def main(args):
if len(args) < 3:
print(get_usage())
sys.exit(1)
votes = sys.argv[1]
outFile = sys.argv[2]
t = testutils.Timer(ENABLE_TIMER)
context = snap.TTableContext()
VoteS = snap.Schema()
VoteS.Add(snap.TStrTAttrPr("UserId", snap.atInt))
VoteS.Add(snap.TStrTAttrPr("AdminId", snap.atInt))
TVotes = snap.TTable.LoadSS("WikiVotes", VoteS, votes, context, '\t',
snap.TBool(False))
t.show("load Votes", TVotes)
GroupBy = snap.TStrV()
GroupBy.Add("UserId")
JointTable = TVotes.SelfSimJoinPerGroup(GroupBy, "AdminId",
DISTANCE_ATTRIBUTE, snap.Jaccard,
0.5)
t.show("SimJoinPerGroup complete", JointTable)
JointTable.SelectAtomic("WikiVotes_1.UserId", "WikiVotes_2.UserId",
snap.NEQ)
t.show("Select complete", JointTable)
testutils.dump(JointTable, 20)
JointTable.SaveSS(outFile)
def getLblGraph(self, fileName):
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("srcLabel", snap.atStr))
schema.Add(snap.TStrTAttrPr("srcId", snap.atInt))
schema.Add(snap.TStrTAttrPr("dstLabel", snap.atStr))
schema.Add(snap.TStrTAttrPr("dstId", snap.atInt))
table = snap.TTable.LoadSS(schema, fileName, context, " ",
snap.TBool(False))
#print table
edgeattrv = snap.TStrV()
edgeattrv.Add("srcLabel")
edgeattrv.Add("dstLabel")
# edgeattrv.Add("edgeattr2")
srcnodeattrv = snap.TStrV()
# srcnodeattrv.Add("srcLabel")
dstnodeattrv = snap.TStrV()
# srcnodeattrv.Add("dstLabel")
# net will be an object of type snap.PNEANet
return snap.ToNetwork(snap.PNEANet, table, "srcId", "dstId",
srcnodeattrv, dstnodeattrv, edgeattrv,
snap.aaFirst)
def parseGraph(filename="./GG-NE/test.tsv"):
edgefilename = filename # A file containing the graph, where each row contains an edge
# and each edge is represented with the source and dest node ids,
# the edge attributes, and the source and destination node attributes
# separated by a tab.
context = snap.TTableContext(
) # When loading strings from different files, it is important to use the same context
# so that SNAP knows that the same string has been seen before in another table.
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("srcID", snap.atInt))
schema.Add(snap.TStrTAttrPr("dstID", snap.atInt))
schema.Add(snap.TStrTAttrPr("weight", snap.atFlt))
table = snap.TTable.LoadSS(schema, edgefilename, context, "\t",
snap.TBool(False))
# In this example, we add both edge attributes to the network,
# but only one src node attribute, and no dst node attributes.
edgeattrv = snap.TStrV()
edgeattrv.Add("weight")
srcnodeattrv = snap.TStrV()
dstnodeattrv = snap.TStrV()
# net will be an object of type snap.PNEANet
G = snap.ToNetwork(snap.PNEANet, table, "srcID", "dstID", srcnodeattrv,
dstnodeattrv, edgeattrv, snap.aaFirst)
labels = pd.read_table("SS-Butterfly_labels.tsv")
G.AddIntAttrN("label")
for index, row in labels.iterrows():
G.AddIntAttrDatN(row["# Node_ID"], row["Species"], "label")
return G
def load_mode_to_graph(mode, filename, Graph, context):
modeId = mode + 'Id'
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr(modeId, snap.atStr))
schema.Add(snap.TStrTAttrPr("datasetId", snap.atStr))
modenet = snap.TTable.LoadSS(schema, filename, context, "\t",
snap.TBool(False))
snap.LoadModeNetToNet(Graph, mode, modenet, modeId, snap.TStrV())
def ttable():
t0=t()
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Col1", snap.atInt))
schema.Add(snap.TStrTAttrPr("Col2", snap.atInt))
table = snap.TTable.LoadSS(schema, NW.twitter, context, "\t", snap.TBool(False))
reportTime(t0, "TTABLE")
def main():
S = snap.Schema()
context = snap.TTableContext()
S.Add(snap.TStrTAttrPr("Animal", snap.atStr))
S.Add(snap.TStrTAttrPr("Size", snap.atStr))
S.Add(snap.TStrTAttrPr("Location", snap.atStr))
