NOTE: This page contains all the examples presented during the lectures, as well as all the assigned projects. Click here to go back to the main page with the course information and schedule.
alice@bu.edu
and bob@bu.edu
, the unique identifier for their team will be alice_bob
, where, in cases with two members, the two usernames are in ascending alphabetical order and separated by an underscore. For a onemember team, it is simply the BU login name of the sole member (e.g., alice
).https://github.com/DataMechanics/course2017sprprojzero
, adding a single folder named using the group identifier (alice
or alice_bob
) that contains a single ASCII text file members.txt
. Each team member should commit a line to that text file specifying a mapping from their GitHub username and their BU username. For example, if Alice and Bob have the GitHub usernames alicegh
and bobgh
, respectively, then the file should look as follows:
alicegh:alice
bobgh:bob
members.txt
file you add above).
import urllib.request
import json
url = "https://data.cityofboston.gov/resource/awu8dc52.json?$limit=10"
response = urllib.request.urlopen(url).read().decode("utf8")
print(json.dumps(json.loads(response), sort_keys=True, indent=2))
Connection reset by peer
error, you may want to use a Python library for the Socrata Open Data API (sodapy) instead.
import json
import sodapy
client = sodapy.Socrata("data.cityofboston.gov", None)
response = client.get("awu8dc52", limit=10)
print(json.dumps(response, sort_keys=True, indent=2))
def union(R, S):
return R + S
def difference(R, S):
return [t for t in R if t not in S]
def intersect(R, S):
return [t for t in R if t in S]
def project(R, p):
return [p(t) for t in R]
def select(R, s):
return [t for t in R if s(t)]
def product(R, S):
return [(t,u) for t in R for u in S]
def aggregate(R, f):
keys = {r[0] for r in R}
return [(key, f([v for (k,v) in R if k == key])) for key in keys]
select
can be used with a predicate to filter a data set.
>>> def red(t): return t == 'tomato'
>>> select(['banana', 'tomato'], red)
['tomato']
>>> X = [('Alice', 22), ('Bob', 19)]
>>> Y = [('Alice', 'F'), ('Bob', 'M')]
>>> product(X,Y)
[(('Alice', 'F'), ('Alice', 22)), (('Alice', 'F'), ('Bob', 19)), (('Bob', 'M'), ('Alice', 22)), (('Bob', 'M'), ('Bob', 19))]
>>> select(product(X,Y), lambda t: t[0][0] == t[1][0])
[(('Alice', 'F'), ('Alice', 22)), (('Bob', 'M'), ('Bob', 19))]
>>> project(select(product(X,Y), lambda t: t[0][0] == t[1][0]), lambda t: (t[0][0], t[0][1], t[1][1]))
[('Alice', 'F', 22), ('Bob', 'M', 19)]
>>> X = [('Alice', 'F', 22), ('Bob', 'M', 19), ('Carl', 'M', 25), ('Eve', 'F', 27)]
>>> project(X, lambda t: (t[1], t[2]))
[('F', 22), ('M', 19), ('M', 25), ('F', 27)]
>>> aggregate(project(X, lambda t: (t[1], t[2])), sum)
[('F', 49), ('M', 44)]
aggregate
function for a particular key.
>>> Y = project(X, lambda t: (t[1], t[2]))
>>> keys = {t[0] for t in Y}
>>> keys
{'F', 'M'}
>>> [v for (k,v) in Y if k == 'F']
[22, 27]
>>> sum([v for (k,v) in Y if k == 'F'])
49
>>> ('F', sum([v for (k,v) in Y if k == 'F']))
('F', 49)
def map(f, R):
return [t for (k,v) in R for t in f(k,v)]
def reduce(f, R):
keys = {k for (k,v) in R}
return [f(k1, [v for (k2,v) in R if k1 == k2]) for k1 in keys]
map
operation applies some function f
to every keyvalue tuple and produces zero or more new keyvalue tuples. A reduce
operation collects all values under the same key and performs an aggregate operation f
on those values. Notice that the operation can be applied to any subset of the tuples in any order, so it is often necessary to use an operation that is associated and commutative.
