):
self.shutdownThread = False
self.event = threading.Event()
self.lock = threading.Lock()
self.sbh = sbol.PartShop(sbh_url)
self.sbh_username = None
self.sbh_password = None
self.housekeeping_thread = \
threading.Thread(target=self.housekeeping)
self.housekeeping_thread.start()
def test_submit_00(self):
RESOURCE = 'https://synbiohub.utah.edu'
doc = sbol.Document()
doc.displayId = 'test_collection'
doc.name = 'test collection'
doc.description = 'a test collection automatically generated ' \
'by the SBOL client library'
ps = sbol.PartShop(RESOURCE)
ps.login(username, password)
response = ps.submit(doc, overwrite=1)
self.assertEqual(response.status_code, 200)
def test_search_general(self):
sbh = sbol2.PartShop(TEST_RESOURCE_MAIN)
# sbh.login(username, password)
results = sbh.search("NAND")
# The response is a list
self.assertEqual(list, type(results))
# There are 25 items in the list (search returns more,
# but by default we get the first 25)
self.assertEqual(25, len(results))
# The response items are all of type Identified
self.assertTrue(all([isinstance(x, sbol2.Identified)
for x in results]))
def get_device_from_synbiohub(self, doc):
# Start an interface to igem's public part shop on
# SynBioHub. Located at `https://synbiohub.org/public/igem`
partshop = sbol2.PartShop('https://synbiohub.org/public/igem')
# Search the part shop for parts from the iGEM interlab study
# using the search term `interlab`
records = partshop.search('interlab')
# Import the medium strength device into your document
self.assertEqual(32, len(doc))
partshop.pull(PROMOTER_URI, doc)
self.assertEqual(35, len(doc))
def test_attach_file(self):
sbol2.Config.setOption('sbol_typed_uris', False)
doc = sbol2.Document()
doc.displayId = 'test_attachment'
doc.name = 'test attachment'
desc = 'a test collection created by the sbol2 unit tests'
doc.description = desc
md = doc.moduleDefinitions.create('attachmd')
sbh = sbol2.PartShop(TEST_RESOURCE)
sbh.login(username, password)
sbh.submit(doc, overwrite=1)
md_uri = '{}/user/{}/{}/{}/{}'.format(sbh.getURL(), sbh.getUser(),
doc.displayId, md.displayId,
md.version)
sbh.attachFile(md_uri, CRISPR_LOCATION)
# SBH will autogenerate an Attachment object, so now we query to find out
# what the URI of that Attachment object is so we can download it
query = '''
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX sbol: <http://sbols.org/v2#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX purl: <http://purl.obolibrary.org/obo/>
SELECT DISTINCT ?attachment_uri
WHERE {{
<{}> sbol:attachment ?attachment_uri
}}'''.format(md_uri)
response = sbh.sparqlQuery(query)
content = json.loads(response.content)
attachment_uri = content['results']['bindings'][0]['attachment_uri'][
'value']
# Save to default filename
sbh.downloadAttachment(attachment_uri)
self.assertTrue(os.path.exists('./crispr_example.xml'))
os.remove('crispr_example.xml')
# Save to new file name
sbh.downloadAttachment(attachment_uri, 'foo.xml')
self.assertTrue(os.path.exists('./foo.xml'))
os.remove('foo.xml')
# Confirm error handling
sbh.remove(attachment_uri)
with self.assertRaises(sbol2.SBOLError) as cm:
sbh.downloadAttachment(attachment_uri)
e = cm.exception
self.assertEqual(e.error_code(),
sbol2.SBOLErrorCode.SBOL_ERROR_NOT_FOUND)
def test_attach_file(self):
doc = sbol2.Document()
doc.displayId = 'test_attachment'
doc.name = 'test attachment'
desc = 'a test collection created by the sbol2 unit tests'
doc.description = desc
md = doc.moduleDefinitions.create('attachmd')
sbh = sbol2.PartShop(TEST_RESOURCE)
sbh.login(username, password)
sbh.submit(doc, overwrite=1)
md_uri = '{}/user/{}/{}/{}/{}'.format(sbh.getURL(), sbh.getUser(),
doc.displayId, md.displayId,
md.version)
sbh.attachFile(md_uri, CRISPR_LOCATION)
def test_uri2url(self):