S.Add(snap.TStrTAttrPr("Number", snap.atInt))
Animals = snap.TTable.LoadSS("Animals", S,
"/dfs/ilfs2/0/ringo/tests/animals.txt",
context, '\t', snap.TBool(False))
# Gets animals with size=big
pred_size = snap.TAtomicPredicate(snap.atStr, snap.TBool(True), snap.EQ,
"Size", "", 0, 0, "big")
node_size = snap.TPredicateNode(pred_size)
# Get animals with location=Australia
pred_location = snap.TAtomicPredicate(snap.atStr, snap.TBool(True),
snap.EQ, "Location", "", 0, 0,
"Australia")
node_location = snap.TPredicateNode(pred_location)
# size=big and location=Australia
node1 = snap.TPredicateNode(snap.AND)
node1.AddLeftChild(node_size)
node1.AddRightChild(node_location)
# Get animals with name==location (fabricated to show a non const case
pred_animal_location = snap.TAtomicPredicate(snap.atStr, snap.TBool(False),
snap.EQ, "Animal", "Location")
node2 = snap.TPredicateNode(pred_animal_location)
# (size=big and location=Australia) or Animal==Location
node_root = snap.TPredicateNode(snap.OR)
node_root.AddLeftChild(node1)
node_root.AddRightChild(node2)
pred = snap.TPredicate(node_root)
Animals.Select(pred)
testutils.dump(Animals)
def test_table_merge(self):
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Col1", snap.atInt))
schema.Add(snap.TStrTAttrPr("Col2", snap.atInt))
schema.Add(snap.TStrTAttrPr("Col3", snap.atFlt))
filename = "data/data-table.txt"
grade_table = snap.TTable.LoadSS(schema, filename, context, "\t", snap.TBool(False))
int_vec = snap.TIntV()
def load_physician_referral_data(infilename):
"""
Load the US physician referral data from specified zipfile
Parameters:
infilename - path name of zipflie to load from
Return value:
SNAP TNGraph object built from the data
"""
tmpdir = tempfile.mkdtemp()
try:
archive = zipfile.ZipFile(infilename, 'r')
archive.extract('physician-shared-patient-patterns-2014-days30.txt',
tmpdir)
filename = os.path.join(
tmpdir, "physician-shared-patient-patterns-2014-days30.txt")
archive.close()
context = snap.TTableContext()
schema = snap.Schema()
## schema.Add(snap.TStrTAttrPr("NPI_1", snap.atInt))
## schema.Add(snap.TStrTAttrPr("NPI_2", snap.atInt))
# the above 2 lines worked with SNAP 4.0.0 on VLSCI
# but now using SNAP 4.1.0
# on hpc.ics.usi.ch find that all ids are -1 so graph wrong.
# Cannot work out why so changed to string not int to try to fix it:
schema.Add(snap.TStrTAttrPr("NPI_1", snap.atStr))
schema.Add(snap.TStrTAttrPr("NPI_2", snap.atStr))
## schema.Add(snap.TStrTAttrPr("count", snap.atInt))
## schema.Add(snap.TStrTAttrPr("unique_bene", snap.atInt))
## schema.Add(snap.TStrTAttrPr("same_day_count", snap.atInt))
# The above 3 lines also worked fine with SNAP 4.0.0 before but
# now fail on SNAP 4.1.0 (seems to be due to spaces in CSV fields,
# not inexplicable like first two which have no spaces) but not using
# them at the moment anyway so easier to just make (unused) strings:
schema.Add(snap.TStrTAttrPr("count", snap.atStr))
schema.Add(snap.TStrTAttrPr("unique_bene", snap.atStr))
schema.Add(snap.TStrTAttrPr("same_day_count", snap.atStr))
table = snap.TTable.LoadSS(schema, filename, context, ",",
snap.TBool(False))
G = snap.ToGraph(snap.PNGraph, table, "NPI_1", "NPI_2", snap.aaFirst)
finally:
cleanup_tmpdir(tmpdir)
return G
def test_table_getitem(self):
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Col1", snap.atInt))
schema.Add(snap.TStrTAttrPr("Col2", snap.atInt))
schema.Add(snap.TStrTAttrPr("Col3", snap.atFlt))
filename = "data/data-table.txt"
grade_table = snap.TTable.LoadSS(schema, filename, context, "\t", snap.TBool(False))
int_vec = snap.TIntV()
int_vec.Add(0)
int_vec.Add(1)
int_vec.Add(2)
int_vec.Add(3)
int_vec.Add(4)