R = [('Alice', 23), ('Bob', 19), ('Carl', 22)]
X = map(lambda k,v: [((k,v), (k,v))] if v > 20 else [], R) # Selection.
Y = reduce(lambda k,vs: k, X) # Keep same tuples (use tuples as unique keys).
R = [('Alice', ('F', 23)), ('Bob', ('M', 19)), ('Carl', ('M', 22))]
X = map(lambda k,v: [(v[0], v[1])], R) # Projection keeps only gender and age.
Y = reduce(lambda k,vs: (k, sum(vs)), X) # Aggregates ages by gender.
R = [('Alice', 23), ('Bob', 19), ('Carl', 22)]
S = [('Alice', 'F'), ('Bob', 'M'), ('Carl', 'M')]
X = map(lambda k,v: [(k, ('Age', v))], R)\
+ map(lambda k,v: [(k, ('Gender', v))], S)
Y = reduce(\
lambda k,vs:\
(k,(vs[0][1], vs[1][1]) if vs[0][0] == 'Age' else (vs[1][1],vs[0][1])),\
X\
)
INPUT = [('Alice', ('F', 19)),\
('Bob', ('M', 23)),\
('Carl', ('M', 20)),\
('Eve', ('F', 27))]
TEMP = map(lambda k,v: [(v[0], v[1])], INPUT)
OUTPUT = reduce(lambda k,vs: (k, sum(vs)), TEMP)
db.INPUT.insert({_id:"Alice", gender:"F", age:19});
db.INPUT.insert({_id:"Bob", gender:"M", age:23});
db.INPUT.insert({_id:"Carl", gender:"M", age:20});
db.INPUT.insert({_id:"Eve", gender:"F", age:27});
db.INPUT.mapReduce(
function() {
emit(this.gender, {age:this.age});
},
function(k, vs) {
var total = 0;
for (var i = 0; i < vs.length; i++)
total += vs[i].age;
return {gender:k, age:total};
},
{out: "OUTPUT"}
);
NCA = [('Alice', 'Boston', 23), ('Bob', 'Boston', 19), ('Carl', 'Seattle', 25)]
CA = [(c,a) for (n,c,a) in NCA]
MIN = aggregate(CA, min)
MIN_NEG = [(c,1*a) for (c,a) in MIN]
MAX = aggregate(CA, max)
RESULT = aggregate(union(MIN_NEG, MAX), sum)
('Alice', ('Boston', 23))
, in the mapping stage we might estimate the range as ('Boston', (23, 23, 0))
where the second and third entries are the minimum and maximum "known so far" given the limited information (a single data point). Then, in the reduce stage, we would combine these estimates.
NCA = [('Alice', ('Boston', 23)), ('Bob', ('Boston', 19)), ('Carl', ('Seattle', 25))]
I = map(lambda k, v: [(v[0], (v[1], v[1], 0))], NCA)
def reducer(k, vs):
age_lo = min([l for (l,h,r) in vs])
age_hi = max([h for (l,h,r) in vs])
age_ran = age_hi  age_lo
return (k, (age_lo, age_hi, age_ran))
RESULT = reduce(reducer, I)
D
containing some voting results broken down by voter, state where the voter participated in voting, and the candidate they chose:
R = sum([1 for (person, state, candidate) in D if state == "Massachusetts" and candidate == "Trump"])
D = [('Commonwealth Ave./Mass Ave.', '20161102', '11:34:00', 3), ...]
