def test_taxonomy(self):
tax = taxonomy.Taxonomy()
self.assertIsInstance(tax, taxonomy.Taxonomy)
self.assertIsInstance(tax.semantic, taxonomy_semantic.TaxonomySemantic)
self.assertIsInstance(tax.types, taxonomy_types.TaxonomyTypes)
self.assertIsInstance(tax.units, taxonomy_units.TaxonomyUnits)
self.assertIsInstance(tax.misc, taxonomy_misc.TaxonomyMisc)
def test_taxonomy(self):
tax = taxonomy.Taxonomy()
self.assertIsInstance(tax, taxonomy.Taxonomy)
self.assertIsInstance(tax.semantic, taxonomy_semantic.TaxonomySemantic)
self.assertIsInstance(tax.types, taxonomy_types.TaxonomyTypes)
self.assertIsInstance(tax.units, taxonomy_units.TaxonomyUnits)
self.assertIsInstance(tax.numeric_types, taxonomy_misc.TaxonomyNumericTypes)
self.assertIsInstance(tax.generic_roles, taxonomy_misc.TaxonomyGenericRoles)
self.assertIsInstance(tax.ref_parts, taxonomy_misc.TaxonomyRefParts)
self.assertIsInstance(tax.documentation, taxonomy_misc.TaxonomyDocstrings)
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import unittest
import taxonomy
#import taxonomy_semantic
from six import string_types
taxonomy_obj = taxonomy.Taxonomy()
tax = taxonomy_obj.semantic
class TestTaxonomySemantic(unittest.TestCase):
def test_concept_details(self):
# Data type checks
ci = tax.get_concept_details("solar:ACDisconnectSwitchMember")
self.assertIsNotNone(ci)
self.assertIsInstance(ci.abstract, bool)
self.assertIsInstance(ci.id, string_types)
# 'six.string_types' is equivalent to "str or unicode" in python2, "str" in python3
self.assertIsInstance(ci.name, string_types)
self.assertIsInstance(ci.nillable, bool)
Orange Button Overview: https://sunspec.org/orange-button-initiative/
Orange Button GitHUb: https://github.com/SunSpecOrangeButton
Orange Button CLI GitHub: https://github.com/SunSpecOrangeButton/core
"""
DASHES = "---------------------------------------------------------------------------------------"
# The following line will cause pyinstaller to work correctly.
# In all likelihood it is sub-optimal however because it would
# preclude adding file input or output as CLI arguments (since
# the working directory changes to the wrong value).
if getattr(sys, 'frozen', False):
os.chdir(sys._MEIPASS)
tax = taxonomy.Taxonomy()
def info(args):
print(INFO)
def generate_identifier(args):
print(identifier.identifier())
def list_concept_info(args):
print()
c = tax.semantic.concept_info(args.concept)
print(c)
if c is not None:
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import unittest
import parser
import taxonomy
from jsondiff import diff
taxonomy = taxonomy.Taxonomy()
parser = parser.Parser(taxonomy)
class TestParser(unittest.TestCase):
# Note: this module is tested differently than others. Sample JSON and XML
# files are imported and then exported and later compared using the string
# methods. Thereafter files are loaded and created but the files contents
# themselves are not examined (it is assumed that this would be picked up
# in the comparisons of the strings).
def test_json(self):
entrypoint = parser.from_JSON_string(TEST_JSON)
out = parser.to_JSON_string(entrypoint)
d = diff(TEST_JSON, out)
import taxonomy
# Create a TCP/IP socket
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
if len(sys.argv) != 2:
print 'Usage: python server.py <port number>'
sys.exit(0)
portNum = int(sys.argv[1])
# Bind the socket to the port
server_address = ('nike.cs.uga.edu', portNum)
print >>sys.stderr, 'starting up on %s port %s' % server_address
sock.bind(server_address)
tester = taxonomy.Taxonomy('')
while True:
#print >>sys.stderr, '\nwasiting to receive message'
data, address = sock.recvfrom(4096)
print >>sys.stderr, 'received %s bytes from %s' % (data, address)
print >>sys.stderr, data
commandList = data.split(' ')
for str in commandList:
print str
if commandList[0] == 'insert' and len(commandList) == 2:
tester.insert(commandList[1])
# sent = sock.sendto('Inserted ' + data, address)
elif commandList[0] == 'list':
class Taxonomy:
'''
Taxonomy represents a Linnean category (order, family, or genus)
If a Taxonomy object's level is 'genus', then its item list contains
strings of the form <species-name> [(<common-name>)]
If the Taxonomy object's level is 'Order' or 'Family', then its item
list contains Taxonomy objects of the next level down.