# unsure about next line!
col2_vec = grade_table[]
def main(args):
if len(args) < 3:
print(get_usage())
sys.exit(1)
yelp = sys.argv[1]
outFile = sys.argv[2]
t = testutils.Timer(ENABLE_TIMER)
context = snap.TTableContext()
YelpS = snap.Schema()
YelpS.Add(snap.TStrTAttrPr("Name", snap.atStr))
YelpS.Add(snap.TStrTAttrPr("City", snap.atStr))
YelpS.Add(snap.TStrTAttrPr("State", snap.atStr))
YelpS.Add(snap.TStrTAttrPr("Latitude", snap.atFlt))
YelpS.Add(snap.TStrTAttrPr("Longitude", snap.atFlt))
TYelp = snap.TTable.LoadSS("Yelp", YelpS, yelp, context, '\t', snap.TBool(True));
t.show("load Yelp", TYelp)
Cols = snap.TStrV()
Cols.Add("Latitude")
Cols.Add("Longitude")
# Get all business within 5 kilometers of each other
JointTable = TYelp.SelfSimJoin(Cols, DISTANCE_ATTRIBUTE, snap.Haversine, 2)
t.show("SimJoin complete", JointTable)
ProjectionV = snap.TStrV()
ProjectionV.Add("Yelp_1.Name")
ProjectionV.Add("Yelp_1.City")
ProjectionV.Add("Yelp_1.State")
ProjectionV.Add("Yelp_2.Name")
ProjectionV.Add("Yelp_2.City")
ProjectionV.Add("Yelp_2.State")
ProjectionV.Add(DISTANCE_ATTRIBUTE)
JointTable.ProjectInPlace(ProjectionV)
t.show("Project complete")
testutils.dump(JointTable, 100);
JointTable.SaveSS(outFile)
def load_crossnet_to_graph(context,
edgeId,
srcName,
dstName,
filepath,
Graph,
prefix="miner"):
srcId = srcName + "SrcId"
dstId = dstName + "DstId"
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr(edgeId, snap.atStr))
schema.Add(snap.TStrTAttrPr("datasetId", snap.atStr))
schema.Add(snap.TStrTAttrPr(srcId, snap.atStr))
schema.Add(snap.TStrTAttrPr(dstId, snap.atStr))
crossnet = snap.TTable.LoadSS(schema, filepath, context, DELIMITER,
snap.TBool(False))
crossName = prefix + "-" + dstName + "-" + srcName
Graph.AddCrossNet(srcName, dstName, crossName, False)
snap.LoadCrossNetToNet(Graph, srcName, dstName, crossName, crossnet, srcId,
dstId, snap.TStrV())
def load_chchse(path):
#load table
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("STITCH 1", snap.atStr))
schema.Add(snap.TStrTAttrPr("STITCH 2", snap.atStr))
schema.Add(snap.TStrTAttrPr("Polypharmacy Side Effect", snap.atStr))
schema.Add(snap.TStrTAttrPr("Side Effect Name", snap.atStr))
table = snap.TTable.LoadSS(schema, path, context, ",", snap.TBool(True))
#reformat CIDs and seIDs as strings
raw_cid1s = snap.TStrV()
cid1s = snap.TIntV()
table.ReadStrCol("STITCH 1", raw_cid1s)
for raw_cid in raw_cid1s:
cid = format_cid(raw_cid)
cid1s.Add(cid)
table.StoreIntCol("cid1", cid1s)
raw_cid2s = snap.TStrV()
cid2s = snap.TIntV()
table.ReadStrCol("STITCH 2", raw_cid2s)
for raw_cid in raw_cid2s:
cid = format_cid(raw_cid)
cid2s.Add(cid)
table.StoreIntCol("cid2", cid2s)
#save table as binary
#cache_path = "../cache/ChChSe-decagon_table.tsv"
#table.Save(snap.TFOut(cache_path))
#TEST: checks the number of side effect types
seVec = snap.TStrV()
table.ReadStrCol("Side Effect Name", seVec)
print len(set(list(seVec)))
return table
def ttableToTmmnet():
# load table
t0 = t()
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("srcID", snap.atInt))
schema.Add(snap.TStrTAttrPr("dstID", snap.atInt))
edge_table = snap.TTable.LoadSS(schema, NW.small, context, "\t",
snap.TBool(False))
t1 = reportTime(t0, "TTABLE")
# convert table to TMMNet
mmnet = snap.TMMNet.New()
edgeattrv = snap.TStrV()
edgeattrv.Add("edgeattr1")
CrossG = snap.LoadCrossNetToNet(mmnet, "Mode1", "Mode2", "Cross1",
edge_table, "srcID", "dstID", edgeattrv)
reportTime(t1, "convert TTABLE to CrossNet")
import snap
#tsv_file = "data-table1.txt"
tsv_file = "data/data-table.txt"
print("writing table")
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("srcID", snap.atInt))
schema.Add(snap.TStrTAttrPr("dstID", snap.atInt))
schema.Add(snap.TStrTAttrPr("distance", snap.atFlt))
#schema.Add(snap.TStrTAttrPr("distance", snap.atStr))
table = snap.TTable.LoadSS(schema, tsv_file, context, "\t", snap.TBool(False))
#FOut = snap.TFOut(table_file)
#table.Save(FOut)
#FOut.Flush()
tmp = table.BegRI()
while tmp < table.EndRI():
#print(str(tmp))
#print(tmp.GetFltAttr('distance'))
print(tmp.GetIntAttr('srcID'), tmp.GetIntAttr('dstID'), tmp.GetFltAttr('distance'))
#print(tmp.GetIntAttr('srcID'), tmp.GetIntAttr('dstID'), tmp.GetStrAttr('distance'))
tmp.Next()
context = snap.TTableContext()
t = testutils.Timer(ENABLE_TIMER)
# a) Compute authority scores
# Load posts
# >>> posts = ringo.load('posts.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("PostId", snap.atInt))
S.Add(snap.TStrTAttrPr("UserId", snap.atInt))
S.Add(snap.TStrTAttrPr("AcceptedAnswerId", snap.atInt))
S.Add(snap.TStrTAttrPr("CreationDate", snap.atStr))
posts = snap.TTable.LoadSS("t1", S, postsFile, context, '\t',
snap.TBool(False))
t.show("load posts", posts)
# Load tags
# >>> tags = ringo.load('tags.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("PostId", snap.atInt))
S.Add(snap.TStrTAttrPr("Tag", snap.atStr))
tags = snap.TTable.LoadSS("t2", S, tagsFile, context, '\t', snap.TBool(False))
t.show("load tags", tags)
# Select
# >>> tags.select('Tags = "python"')
tags.SelectAtomicStrConst("Tag", "python", snap.EQ)
t.show("select", tags)
# In[3]:
print time.ctime(), "computing pagerank ..."