M = project(D, lambda i, date, time, cars: [(i, cars)])
R = aggregate(M, max)
H = [(i,d,t) for ((i,m), (j,d,t,c)) in product(R, D) if i==j and m==c]
def dist(p, q):
(x1,y1) = p
(x2,y2) = q
return (x1x2)**2 + (y1y2)**2
def plus(args):
p = [0,0]
for (x,y) in args:
p[0] += x
p[1] += y
return tuple(p)
def scale(p, c):
(x,y) = p
return (x/c, y/c)
M = [(13,1), (2,12)]
P = [(1,2),(4,5),(1,3),(10,12),(13,14),(13,9),(11,11)]
OLD = []
while OLD != M:
OLD = M
MPD = [(m, p, dist(m,p)) for (m, p) in product(M, P)]
PDs = [(p, dist(m,p)) for (m, p, d) in MPD]
PD = aggregate(PDs, min)
MP = [(m, p) for ((m,p,d), (p2,d2)) in product(MPD, PD) if p==p2 and d==d2]
MT = aggregate(MP, plus)
M1 = [(m, 1) for ((m,p,d), (p2,d2)) in product(MPD, PD) if p==p2 and d==d2]
MC = aggregate(M1, sum)
M = [scale(t,c) for ((m,t),(m2,c)) in product(MT, MC) if m == m2]
print(sorted(M))
[(m, p) for ((m,p,d), (p2,d2)) in product(MPD, PD) if p==p2 and d==d2]
first filters product(MPD, PD)
using a selection criteria if p==p2 and d==d2
and then performs a projection from tuples of the form ((m,p,d), (p2,d2))
to tuples of the form (m, p)
to obtain the result.
N = ['a','b','c','d','e','f']
E = [('a','b'),('b','c'),('a','c'),('c','d'),('d','e'),('e','f'),('b','f')]
oo = float('inf') # This represents infinite distance.
P = product(N,N)
I = [((x,y),oo if x != y else 0) for (x,y) in P] # Zero distance to self, infinite distance to others.
D = [((x,y),1) for (x,y) in E] # Edgeconnected nodes are one apart.
OUTPUT = aggregate(union(I,D), min)
STEP = []
while sorted(STEP) != sorted(OUTPUT):
STEP = OUTPUT
P = product(STEP, STEP) # All pairs of edges.
NEW = union(STEP,[((x,v),k+m) for (((x,y),k),((u,v),m)) in P if u == y]) # Add distances of connected edge pairs.
OUTPUT = aggregate(NEW, min) # Keep only shortest nodenode distance entries.
SHORTEST = OUTPUT
db.system.js.save({ _id:"dist" , value:function(u, v) {
return Math.pow(u.x  v.x, 2) + Math.pow(u.y  v.y, 2);
}});
function flatten(A) {
db[A].find().forEach(function(a) { db[A].update({_id: a._id}, a.value); });
}
function prod(A, B, AB) {
db[AB].remove({});
db.createCollection(AB);
db[A].find().forEach(function(a) {
db[B].find().forEach(function(b) {
db[AB].insert({left:a, right:b});
});
});
}
function union(A, B, AB) {
db[AB].remove({});
db.createCollection(AB);
db[A].find().forEach(function(a) {
db[AB].insert(a);
});
db[B].find().forEach(function(b) {
db[AB].insert(b);
});
}
function hash_means(M, HASH) {
db[M].mapReduce(
function() { emit("hash", {hash: this.x + this.y}); },
function(k, vs) {
var hash = 0;
vs.forEach(function(v) {
hash += v.hash;
});
return {hash: hash};
},
{out: HASH}
);
}
// We'll only perform a single product operation. Using mapreduce, we can perform
// argmax and argmin more easily. We can also use mapreduce to compare progress.
db.M.remove({});
db.M.insert([{x:13,y:1},{x:2,y:12}]);
db.P.remove({});
db.P.insert([{x:1,y:2},{x:4,y:5},{x:1,y:3},{x:10,y:12},{x:13,y:14},{x:13,y:9},{x:11,y:11}]);
var iterations = 0;
do {
// Compute an initial hash of the means in order to have a baseline
// against which to compare when deciding whether to loop again.
hash_means("M", "HASHOLD");
prod("M", "P", "MP");
// For each point, find the distance to the shortest mean. The output after
// flattening has entries of the form {_id:{x:?, y:?}, m:{x:?, y:?}, d:?}
// where the identifier is the point.
db.MPs.remove({});
db.MP.mapReduce(
function() {
var point = {x:this.right.x, y:this.right.y};
var mean = {x:this.left.x, y:this.left.y};
emit(point, {m:mean, d:dist(point, mean)});
},
function(point, vs) {
// Each entry in vs is of the form {m:{x:?, y:?}, d:?}.