'''
def __init__(self, category, level='Order'):
import pickle
import os.path
'''
Create a new Taxonomy based on 'category'
if 'level' is 'Order' and a serialization file
for this order exists, then populate this object from
that file; otherwise, create an empty Taxonomy
category: the name of an order, a family, or a genus
level: one of 'Order', 'Family', or 'Genus'
'''
self.errorMessageStatement = 'Insertion OK'
if level == 'Order':
# does the file already exist?
if (os.path.isfile(category + ".p")):
self.itemList = pickle.load(open(category + ".p", "rb"))
self.level = 'Order'
self.itemList = []
self.categoryName = category
else:
# just make an empty taxonomy object
self.categoryName = category
self.level = level
self.itemList = []
def addSpecies(self, species):
'''
Add a species to this taxonomy and return True. The level of this
taxonomy must be 'genus'. If not, set an error message and return False.
'''
if self.level != 'Genus':
self.errorMessageStatement = 'Taxonomy is not of level Genus.'
return False
else:
self.itemList.append(species)
self.serialize()
return True
def addTaxonomy(self, subTaxonomy):
'''
Add a sub-taxonomy to this taxonomy and return True. The sub-taxonomy must
be at one level below this taxonomy. If not, set an error message and return False.
'''
# checks to see one level below
if self.level == 'Order' and subTaxonomy.level != 'Family':
self.errorMessageStatement = 'Subtaxonomy was not one level below.'
return False
if self.level == 'Family' and subTaxonomy.level != 'Genus':
self.errorMessageStatement = 'Subtaxonomy was not one level below.'
return False
self.itemList.append(subTaxonomy)
self.serialize()
return True
def errorMessage(self):
'''
Return the error message generated by the last insertion, or
'Insertion OK' if the last insertion did not create an error
'''
return self.errorMessageStatement
def insert(self, path):
'''
Insert the species that is the last element of 'path' into
this object,creating order, family, or genus Taxonomy objects
as needed. If the length of path does not match the level of this
Taxonomy object, set an error message ,abort the insertion, and
return False; otherwise return True after successful insertion.
This Taxonomy Level Expected path length
Order 3
Family 2
Genus 1
path: front-slash-separated list of categories.