PRankH = snap.TIntFltH()
snap.GetPageRankMP(net, PRankH, 0.85, 1e-4, 100)
t.show("prank", PRankH)
r.show("__PRankH__")
print time.ctime()
# In[4]:
print time.ctime(), "creating TTable with PageRank ..."
PRankT = snap.TTable(PRankH, "PaperID", "PageRankScore", context, snap.TBool(True))
t.show("prankt", PRankT)
r.show("__PRankT__")
print time.ctime()
# In[5]:
print time.ctime(), "Creating table after join ..."
PaperPRankJoinT = papers.Join("PaperID", PRankT, "PaperID")
t.show("paperprankjoint", PaperPRankJoinT)
r.show("__PaperPRankJoinT__")
print time.ctime()
# In[6]:
pass
context = snap.TTableContext()
t = testutils.Timer(ENABLE_TIMER)
# a) Compute authority scores
# Load posts
# >>> t1 = ringo.load('posts.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("PostId", snap.atInt))
S.Add(snap.TStrTAttrPr("UserId", snap.atInt))
S.Add(snap.TStrTAttrPr("AnswerId", snap.atInt))
t1 = snap.TTable.LoadSS("t1", S, os.path.join(srcdir, POSTS_FILE), context,
'\t', snap.TBool(False))
t.show("load posts", t1)
# Load tags
# >>> t2 = ringo.load('tags.tsv')
#S = snap.Schema()
#S.Add(snap.TStrTAttrPr("PostId", snap.atInt))
#S.Add(snap.TStrTAttrPr("Tag", snap.atStr))
#t2 = snap.TTable.LoadSS("t2", S, os.path.join(srcdir, TAGS_FILE), context, '\t', snap.TBool(False))
#t.show("load tags", t2)
# Select
# >>> t.select('Tag = "python"'')
#t2.SelectAtomicStrConst("Tag", "python", snap.EQ)
#t.show("select", t2)
if args.loglevel:
numeric_level = getattr(logging, args.loglevel.upper(), None)
logging.basicConfig(level=numeric_level)
context = snap.TTableContext()
# Construct the graph
logging.info('Building Multi-Modal Network')
Graph = snap.TMMNet.New()
# Loading Modes
try:
chemical_mode_file = config.get('Modes', 'Chemical')
cmschema = snap.Schema()
cmschema.Add(snap.TStrTAttrPr("ChemicalId", snap.atStr))
cmschema.Add(snap.TStrTAttrPr("datasetId", snap.atStr))
chemical_mode = snap.TTable.LoadSS(cmschema, chemical_mode_file, context, "\t", snap.TBool(False))
logging.info('Done loading Chemical Mode')
snap.LoadModeNetToNet(Graph, "Chemical", chemical_mode, "ChemicalId", snap.TStr64V())
except ConfigParser.NoOptionError:
logging.info('Skipping Chemical Mode')
try:
function_mode_file = config.get('Modes', 'Function')
fmschema = snap.Schema()
fmschema.Add(snap.TStrTAttrPr("FunctionId", snap.atStr))
fmschema.Add(snap.TStrTAttrPr("datasetId", snap.atStr))
function_mode = snap.TTable.LoadSS(fmschema, function_mode_file, context, "\t", snap.TBool(False))
logging.info('Done loading Function Mode')
snap.LoadModeNetToNet(Graph, "Function", function_mode, "FunctionId", snap.TStr64V())
except ConfigParser.NoOptionError:
logging.info('Skipping Function Mode')
print("G3 nodes", G3.GetNodes())
print("G3 edges", G3.GetEdges())
t = printtime(t, "saving the graph to binary")
FOut = snap.TFOut(binname)
G1.Save(FOut)
FOut.Flush()
t = printtime(t, "reading the graph from binary")
FIn = snap.TFIn(binname)
G4 = snap.TUNGraph.Load(FIn)
print("G4 nodes", G4.GetNodes())
print("G4 edges", G4.GetEdges())
t = printtime(t, "reading the graph as table")
context = snap.TTableContext()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("SrcID", snap.atInt))
schema.Add(snap.TStrTAttrPr("DstID", snap.atInt))
T1 = snap.TTable.LoadSS(schema, txtname, context, "\t", snap.TBool(False))
print("T1 rows", T1.GetNumRows())
t = printtime(t, "converting table to graph")
G5 = snap.ToGraph(snap.PUNGraph, T1, "SrcID", "DstID", snap.aaFirst)