// We return the one that is closest to point.
var j = 0;
vs.forEach(function(v, i) {
if (v.d < vs[j].d)
j = i;
});
return vs[j];
},
{out: "MPs"}
);
flatten("MPs");
// For each mean (i.e., key), compute the average of all the points that were
// "assigned" to that mean (because it was the closest mean to that point).
db.MPs.mapReduce(
function() {
// The key is the mean and the value is the point together with its counter.
var point_with_count = {x:this._id.x, y:this._id.y, c:1};
var mean = this.m;
emit(mean, point_with_count);
},
function(key, vs) {
// Remember that the reduce operations will be applied to the values for each key
// in some arbitrary order, so our aggregation operation must be commutative (in
// this case, it is vector addition).
var x = 0, y = 0, c = 0;
vs.forEach(function(v, i) {
x += v.x;
y += v.y;
c += v.c;
});
return {x:x, y:y, c:c};
},
{ finalize: function(k, v) { return {x: v.x/v.c, y: v.y/v.c}; },
out: "M"
}
);
flatten("M");
// Compute the hash of the new set of means.
hash_means("M", "HASHNEW");
// Extract the two hashes in order to compare them in the loop condition.
var hashold = db.HASHOLD.find({}).limit(1).toArray()[0].value.hash;
var hashnew = db.HASHNEW.find({}).limit(1).toArray()[0].value.hash;
print(hashold);
print(hashnew);
print(iterations);
iterations++;
} while (hashold != hashnew);
.updateMany()
to distribute the means to all the points at the beginning of each iteration. This leads to a much more concise (and, for a small number of means, efficient) implementation of the algorithm than what is presented in a previous example. In particular, it is no longer necessary to encode a production operation within MongoDB.
db.system.js.save({ _id:"dist" , value:function(u, v) {
return Math.pow(u.x  v.x, 2) + Math.pow(u.y  v.y, 2);
}});
db.P.insert([{x:1,y:2},{x:4,y:5},{x:1,y:3},{x:10,y:12},{x:13,y:14},{x:13,y:9},{x:11,y:11}]);
var means = [{x:13,y:1}, {x:2,y:12}];
do {
db.P.updateMany({}, {$set: {means: means}}); // Add a field to every object.
db.P.mapReduce(
function() {
var closest = this.means[0];
for (var i = 0; i < this.means.length; i++)
if (dist(this.means[i], this) < dist(closest, this))
closest = this.means[i];
emit(closest, {x:this.x, y:this.y, c:1});
},
function(key, vs) {
var x = 0, y = 0, c = 0;
vs.forEach(function(v, i) {
x += v.x;
y += v.y;
c += v.c;
});
return {x:x, y:y, c:c};
},
{ finalize: function(k, v) { return {x: v.x/v.c, y: v.y/v.c}; },
out: "M"
}
);
means = db.M.find().toArray().map(function(r) { return {x:r.value.x, y:r.value.y}; });
printjson(means);
} while (true);
import pymongo
import bson.code
client = pymongo.MongoClient()
db = client.local
db.system.js.save({'_id':'dist', 'value': bson.code.Code("""
function(u, v) {
return Math.pow(u.x  v.x, 2) + Math.pow(u.y  v.y, 2);
}
""")})
db.P.insert_many([{'x':1,'y':2},{'x':4,'y':5},{'x':1,'y':3},{'x':10,'y':12},\
{'x':13,'y':14},{'x':13,'y':9},{'x':11,'y':11}])
means = [{'x':13,'y':1}, {'x':2,'y':12}]
while True:
db.P.update_many({}, {'$set': {'means': means}})
mapper = bson.code.Code("""
function() {
var closest = this.means[0];
for (var i = 0; i < this.means.length; i++)
if (dist(this.means[i], this) < dist(closest, this))
closest = this.means[i];
emit(closest, {x:this.x, y:this.y, c:1});
}
""")
reducer = bson.code.Code("""
function(key, vs) {
var x = 0, y = 0, c = 0;
vs.forEach(function(v, i) {
x += v.x;
y += v.y;
c += v.c;
});
return {x:x, y:y, c:c};
}
""")
finalizer = bson.code.Code("""
function(k, v) { return {x: v.x/v.c, y: v.y/v.c}; }
""")
db.P.map_reduce(mapper, reducer, "M", finalize = finalizer)
means = [{'x':t['value']['x'], 'y':t['value']['y']} for t in db.M.find()]
print(means)
 = 
 
 = 

 ↦ 
 ↦ 

 ↦ 
 
 ↦ 

 = 
 
 = 

data set transformations

f
).