# This tests an internal method that underlies `remove` and
# `pull`. No spoofing in these tests.
part_shop = sbol.PartShop(TEST_RESOURCE_MAIN)
uri = 'https://synbiohub.org/design/CAT_C0378/1'
url = part_shop._uri2url(uri)
self.assertEqual(url, uri)
uri = 'https://example.org/design/CAT_C0378/1'
try:
url = part_shop._uri2url(uri)
except sbol.SBOLError as err:
self.assertEqual(err.error_code(),
sbol.SBOLErrorCode.SBOL_ERROR_INVALID_ARGUMENT)
else:
self.fail('Expected SBOLError')
def test_search_general_offset_limit(self):
# Test a general search using offset and limit
# This comes from a documentation example that was failing
sbh = sbol2.PartShop(TEST_RESOURCE_MAIN)
offset = 10
limit = 20
results = sbh.search('plasmid', sbol2.SBOL_COMPONENT_DEFINITION,
offset, limit)
# The response is a list
self.assertEqual(list, type(results))
# There are `limit` items in the list (search returns more,
# but by default we get the first `limit`)
self.assertEqual(limit, len(results))
# The response items are all of type Identified
self.assertTrue(all([isinstance(x, sbol2.Identified)
for x in results]))
def test_getUser(self):
url = 'https://example.org'
partShop = sbol.PartShop(url)
self.assertTrue(hasattr(partShop, 'getUser'))
self.assertEqual(partShop.getUser(), '')
user = '******'
password = '******'
# Depending on DNS we might get one of two errors. Detect both
# and handle them gracefully. If neither of the expected
# errors is raised, then fail the test.
try:
partShop.login(user, password)
except requests.exceptions.ConnectionError:
pass
except sbol.sbolerror.SBOLError as err:
self.assertEqual(err.error_code(),
sbol.SBOLErrorCode.SBOL_ERROR_BAD_HTTP_REQUEST)
self.assertEqual(partShop.getUser(), user)
def test_search_exact(self):
igem = sbol.PartShop(TEST_RESOURCE_MAIN)
limit = 10
results = igem.search(sbol2.SO_PROMOTER,
sbol2.SBOL_COMPONENT_DEFINITION,
sbol2.SBOL_ROLES, 0, limit)
# The response is a list
self.assertEqual(list, type(results))
# The response contains _limit_ items
self.assertEqual(limit, len(results))
# The response items are all of type Identified
self.assertTrue(all([isinstance(x, sbol2.Identified)
for x in results]))
doc = sbol2.Document()
igem.pull([x.identity for x in results], doc, False)
self.assertEqual(10, len(doc))
for cd in doc.componentDefinitions:
self.assertIn(sbol2.SO_PROMOTER, cd.roles)
def test_gsoc_example_1_display_id(self):
# See issue #240
collection = 'https://synbiohub.org/public/igem/igem_collection/1'
display_id = 'BBa_E0040'
query = sbol2.SearchQuery()
query[sbol2.SBOL_COLLECTION] = collection
query[sbol2.SBOL_DISPLAY_ID] = display_id
# GSOC is always looking for DNA Region
query[sbol2.SBOL_TYPES] = sbol2.BIOPAX_DNA
part_shop = sbol2.PartShop(GSOC_SBH_URL)
response = part_shop.search(query)
# At least one item in return should be the
# expected return: https://synbiohub.org/public/igem/BBa_E0040/1
identities = [r.identity for r in response]
self.assertIn('https://synbiohub.org/public/igem/BBa_E0040/1',
identities)
#
# All items in response should have name == GFP exactly.
display_ids = [r.displayId == display_id for r in response]
self.assertTrue(all(display_ids))
def test_sparqlQuery_00(self):
ps = sbol.PartShop(TEST_RESOURCE_MAIN)
response = ps.login('johndoe', 'test')
self.assertEqual(response.status_code, 200)
query = '''
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX sbol: <http://sbols.org/v2#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX purl: <http://purl.obolibrary.org/obo/>
SELECT ?p ?o
WHERE {
<https://synbiohub.org/public/igem/BBa_K318030/1> ?p ?o
}
'''
response = ps.sparqlQuery(query)
# print(response.text)
self.assertEqual(response.status_code, 200)
def test_uri2url_spoofed(self):
# Test with a spoofed url
#
# Spoofed URLs had been an issue in `pull` before extracting
# the `_uri2url` method
part_shop = sbol.PartShop(TEST_RESOURCE_MAIN,
spoofed_url='https://example.org')
uri = 'https://synbiohub.org/design/CAT_C0378/1'
url = part_shop._uri2url(uri)
self.assertEqual(url, uri)
# _uri2url should change the spoofed URI to the resource URL
uri = 'https://example.org/design/CAT_C0378/1'
expected = 'https://synbiohub.org/design/CAT_C0378/1'
url = part_shop._uri2url(uri)
self.assertEqual(url, expected)
# URI is not in spoofed or resource domains
uri = 'https://example.com/design/CAT_C0378/1'
try:
url = part_shop._uri2url(uri)
except sbol.SBOLError as err:
self.assertEqual(err.error_code(),
sbol.SBOLErrorCode.SBOL_ERROR_INVALID_ARGUMENT)
else:
self.fail('Expected SBOLError')