'''
# to see if there is an existing species, otherwise add it
temp = path.split('/')
if self.level == 'Genus':
if len(temp) != 1:
self.errorMessageStatement = 'Error inserting ' + path + ' into ' + self.categoryName + ': wrong length'
return False
else:
self.itemList.append(temp[0])
self.serialize()
return True
if self.level == 'Family':
if len(temp) != 2:
self.errorMessageStatement = 'Error inserting ' + path + ' into ' + self.categoryName + ': wrong length'
return False
for item in self.itemList:
if item.categoryName == temp[0]:
# in the event genus already exists
for _item in item.itemList:
if _item == temp[1]:
# species already exists in heirarchy
return True
# species does not exist, but the genus does
item.itemList.append(temp[0])
return True
# in the event no genus exists in the family
newGenus = Taxonomy(temp[0], 'Genus')
newGenus.itemList.append(temp[1])
self.itemList.append(newGenus)
self.serialize()
return True
# error check on order
if self.level == 'Order':
if len(temp) != 3:
self.errorMessageStatement = 'Error inserting ' + path + ' into ' + self.categoryName + ': wrong length'
return False
print '\n'
# iterate through family objects in order to see match
for item in self.itemList:
# check if there is a family that already exists
if item.categoryName == temp[0]:
# there is already a family object with the same category name
for _item in item.itemList:
# for every genus in this family object
if _item.categoryName == temp[1]:
# genus already exists in this family object
for _item_ in _item.itemList:
# for every species string in this genus
if _item_ == temp[2]:
# this species already exists in the genus
return True
# genus exists but the species does not
_item.itemList.append(temp[2])
return True
# there is a family object, but no genus or therefore species
newGenus = Taxonomy(temp[1], 'Genus')
newGenus.itemList.append(temp[2])
_item.itemList.append(newGenus)
return True
# adds a family with a new genus and new species in that genus
newFamily = Taxonomy(temp[0], 'Family')
_newGenus = Taxonomy(temp[1], 'Genus')
_newGenus.itemList.append(temp[2])
self.itemList.append(newFamily)
newFamily.itemList.append(_newGenus)
self.serialize()
return True
def list(self):
'''
Return a string representing the contents of this Taxonomy
and its sub-Taxonomies, in the format
top-category-name (subitem1, subitem2,...),
where subitem1, subitem2... are either strings representing species,
in the form <latin-name> [(common-name)], or sublists representing
Taxonomies.
'''
# iterates through objects in an order's item list
if self.level == 'Order':
listSpecies = ""
listSpecies += self.categoryName
for family in self.itemList:
listSpecies += " (" + family.categoryName
for genus in family.itemList:
listSpecies += " (" + genus.categoryName
for species in genus.itemList:
listSpecies += " (" + species
listSpecies += ")"
listSpecies += ")"
listSpecies += ")"
return listSpecies
# iteratees through the items of a family
if self.level == 'Family':
listSpecies = ""
listSpecies += self.categoryName
for genus in self.itemList:
listSpecies += " (" + genus.categoryName
for species in genus.itemList:
listSpecies += " (" + species
listSpecies += ")"
listSpecies += ")"
return listSpecies
# iterates through items in a genus
if self.level == 'Genus':
listSpecies = ""
listSpecies += self.categoryName
for species in self.itemList:
listSpecies += " (" + species
listSpecies += ")"
return listSpecies
def serialize(self):
import pickle
'''
Save contents of this object using pickle
'''
pickle.dump(self.itemList, open(self.categoryName + ".p", "wb"))
if __name__ == "__main__":
import taxonomy
import unittest
import sys
'''Test adding a species to a genus with no errors'''
genus1 = taxonomy.Taxonomy('')
while (1):
userInput = raw_input('> ')
commandList = []
commandList = userInput.split(' ')
for str in commandList:
print(str + ' ')
if userInput.strip() == 'quit' or userInput.strip() == 'exit':
print 'Closing application'
sys.exit(0)
if commandList[0] == 'insert':
genus1.insert(commandList[1])
if commandList[0] == 'list':
print(genus1.list())
else:
print('The command ' + userInput + ' does not exist.')
From home run: $ ssh -fNL 27028:localhost:27018 gbwl $ ssh -fNL 27027:localhost:27017 gbwl where gbwl is [email protected] -W wl-cmadmin.scripps.edu:22 """ #HOST = 'localhost' HOST = 'wl-cmadmin' from pymongo import MongoClient from itertools import chain from collections import Counter import taxonomy t = taxonomy.Taxonomy(host=HOST, port=27017) client = MongoClient(HOST, 27017) taxDB = client.TaxDB_072114.TaxDB_072114 hashDB = client.HashDB_072114.HashDB_072114 domainDB = client.DomainDB_072114.DomainDB_072114 protDB = MongoClient(HOST, 27018).ProtDB_072114.ProtDB_072114 from file_processing import blazmass_tools from file_processing.dta import build_proteins_from_peptides def get_domains(p): hashes = [ x['_id'] for x in hashDB.find({'pID': {