from itertools import combinations, chain
def powerset(iterable):
"powerset([1,2,3]) > () (1,) (2,) (3,) (1,2) (1,3) (2,3) (1,2,3)"
s = list(iterable)
return chain.from_iterable(combinations(s, r) for r in range(len(s)+1))
def general_prov(f, X, y):
for Y in reversed(powerset(X)): # From largest to smallest subset.
if list(f(list(Y))) == [y]:
return Y
def context_free_prov(f, X, y):
# Build the partitions of the input data set.
partitions = []
for (x_key, x_val) in X:
found = False
for i in range(0,len(partitions)):
if len(f(partitions[i] + [(x_key, x_val)])) == 1:
partitions[i].append((x_key, x_val))
found = True
break
# Create a new partition if adding to any other
# partition increases the size of the output data set.
if found == False:
partitions.append([(x_key, x_val)])
# Find the corresponding partition.
for partition in partitions:
if y in f(partition):
return partition
def key_preserving_prov(f, X, y):
keymap = {}
# Build up the map from input data set
# keys to output data set keys.
for (x_key, x_val) in X:
(y_key, y_val) = f([(x_key, x_val)])[0]
keymap[x_key] = y_key
(y_key, y_val) = y
# Collect all the tuples that contribute
# to the target result.
pre_image = set()
for (x_key, x_val) in X:
if keymap[x_key] == y_key:
pre_image.add((x_key, x_val))
return pre_image
prov
Python package to programmatically assemble a course granularity provenance record that conforms to the PROV standard and describes a particular execution of this script.
doc = prov.model.ProvDocument()
doc.add_namespace('alg', 'http://datamechanics.io/algorithm/alice_bob/') # The scripts in / format.
doc.add_namespace('dat', 'http://datamechanics.io/data/alice_bob/') # The data sets in / format.
doc.add_namespace('ont', 'http://datamechanics.io/ontology#')
doc.add_namespace('log', 'http://datamechanics.io/log#') # The event log.
doc.add_namespace('bdp', 'https://data.cityofboston.gov/resource/')
this_script = doc.agent('alg:example', {prov.model.PROV_TYPE:prov.model.PROV['SoftwareAgent'], 'ont:Extension':'py'})
resource = doc.entity('bdp:wc8wnujj',
{'prov:label':'311, Service Requests',
prov.model.PROV_TYPE:'ont:DataResource', 'ont:Extension':'json'}
)
this_run = doc.activity(
'log:a'+str(uuid.uuid4()), startTime, endTime,
{prov.model.PROV_TYPE:'ont:Retrieval', 'ont:Query':'?type=Animal+Found&$select=type,latitude,longitude,OPEN_DT'}
)
doc.wasAssociatedWith(this_run, this_script)
doc.used(this_run, resource, startTime)
found = doc.entity('dat:found', {prov.model.PROV_LABEL:'Animals Found', prov.model.PROV_TYPE:'ont:DataSet'})
doc.wasAttributedTo(found, this_script)
doc.wasGeneratedBy(found, this_run, endTime)
doc.wasDerivedFrom(found, resource, this_run, this_run, this_run)
doc.serialize()
.alice_bob
(in accordance with the requirements specified in Project #0).https://github.com/DataMechanics/course2017sprproj
. Note that we may commit and push a few additional fixes or updates to this repository before the deadline, so check for updates and pull them into your fork on a regular basis. Set up a MongoDB and Python environment as necessary for the project (including the installation of all dependencies). You should be able to run the setup.js
script to prepare the repository, and then to start your MongoDB server with authentication enabled and run the alice_bob/example.py
example script.alice_bob
within the toplevel directory of the project. All the code constituting your submission, including all of your scripts and algorithm files (i.e., for retrieval of data and for transforming data already within the repository), should be placed within this folder. Do not place data files within this folder, or submit any data sets or data files via GitHub.dml.Algorithm
base class (such that the class name matches exactly the filename). Consult alice_bob/example.py
for a working example script and algorithm.