print("G5 nodes", G5.GetNodes())
print("G5 edges", G5.GetEdges())
printtime(t, "done")
if not dstDir is None:
try:
os.makedirs(dstDir)
except OSError:
pass
context = snap.TTableContext()
t = testutils.Timer(ENABLE_TIMER)
# Load data
# >>> authors = ringo.load('authors.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("Key", snap.atStr))
S.Add(snap.TStrTAttrPr("Author", snap.atStr))
authors = snap.TTable.LoadSS("1", S, authorFile, context, '\t', snap.TBool(False))
t.show("load authors table", authors)
# >>> year = ringo.load('year.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("Key", snap.atStr))
S.Add(snap.TStrTAttrPr("Year", snap.atInt))
year = snap.TTable.LoadSS("2", S, yearFile, context, '\t', snap.TBool(False))
t.show("load year table", year)
# Select
# >>> year.select('Year >= 2005')
year.SelectAtomicIntConst("Year", 2005, snap.GTE)
t.show("select", year)
# Join
def get_commits_graph(path):
context = snap.TTableContext()
e_schema = snap.Schema()
e_schema.Add(snap.TStrTAttrPr("source", snap.atStr))
e_schema.Add(snap.TStrTAttrPr("target", snap.atStr))
e_schema.Add(snap.TStrTAttrPr("weight", snap.atStr))
n_schema = snap.Schema()
n_schema.Add(snap.TStrTAttrPr("id", snap.atStr))
n_schema.Add(snap.TStrTAttrPr("username", snap.atStr))
n_schema.Add(snap.TStrTAttrPr("size", snap.atStr))
edgetable = snap.TTable.LoadSS(e_schema, path + '{}_edges.csv'.format(pname), context, ",", snap.TBool(True))
nodetable = snap.TTable.LoadSS(n_schema, path + '{}_nodes.csv'.format(pname), context, ",", snap.TBool(True))
edgeattrv = snap.TStrV()
nodeattrv = snap.TStrV()
net = snap.ToNetwork(snap.PNEANet, edgetable, "source", "target", edgeattrv, nodetable, "id", nodeattrv, snap.aaFirst)
snap.DelSelfEdges(net)
snap.SaveEdgeList(net, 'temp/commits_temp_edgelist.csv')
Data = open('temp/commits_temp_edgelist.csv', 'r')
Graphtype = nx.Graph()
G = nx.parse_edgelist(Data, delimiter='\t', create_using=Graphtype, nodetype=int, data=(('weight', float),), comments='#')
return G
import testutils
if __name__ == '__main__':
if len(sys.argv) < 2:
print """Usage: """ + sys.argv[0] + """ <srcfile>
srcfile: posts.tsv file from StackOverflow dataset"""
sys.exit(1)
srcfile = sys.argv[1]
context = snap.TTableContext()
t = testutils.Timer()
r = testutils.Resource()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Id", snap.atInt))
schema.Add(snap.TStrTAttrPr("OwnerUserId", snap.atInt))
schema.Add(snap.TStrTAttrPr("AcceptedAnswerId", snap.atInt))
schema.Add(snap.TStrTAttrPr("CreationDate", snap.atInt))
schema.Add(snap.TStrTAttrPr("Score", snap.atInt))
table = snap.TTable.LoadSS("1", schema, srcfile, context, "\t", snap.TBool(False))
t.show("load text", table)
r.show("__loadtext__")
table = table.IsNextK("CreationDate", 1, "OwnerUserId")
t.show("isnextk", table)
r.show("__isnextk__")
# In[4]:
# Compute PageRank from references graph.
print time.ctime(), "Computing pagerank ..."
PRankH = snap.TIntFltH()
snap.GetPageRankMP(net, PRankH, 0.85, 1e-4, 100)
t.show("prank", PRankH)
r.show("__PRankH__")
print time.ctime()
# In[5]:
# Create a TTable with PageRank
print time.ctime(), "Creating TTable with PageRank ..."
PRankT = snap.TTable(PRankH, "PaperID", "PageRankScore", context,
snap.TBool(True))
t.show("prankt", PRankT)
r.show("__PRankT__")
print time.ctime()
# In[ ]:
# Moving InDegV into a HashTable to construct a TTable
print time.ctime(), "Creating TTable with InDegV ..."
