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This resolves for UD-467 For ndexstringloader Hardcode the following …
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…network attributes instead of pulling them from the style file.
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@vrynkov
vrynkov committed Jul 11, 2019
1 parent bc83715 commit 95e5db6
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Showing 2 changed files with 118 additions and 48 deletions.
95 changes: 61 additions & 34 deletions ndexstringloader/ndexloadstring.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -495,48 +495,75 @@ def run(self):

return 0

def _generate_CX_file(self, file_name, network_name):
new_cx_file = file_name + '.cx'

logger.debug('generating CX file for network {}...'.format(network_name))
def _init_network_attributes(self):
net_attributes = {}

with open(file_name, 'r') as tsvfile:
net_attributes['name'] = 'STRING - Human Protein Links - High Confidence (Score >= ' \
+ str(self._cutoffscore) + ')'

with open(new_cx_file, "w") as out:
loader = StreamTSVLoader(self._load_plan, self._template)
net_attributes['description'] = '<br>This network contains high confidence (score >= ' \
+ str(self._cutoffscore) + ') human protein links with combined scores. ' \
+ 'Edge color was mapped to the combined score value using a gradient from light grey ' \
+ '(low Score) to black (high Score).'

net_attributes['rights'] = 'Attribution 4.0 International (CC BY 4.0)'

net_attributes['rightsHolder'] = 'STRING CONSORTIUM'

net_attributes['version'] = self._string_version

description = '<br>This network contains high confidence (score >= ' \
+ str(self._cutoffscore) + ') human protein links with combined scores. Edge color was mapped to ' \
+ 'the combined score value using a gradient from light grey (low Score) to black (high Score).'
net_attributes['organism'] = 'Homo sapiens (human)'

reference = '<p>Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, ' \
+ 'Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C.<br><b> ' \
net_attributes['networkType'] = ['interactome', 'ppi']

net_attributes['reference'] = '<p>Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, ' \
+ 'Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C.<br><b> ' \
+ 'The STRING database in 2017: quality-controlled protein-protein association networks, ' \
+ 'made broadly accessible.</b><br>Nucleic Acids Res. 2017 Jan; ' \
+ '45:D362-68.<br> <a target="_blank" href="https://doi.org/10.1093/nar/gkw937">' \
+ 'DOI:10.1093/nar/gkw937</a></p>'

net_attributes['prov:wasDerivedFrom'] = \
'https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz'

net_attributes['prov:wasGeneratedBy'] = \
'<a href="https://github.com/ndexcontent/ndexstringloader" target="_blank">ndexstringloader ' \
+ str(ndexstringloader.__version__) + '</a>'

net_attributes['__iconurl'] = self._iconurl

return net_attributes



def _generate_CX_file(self, network_attributes):
file_name = self._output_tsv_file_name
new_cx_file = file_name + '.cx'

logger.debug('generating CX file for network {}...'.format(network_attributes['name']))

with open(file_name, 'r') as tsvfile:

with open(new_cx_file, "w") as out:
loader = StreamTSVLoader(self._load_plan, self._template)

loader.write_cx_network(tsvfile, out,
[
{'n': 'name', 'v': network_name},
{'n': 'description', 'v': description},
{'n': 'rights', 'v': 'Attribution 4.0 International (CC BY 4.0)'},
{'n': 'rightsHolder', 'v': 'STRING CONSORTIUM'},
{'n': 'version', 'v': self._string_version},
{'n': 'organism', 'v': 'Human, 9606, Homo sapiens '},
{'n': 'networkType', 'v': ['interactome', 'ppi'], 'd': 'list_of_string'},
{'n': 'reference', 'v': reference},
{'n': 'prov:wasDerivedFrom', 'v':
'https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz'
},
{'n': 'prov:wasGeneratedBy', 'v':
'<a href="https://github.com/ndexcontent/ndexstringloader" target="_blank">ndexstringloader ' + str(
ndexstringloader.__version__) + '</a>'},

{'n': '__iconurl', 'v': self._iconurl}
{'n': 'name', 'v': network_attributes['name']},
{'n': 'description', 'v': network_attributes['description']},
{'n': 'rights', 'v': network_attributes['rights']},
{'n': 'rightsHolder', 'v': network_attributes['rightsHolder']},
{'n': 'version', 'v': network_attributes['version']},
{'n': 'organism', 'v': network_attributes['organism']},
{'n': 'networkType', 'v': network_attributes['networkType'], 'd': 'list_of_string'},
{'n': 'reference', 'v': network_attributes['reference']},
{'n': 'prov:wasDerivedFrom', 'v': network_attributes['prov:wasDerivedFrom']},
{'n': 'prov:wasGeneratedBy', 'v': network_attributes['prov:wasGeneratedBy']},
{'n': '__iconurl', 'v': network_attributes['__iconurl']}
])

logger.debug('CX file for network {} generated\n'.format(network_name))
logger.debug('CX file for network {} generated\n'.format(network_attributes['name']))
return new_cx_file


Expand Down Expand Up @@ -594,15 +621,15 @@ def get_network_uuid(self, network_name):

def load_to_NDEx(self):

file_name = self._output_tsv_file_name
network_name = 'STRING - Human Protein Links - ' \
'High Confidence (Score > ' +\
str(self._cutoffscore) + ')'

if self.create_ndex_connection() is None:
return 2

cx_file_name = self._generate_CX_file(file_name, network_name)

network_attributes = self._init_network_attributes()

cx_file_name = self._generate_CX_file(network_attributes)

network_name = network_attributes['name']

network_id = self.get_network_uuid(network_name)