class example(dml.Algorithm):
contributor = 'alice_bob'
reads = []
writes = ['alice_bob.lost', 'alice_bob.found']
@staticmethod
def execute(trial = False):
...
@staticmethod
def provenance(doc = prov.model.ProvDocument(), startTime = None, endTime = None):
...
README.md
file within your directory (along with any documentation you may write in that file).dml.Algorithm
subclasses and defining their reads
and writes
fields, as well as their execute
methods). Any authentication credentials your scripts use should be included in the file auth.json
(such that the file conforms to the auth.schema.json
schema). All your scripts should retrieve the credential information they need from your copy of the file by using the existing dml
functionality for doing so.auth.json
file and do not include hardcoded authentication credentials in your code. We already added it to the .gitignore
file to ensure you do not accidentially submit the credentials file. The course staff will use their own authentication credentials when running your code. Your README.md
file should list any idiosyncratic details associated with the services and/or credentials needed to run your scripts.
README.md
file how to obtain and run those tools).provenance()
method). Each algorithm should generate a single provenance document when its provenance()
method is invoked.
 = 

 

def argmax(X, f):
Y = [f(x) for x in X] # Projection.
y_max = aggregate(Y, max)
XF = [(x, f(x)) for x in X] # Projection.
xs = [x for (x,y) in XF if y == y_max] # Selection.
return xs[0]

import z3
(x1,x2,x3,x4,x5,x6,x7) = [z3.Real('x'+str(i)) for i in range(1,8)]
S = z3.Solver()
# Only allow nonnegative flows.
for x in (x1,x2,x3,x4,x5,x6,x7):
S.add(x >= 0)
# Edge capacity constraints.
S.add(x2 <= 7, x3 <= 8, x4 <= 6)
S.add(x5 <= 3, x6 <= 4, x7 <= 5)
# Constraints derived from graph topology.
S.add(x1 <= x2+x3, x2 <= x4+x5, x3+x4 <= x6, x5+x6 <= x7)
S.add(x1 > 0) # We want a positive flow.
