def get_similarity_network(self):
plot = None
try:
cwd = os.path.abspath(os.path.dirname(__file__))
query_path = os.path.join(cwd, self.queries_file)
project_cypher = query_utils.read_queries(query_path)
query = query_utils.get_query(project_cypher,
query_id="projects_subgraph")
list_projects = []
driver = connector.getGraphDatabaseConnectionConfiguration()
if "other_id" in self.similar_projects:
list_projects = self.similar_projects[
"other_id"].values.tolist()
list_projects.append(self.identifier)
list_projects = ",".join(['"{}"'.format(i) for i in list_projects])
query = query.replace("LIST_PROJECTS", list_projects)
path = connector.sendQuery(driver, query, parameters={}).data()
G = acore_utils.neo4j_path_to_networkx(path, key='path')
args = {}
style, layout = self.get_similarity_network_style()
args['stylesheet'] = style
args['layout'] = layout
args['title'] = "Projects subgraph"
net, mouseover = acore_utils.networkx_to_cytoscape(G)
plot = viz.get_cytoscape_network(net, "projects_subgraph", args)
except Exception as err:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
logger.error(
"Error: {}. Reading queries from file {}: {}, file: {},line: {}"
.format(err, query_path, sys.exc_info(), fname,
exc_tb.tb_lineno))
return plot
def get_project_information(driver, project_id):
query_name = 'project_graph'
queries = []
data = []
res = []
try:
query = ''
data_upload_cypher = get_data_upload_queries()
for section in data_upload_cypher[query_name]:
code = section['query']
queries.extend(
code.replace("PROJECTID", project_id).split(';')[0:-1])
for query in queries:
result = connector.sendQuery(driver, query + ";")[0]
data.append(result)
except Exception as err:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
logger.error(
"Error: {}. Creating analytical samples: Query name ({}) - Query ({}), error info: {}, file: {},line: {}"
.format(err, query_name, query, sys.exc_info(), fname,
exc_tb.tb_lineno))
if data:
for i, j in enumerate(data):
df = pd.DataFrame([data[i]], columns=data[i].keys())
header = '_'.join(df.columns[0].split('_', 1)[1:]).capitalize()
df.rename(columns={df.columns[0]: 'project'}, inplace=True)
res.append(
viz.get_table(df,
identifier='new_project_{}'.format(header),
args={
'title':
'{} data uploaded for project {}'.format(
header, project_id)
}))
else:
res = None
logger.error(
"Error: No data was uploaded for project: {}. Review your experimental design and data files and the logs for errors."
.format(project_id))
return res
def remove_project(self,
host="localhost",
port=7687,
user="******",
password="******"):
try:
cwd = os.path.abspath(os.path.dirname(__file__))
query_path = os.path.join(cwd, self.queries_file)
project_cypher = query_utils.read_queries(query_path)
query = query_utils.get_query(project_cypher,
query_id="remove_project")
driver = connector.connectToDB(host, port, user, password)
queries = query.replace("PROJECTID", self.identifier)
for query in queries.split(';')[:-1]:
result = connector.sendQuery(driver,
query + ';',
parameters={}).data()
except Exception as err:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
logger.error(
"Error removing project {}. Query file: {},line: {}, error: {}"
.format(self.identifier, fname, exc_tb.tb_lineno, err))
def get_db_schema():
"""
Retrieves the database schema
:return: network with all the database nodes and how they are related
"""
style = [{
'selector': 'node',
'style': {
'label': 'data(name)',
'background-color': 'data(color)',
'text-valign': 'center',
'text-halign': 'center',
'border-color': 'gray',
'border-width': '1px',
'width': 55,
'height': 55,
'opacity': 0.8,
'font-size': '14'
}
}, {
'selector': 'edge',
'style': {
'label': 'data(label)',
'curve-style': 'bezier',
'opacity': 0.7,
'width': 0.4,
'font-size': '5'
}
}]
layout = {
'name': 'cose',
'idealEdgeLength': 100,
'nodeOverlap': 20,
'refresh': 20,
'randomize': False,
'componentSpacing': 100,
'nodeRepulsion': 400000,
'edgeElasticity': 100,
'nestingFactor': 5,
'gravity': 80,
'numIter': 1000,
'initialTemp': 200,
'coolingFactor': 0.95,
'minTemp': 1.0
}
query_name = 'db_schema'
cypher = get_query()
if query_name in cypher:
if 'query' in cypher[query_name]:
query = cypher[query_name]['query']
path = connector.sendQuery(driver, query, parameters={}).data()
G = utils.neo4j_schema_to_networkx(path)
args = {'height': '1000px'}
args['stylesheet'] = style
args['layout'] = layout
args['title'] = "Database Schema"
net, mouseover = utils.networkx_to_cytoscape(G)
plot = viz.get_cytoscape_network(net, "db_schema", args)
return plot