InDegH = snap.TIntH()
for item in InDegV:
InDegH.AddDat(item.GetVal1(), item.GetVal2())
print time.ctime()
InDegT = snap.TTable(InDegH, "PaperID", "InDeg", context, snap.TBool(True))
print time.ctime()
try:
os.makedirs(dstDir)
except OSError:
pass
context = snap.TTableContext()
t = testutils.Timer(ENABLE_TIMER)
# Load data
# >>> authors = ringo.load('authors.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("Key", snap.atStr))
S.Add(snap.TStrTAttrPr("Author", snap.atStr))
authors = snap.TTable.LoadSS("1", S, authorFile, context, '\t',
snap.TBool(False))
t.show("load author table", authors)
# >>> year = ringo.load('year.tsv')
S = snap.Schema()
S.Add(snap.TStrTAttrPr("Key", snap.atStr))
S.Add(snap.TStrTAttrPr("Year", snap.atInt))
year = snap.TTable.LoadSS("2", S, yearFile, context, '\t', snap.TBool(False))
t.show("load year table", year)
# Select
# >>> year.select('Year >= 2005')
year.SelectAtomicIntConst("Year", 2005, snap.GTE)
t.show("select", year)
# Join
import sys
import os
import snap
#Load Tables
context = snap.TTableContext()
friends_file = "friends.txt"
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Student1ID", snap.atInt))
schema.Add(snap.TStrTAttrPr("Student2ID", snap.atInt))
friends_table = snap.TTable.LoadSS(schema, friends_file, context, "\t", snap.TBool(False))
enrollments_file = "enrollments.txt"
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("StudentID", snap.atInt))
schema.Add(snap.TStrTAttrPr("CourseID", snap.atInt))
enrollments_table = snap.TTable.LoadSS(schema, enrollments_file, context, "\t", snap.TBool(False))
advisors_file = "advisors.txt"
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("StudentID", snap.atInt))
schema.Add(snap.TStrTAttrPr("ProfID", snap.atInt))
advisors_table = snap.TTable.LoadSS(schema, advisors_file, context, "\t", snap.TBool(False))
prereqs_file = "prereqs.txt"
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("CourseID", snap.atInt))
schema.Add(snap.TStrTAttrPr("PrereqCourseID", snap.atInt))
prereqs_table = snap.TTable.LoadSS(schema, prereqs_file, context, "\t", snap.TBool(False))
def main(args):
if len(args) < 3:
print(get_usage())
sys.exit(1)
root = sys.argv[1]
mid_date = sys.argv[2]
mid_ticks = utils.date_to_ticks(mid_date)
file_cache = {
TCOLLAB: None,
TPULL: None,
TREPO: None,
TFOLLOW: None,
TWATCH: None,
TFORK: None
}
for file in os.listdir(root):
if file.endswith(".tsv"):
file_cache[file] = os.path.join(root, file)
print file_cache[file]
for key, val in file_cache.iteritems():
if val == None:
print("One of the required files not found.")
print(get_usage())
sys.exit(1)
t = testutils.Timer(ENABLE_TIMER)
context = snap.TTableContext()
S1 = snap.Schema()
S1.Add(snap.TStrTAttrPr("userid1", snap.atStr))
S1.Add(snap.TStrTAttrPr("userid2", snap.atStr))
S1.Add(snap.TStrTAttrPr("created_at", snap.atInt))
Tfollow = snap.TTable.LoadSS("Tfollow", S1, file_cache[TFOLLOW], context,
'\t', snap.TBool(False))
t.show("load follow")
S2 = snap.Schema()
S2.Add(snap.TStrTAttrPr("userid", snap.atStr))
S2.Add(snap.TStrTAttrPr("owner", snap.atStr))
S2.Add(snap.TStrTAttrPr("name", snap.atStr))
S2.Add(snap.TStrTAttrPr("created_at", snap.atInt))
Tcollab = snap.TTable.LoadSS("Tcollab", S2, file_cache[TCOLLAB], context,
'\t', snap.TBool(False))
t.show("load collab")
S3 = snap.Schema()
S3.Add(snap.TStrTAttrPr("userid", snap.atStr))
S3.Add(snap.TStrTAttrPr("owner", snap.atStr))
S3.Add(snap.TStrTAttrPr("name", snap.atStr))
S3.Add(snap.TStrTAttrPr("pullid", snap.atInt))
S3.Add(snap.TStrTAttrPr("status", snap.atStr))
S3.Add(snap.TStrTAttrPr("created_at", snap.atInt))
Tpull = snap.TTable.LoadSS("Tpull", S3, file_cache[TPULL], context, '\t',
snap.TBool(False))
t.show("load pull")
# If (u,v) collaborated on the same repository - determined by the owner, name pair,
# are added as collaborators.
#TODO Better column renaming
V = snap.TStrV()
V.Add("created_at")
Tcollab.Order(V, "", snap.TBool(False), snap.TBool(True))
V.Clr()
V.Add("owner")
V.Add("name")
V.Add("userid")
Tcollab.Group(V, "UserRepoId")
V.Clr()
V.Add("UserRepoId")
Tcollab.Unique(V)
Tcollab_merge = Tcollab.SelfJoin("owner")
Tcollab_merge.SelectAtomic("Tcollab_1.name", "Tcollab_2.name", snap.EQ)
Tcollab_merge.SelectAtomic("Tcollab_1.userid", "Tcollab_2.userid",
snap.NEQ)