print(S.check())
print(S.model())
flow = 0
for i in range(5, 1, 1):
S.push()
S.add(x1 >= (2**i + flow))
if str(S.check()) != 'unsat':
flow += 2**i
S.pop()
S.add(x1 >= flow)
print(S.model())
def dot(xs, ys):
return sum([x*y for (x,y) in zip(xs, ys)])
x = [x1,x2,x3,x4,x5,x6,x7]
M = [
[ 0,1, 0, 0, 0, 0, 0],
[ 0, 0,1, 0, 0, 0, 0],
[ 0, 0, 0,1, 0, 0, 0],
[ 0, 0, 0, 0,1, 0, 0],
[ 0, 0, 0, 0, 0,1, 0],
[ 0, 0, 0, 0, 0, 0,1],
[ 1, 0, 0, 0, 0, 0, 0],
[ 0, 1, 0, 0, 0, 0, 0],
[ 0, 0, 1, 0, 0, 0, 0],
[ 0, 0, 0, 1, 0, 0, 0],
[ 0, 0, 0, 0, 1, 0, 0],
[ 0, 0, 0, 0, 0, 1, 0],
[ 0, 0, 0, 0, 0, 0, 1],
[1, 1, 1, 0, 0, 0, 0],
[ 0,1, 0, 1, 1, 0, 0],
[ 0, 0,1,1, 0, 1, 0],
[ 0, 0, 0, 0,1,1, 1]
]
b = [7,8,6,3,4,5,
0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0]
S = z3.Solver()
for i in range(len(M)):
S.add(b[i] <= dot(M[i], x))
print(S.check())
print(S.model())
from scipy.optimize import linprog
M = [
[ 1,1,1, 0, 0, 0, 0],
[ 0, 1, 0,1,1, 0, 0],
[ 0, 0, 1, 1, 0,1, 0],
[ 0, 0, 0, 0, 1, 1,1],
]
b = [0, 0, 0, 0]
c = [1, 0, 0, 0, 0, 0, 0]
bounds = [(0, None), (0, 7), (0, 8), (0, 6), (0, 3), (0, 4), (0, 5)]
result = linprog(c, A_ub = M, b_ub = b, bounds=bounds, options={"disp": True})
print(result)
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⋮  
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from random import shuffle
from math import sqrt
data = [(18, 28), (24, 18), (27, 31), (14, 15), (46, 23),
(36, 19), (27, 10), (34, 25), (19, 15), (13, 13),
(4, 2), (17, 20), (28, 12), (36, 11), (26, 14),
(19, 19), (24, 13), (25, 6), (20, 8), (17, 22),
(18, 8), (25, 12), (28, 27), (31, 28), (35, 22),
(17, 8), (19, 19), (23, 23), (22, 11)]
x = [xi for (xi, yi) in data]
y = [yi for (xi, yi) in data]
def permute(x):
shuffled = [xi for xi in x]
shuffle(shuffled)
return shuffled
def avg(x): # Average
return sum(x)/len(x)
def stddev(x): # Standard deviation.
m = avg(x)
return sqrt(sum([(xim)**2 for xi in x])/len(x))
def cov(x, y): # Covariance.
return sum([(xiavg(x))*(yiavg(y)) for (xi,yi) in zip(x,y)])/len(x)
def corr(x, y): # Correlation coefficient.
if stddev(x)*stddev(y) != 0:
return cov(x, y)/(stddev(x)*stddev(y))
def p(x, y):
c0 = corr(x, y)
corrs = []
for k in range(0, 2000):
y_permuted = permute(y)
corrs.append(corr(x, y_permuted))
return len([c for c in corrs if abs(c) > c0])/len(corrs)
scipy.stats.pearsonr()
function will return the correlation coefficient and the pvalue.
import scipy.stats
print(scipy.stats.pearsonr(x, y))
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alice_bob
in accordance with Project #0. Teams consisting of up to four people are permitted for this project.https://github.com/DataMechanics/course2017sprproj
.
README.md
file within your directory (you may only need to update your existing file).README.md
file how to obtain and run those tools). As in Project #1, your algorithms should be implemented within scripts that extend the dml.Algorithm
base class, should follow reasonable modularity and encapsulation practices, and should perform logically related operations.provenance()
method is invoked.trial
parameter of the execute()
method is set to True
. In trial mode, the algorithm should complete its execution very quickly (in at most a few seconds) by operating on a very small portion of the input data set(s). However, it should still run through most (or, ideally, all) the code paths in the algorithm definition when it does so. This will make it possible to easily test the algorithm without running it on the entire data set.
import jsonschema
from flask import Flask, jsonify, abort, make_response, request
from flask.ext.httpauth import HTTPBasicAuth
app = Flask(__name__)
auth = HTTPBasicAuth()
users = [
{ 'id': 1, 'username': u'alice' },
{ 'id': 2, 'username': u'bob' }
]
schema = {
"type": "object",
"properties": {"username" : {"type": "string"}},
"required": ["username"]
}
@app.route('/client', methods=['OPTIONS'])
def show_api():
return jsonify(schema)
@app.route('/client', methods=['GET'])
@auth.login_required
def show_client():
return open('client.html','r').read()
@app.route('/app/api/v0.1/users', methods=['GET'])
def get_users(): # Serverside reusable name for function.