Expand Down
71 changes: 57 additions & 14 deletions tests/test_ndexloadstring.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import unittest
from ndexutil.config import NDExUtilConfig
from ndexstringloader.ndexloadstring import NDExSTRINGLoader
import ndexstringloader


class Param(object):
Expand All @@ -36,11 +37,11 @@ def setUp(self):
'conf': None,
'profile': None,
'loadplan': None,
'stringversion': None,
'stringversion': '11.0',
'args': None,
'datadir': None,
'datadir': tempfile.mkdtemp(),
'cutoffscore': 0.7,
'iconurl': None
'iconurl': 'https://home.ndexbio.org/img/STRING-logo.png'
}

self._args = dotdict(self._args)
Expand All @@ -51,9 +52,9 @@ def tearDown(self):
"""Tear down test fixtures, if any."""

@unittest.skip("skip it now - will add later")
def test_parse_config(self):
def test_0010_parse_config(self):

temp_dir = tempfile.mkdtemp()
temp_dir = self._args['datadir']
try:
p = Param()
p.profile = 'test_conf_section'
Expand All @@ -76,7 +77,7 @@ def test_parse_config(self):
shutil.rmtree(temp_dir)

@unittest.skip("skip it now - uncomment later")
def test_remove_duplicate_edges(self):
def test_0020_remove_duplicate_edges(self):

# some duplicate records in the same format as in STRING 9606.protein.links.full.v11.0.txt
duplicate_records = [
Expand Down Expand Up @@ -120,14 +121,13 @@ def test_remove_duplicate_edges(self):
}
}

temp_dir = tempfile.mkdtemp()
temp_dir = self._args['datadir']
temp_file = 'tmp.txt'
temp_file_1 = 'tmp1.txt'

try:
f = os.path.join(temp_dir, temp_file)

self._args.datadir = temp_dir
self._full_name_file = f

self._output_tsv_file_name = os.path.join(temp_dir, temp_file_1)
Expand Down Expand Up @@ -178,7 +178,7 @@ def test_remove_duplicate_edges(self):
shutil.rmtree(temp_dir)

@unittest.skip("skip it now - uncomment later")
def test_exception_on_duplicate_edge_with_different_scores(self):
def test_0030_exception_on_duplicate_edge_with_different_scores(self):


# some duplicate records in the same format as in STRING 9606.protein.links.full.v11.0.txt
Expand All @@ -201,14 +201,13 @@ def test_exception_on_duplicate_edge_with_different_scores(self):

for i in range(0, 2):

temp_dir = tempfile.mkdtemp()
temp_dir = self._args['datadir']
temp_file = 'tmp.txt'
temp_file_1 = 'tmp1.txt'

try:
f = os.path.join(temp_dir, temp_file)

self._args.datadir = temp_dir
self._full_name_file = f

self._output_tsv_file_name = os.path.join(temp_dir, temp_file_1)
Expand Down Expand Up @@ -242,13 +241,57 @@ def test_exception_on_duplicate_edge_with_different_scores(self):

finally:
shutil.rmtree(temp_dir)
self._args['datadir'] = tempfile.mkdtemp()

# re-init dudplicates and re-rerun the teast
# re-init duplicates and re-rerun the teast
duplicate_records = [
'9606.ENSP00000238651 9606.ENSP00000364486 0 0 0 0 0 0 45 0 0 800 0 0 0 801',
'9606.ENSP00000364486 9606.ENSP00000238651 0 0 0 0 0 0 45 0 0 800 0 0 0 800'
]


def test_get_network_uuid(self):
pass
def test_0040_init_network_atributes(self):
net_attributes = {}

cutoffscore = str(self._args['cutoffscore'])

net_attributes['name'] = 'STRING - Human Protein Links - High Confidence (Score >= ' + cutoffscore + ')'

net_attributes['description'] = '<br>This network contains high confidence (score >= ' \
+ cutoffscore + ') human protein links with combined scores. ' \
+ 'Edge color was mapped to the combined score value using a gradient from light grey ' \
+ '(low Score) to black (high Score).'

net_attributes['rights'] = 'Attribution 4.0 International (CC BY 4.0)'

net_attributes['rightsHolder'] = 'STRING CONSORTIUM'

net_attributes['version'] = self._args['stringversion']

net_attributes['organism'] = 'Homo sapiens (human)'

net_attributes['networkType'] = ['interactome', 'ppi']

net_attributes['reference'] = '<p>Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, ' \
+ 'Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C.<br><b> ' \
+ 'The STRING database in 2017: quality-controlled protein-protein association networks, ' \
+ 'made broadly accessible.</b><br>Nucleic Acids Res. 2017 Jan; ' \
+ '45:D362-68.<br> <a target="_blank" href="https://doi.org/10.1093/nar/gkw937">' \
+ 'DOI:10.1093/nar/gkw937</a></p>'

net_attributes['prov:wasDerivedFrom'] = \
'https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz'

net_attributes['prov:wasGeneratedBy'] = \
'<a href="https://github.com/ndexcontent/ndexstringloader" target="_blank">ndexstringloader ' \
+ str(ndexstringloader.__version__) + '</a>'

net_attributes['__iconurl'] = self._args['iconurl']


loader = NDExSTRINGLoader(self._args)

# get network attributes from STRING loader object
network_attributes = loader._init_network_attributes()

self.assertDictEqual(net_attributes, network_attributes, 'unexpected network properties')

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