# BUGBUG - Commenting this line will mean created_at is not present in Tcollab_merge.
# However, the ProjectInPlace will not complain and silently exclude created_at from the
# result. This leads to the Index:-1 error in SelectAtomicIntConst on created_at later in the code.
Tcollab_merge.ColMin("Tcollab_1.created_at", "Tcollab_2.created_at",
"created_at")
V = snap.TStrV()
V.Add("Tcollab_1.userid")
V.Add("Tcollab_2.userid")
V.Add("created_at")
Tcollab_merge.ProjectInPlace(V)
Tcollab_merge.Rename("Tcollab_1.userid", "userid1")
Tcollab_merge.Rename("Tcollab_2.userid", "userid2")
t.show("merge collab", Tcollab_merge)
#testutils.dump(Tcollab_merge, 50)
# If (u,v) worked on the same pull request on the same repository, they are added
# as (soft) collaborators.
V = snap.TStrV()
V.Add("created_at")
Tpull.Order(V, "", snap.TBool(False), snap.TBool(True))
V.Clr()
V.Add("owner")
V.Add("name")
V.Add("userid")
Tpull.Group(V, "UserRepoId")
V.Clr()
V.Add("UserRepoId")
Tpull.Unique(V)
Tpull_merge = Tpull.SelfJoin("owner")
Tpull_merge.SelectAtomic("Tpull_1.name", "Tpull_2.name", snap.EQ)
Tpull_merge.SelectAtomic("Tpull_1.pullid", "Tpull_2.pullid", snap.EQ)
Tpull_merge.SelectAtomic("Tpull_1.userid", "Tpull_2.userid", snap.NEQ)
Tpull_merge.ColMin("Tpull_1.created_at", "Tpull_2.created_at",
"created_at")
V = snap.TStrV()
V.Add("Tpull_1.userid")
V.Add("Tpull_2.userid")
V.Add("created_at")
Tpull_merge.ProjectInPlace(V)
Tpull_merge.Rename("Tpull_1.userid", "userid1")
Tpull_merge.Rename("Tpull_2.userid", "userid2")
t.show("merge pull", Tpull_merge)
# BUGBUG: UnionAll is returning unexpected result at this point
#Tmerge = Tcollab_merge.UnionAll(Tpull_merge, "Tmerge")
Tmerge = Tpull_merge
# Select the base and delta tables from the merged table.
Tbase = snap.TTable.New(Tmerge, "Base")
Tdelta = snap.TTable.New(Tmerge, "Delta")
Tbase.SelectAtomicIntConst("created_at", mid_ticks, snap.LTE)
Tdelta.SelectAtomicIntConst("created_at", mid_ticks, snap.GTE)
#TODO: Union Tbase with collab and pull to include (userid, owner) edge
t.show("collab union")
# Convert base table to base graph
Gbase = snap.ToNetwork(snap.PNEANet, Tbase, "userid1", "userid2",
snap.aaFirst)
Gdelta = snap.ToNetwork(snap.PNEANet, Tdelta, "userid1", "userid2",
snap.aaFirst)
t.show("base graph", Gbase)
t.show("delta graph", Gdelta)
NITERS = 20
total_preck = 0
print("Userid\tPrec@%d\tAverage Index" % (N_TOP_RECOS))
# Random walk with restarts
# BUGBUG: Returns the same id everytime
# userid = Gbase.GetRndNId()
for i in range(NITERS):
# Randomly choose a starting node
userid = random.choice([node.GetId() for node in Gbase.Nodes()])
user = Gbase.GetNI(userid)
# Perform random walk with restarts on base graph
HT = snap.TIntFltH()
snap.GetRndWalkRestart_PNEANet(Gbase, ALPHA, userid, HT)
HT.SortByDat(False)
j = 0
cnt = 0
preck = 0
average_index = -1
# Calculate precision
while cnt < N_TOP_RECOS and j < HT.Len():
recoid = HT.GetKey(j)
pagerank = HT.GetDat(recoid)
#print recoid, pagerank
if recoid != userid:
# If the edge is not in base graph but is present in delta graph, we made an accurate prediction.
if not Gbase.IsEdge(userid, recoid) and Gdelta.IsNode(
userid) and Gdelta.IsNode(recoid) and (Gdelta.IsEdge(
userid, recoid) or Gdelta.IsEdge(recoid, userid)):
preck += 1
cnt += 1
j += 1
# Calculate average index
try:
node = Gdelta.GetNI(userid)
edges = [nid for nid in node.GetOutEdges()
] + [nid for nid in node.GetInEdges()]
#print edges
#print([HT.GetKeyId(nid) for nid in edges])
index = 0
for nid in edges:
index += HT.GetKeyId(nid)
average_index = index / len(edges)
except:
# Node not present in delta graph implies no new edges formed
pass
total_preck += preck
print("%d\t%d\t%f" % (userid, preck, average_index))
#rank = snap.TTable.New("Rank", HT, "User", PAGE_RANK_ATTRIBUTE, context, snap.TBool(True))
print("Average Precision@%d = %f" %
(N_TOP_RECOS, total_preck / float(NITERS)))
import snap
graphfilename = "C:\Python27\HW1\wiki-vote.txt"
schema = snap.Schema()
context = snap.TTableContext()
schema.Add(snap.TStrTAttrPr("srcID", snap.atStr))
schema.Add(snap.TStrTAttrPr("dstID", snap.atStr))
sample_table = snap.TTable.LoadSS(schema, graphfilename, context, "\t",
snap.TBool(False))
# graph will be an object of type snap.PNGraph
graph = snap.ToGraph(snap.PNGraph, sample_table, "srcID", "dstID",
snap.aaFirst)
#no of nodes
Count = snap.CntNonZNodes(graph)
print "Count of nodes with degree greater than 0 is %d" % Count
#no of edges
Count = snap.CntOutDegNodes(graph, 0)
print "Count of nodes with out-degree 0 is %d" % Count
#no of nodes with zero in-degree
Count = snap.CntInDegNodes(graph, 0)
print "Count of nodes with in-degree 0 is %d" % Count
#no of directed edges
Count = snap.CntUniqDirEdges(graph)
print "Count of directed edges is %d" % Count
#no of undirected edges
Count = snap.CntUniqUndirEdges(graph)
print "Count of undirected edges is %d" % Count
#no of self edges
Count = snap.CntSelfEdges(graph)
print "Count of self edges is %d" % Count
dstfile = sys.argv[2]
context = snap.TTableContext()
t = testutils.Timer()
r = testutils.Resource()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Id", snap.atInt))
schema.Add(snap.TStrTAttrPr("OwnerUserId", snap.atInt))
schema.Add(snap.TStrTAttrPr("AcceptedAnswerId", snap.atInt))
schema.Add(snap.TStrTAttrPr("CreationDate", snap.atInt))
schema.Add(snap.TStrTAttrPr("Score", snap.atInt))
schema.Add(snap.TStrTAttrPr("Tag", snap.atStr))
table = snap.TTable.LoadSS("1", schema, srcfile, context, "\t",
snap.TBool(False))
t.show("load posts text", table)
r.show("__loadpoststext__")
questions = snap.TTable.New("2", table.GetSchema(), context)
table.SelectAtomicStrConst("Tag", "python", snap.EQ, questions)
t.show("select tag = 'python'", questions)
r.show("__selecttagpython__")
questions.SelectAtomicIntConst("AcceptedAnswerId", 0, snap.NEQ)
t.show("select questions", questions)
r.show("__selectquestions__")
table.SelectAtomicIntConst("AcceptedAnswerId", 0, snap.EQ)
t.show("select answers", table)
r.show("__selectanswers__")
if __name__ == '__main__':
if len(sys.argv) < 3:
print "Usage: " + sys.argv[0] + " <srcfile1> <srcfile2>"
sys.exit(1)
srcfile1 = sys.argv[1]
srcfile2 = sys.argv[2]
context = snap.TTableContext()
t = testutils.Timer()
r = testutils.Resource()
FIn = snap.TFIn(srcfile1)
t1 = snap.TTable.Load(FIn, context)
t.show("load bin", t1)
r.show("__loadbin__")
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Index", snap.atInt))
t2 = snap.TTable.LoadSS(schema, srcfile2, context, "\t", snap.TBool(False))
t.show("load text", t2)
r.show("__loadtext__")
t3 = t1.Join("Src", t2, "Index")
t.show("join", t3)
r.show("__join__")
postsfile = sys.argv[1]
tagsfile = sys.argv[2]
context = snap.TTableContext()
t = testutils.Timer()
r = testutils.Resource()
schema = snap.Schema()
schema.Add(snap.TStrTAttrPr("Id", snap.atInt))
schema.Add(snap.TStrTAttrPr("OwnerUserId", snap.atInt))
schema.Add(snap.TStrTAttrPr("AcceptedAnswerId", snap.atInt))
schema.Add(snap.TStrTAttrPr("CreationDate", snap.atInt))
schema.Add(snap.TStrTAttrPr("Score", snap.atInt))
posts = snap.TTable.LoadSS(schema, postsfile, context, "\t",
snap.TBool(False))
t.show("load posts text", posts)
r.show("__loadpoststext__")
S = snap.Schema()
S.Add(snap.TStrTAttrPr("PostId", snap.atInt))
S.Add(snap.TStrTAttrPr("Tag", snap.atStr))
tags = snap.TTable.LoadSS(S, tagsfile, context, '\t', snap.TBool(False))
t.show("load tags text", tags)
r.show("__loadtagstext__")
table = posts.Join("Id", tags, "PostId")
t.show("join", table)
r.show("__join__")
table = table.Join("AcceptedAnswerId", posts, "Id")