print("I'm responding.")
return jsonify({'users': users})
@app.route('/app/api/v0.1/users/', methods=['GET'])
def get_user(user_id):
user = [user for user in users if user['id'] == user_id]
if len(user) == 0:
abort(404)
return jsonify({'user': user[0]})
@app.errorhandler(404)
def not_found(error):
return make_response(jsonify({'error': 'Not found foo.'}), 404)
@app.route('/app/api/v0.1/users', methods=['POST'])
def create_user():
print(request.json)
if not request.json:
print('Request not valid JSON.')
abort(400)
try:
jsonschema.validate(request.json, schema)
user = { 'id': users[1]['id'] + 1, 'username': request.json['username'] }
users.append(user)
print(users)
return jsonify({'user': user}), 201
except:
print('Request does not follow schema.')
abort(400)
@auth.get_password
def foo(username):
if username == 'alice':
return 'ecila'
return None
@auth.error_handler
def unauthorized():
return make_response(jsonify({'error': 'Unauthorized access.'}), 401)
if __name__ == '__main__':
app.run(debug=True)
<script>
function postSomething() {
var http = new XMLHttpRequest();
var url = "http://localhost:5000/app/api/v0.1/users";
var json = JSON.stringify({'name':'carl'});
http.open("POST", url, true);
http.setRequestHeader("Contenttype", "application/json");
http.onreadystatechange = function() {
if (http.readyState == 4 && http.status == 200) {
console.log(http.responseText);
}
}
http.send(json);
}
</script>
<button onclick="postSomething();">Post new user</button>
README.md
file within your repository, though HTML or PDF are also acceptable). It is expected that the report should come out to at least 35 pages (if printed in a 12point font on 8.5 by 11 in. sheets), but there's no upper limit on length.[1]  "World's population increasingly urban with more than half living in urban areas". https://www.un.org/development/desa/en/news/population/worldurbanizationprospects.html 
[2]  Luís M. A. Bettencourt, José Lobo, Dirk Helbing, Christian Kühnert, and Geoffrey B. West. "Growth, innovation, scaling, and the pace of life in cities". Proceedings of the National Academy of Sciences of the United States of America 2007;104(17):73017306. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852329/ 
[3]  Robert Albright, and Alan Demers, Johannes Gehrke, Nitin Gupta, Hooyeon Lee, Rick Keilty, Gregory Sadowski, Ben Sowell, and Walker White. "SGL: A Scalable Language for Datadriven Games". Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data 2008. http://www.cs.cornell.edu/~sowell/2008sigmodgamesdemo.pdf 
[4]  Walker White, Benjamin Sowell, Johannes Gehrke, and Alan Demers. "Declarative Processing for Computer Games". Proceedings of the 2008 ACM SIGGRAPH Symposium on Video Games 2008. http://www.cs.cornell.edu/~sowell/2008sandboxdeclarative.pdf 
[5]  W3C Working Group. "PROV Model Primer". https://www.w3.org/TR/provprimer/ 
[6]  Robert Ikeda and Jennifer Widom. "Data Lineage: A Survey". http://ilpubs.stanford.edu:8090/918/1/lin_final.pdf 
[7]  Y. Cui and J. Widom. "Lineage Tracing for General Data Warehouse Transformations". The VLDB Journal 2003;12(1):4158. http://ilpubs.stanford.edu:8090/525/1/20015.pdf 
[8]  Gerd Gigerenzer. "Mindless statistics". The Journal of SocioEconomics 2004;33(5):587606. http://www.unh.edu/halelab/BIOL933/papers/2004_Gigerenzer_JSE.pdf 
[9]  Nihar B. Shah and Dengyong Zhou. "Double or Nothing: Multiplicative Incentive Mechanisms for Crowdsourcing". CoRR 2014. http://www.eecs.berkeley.edu/~nihar/publications/double_or_nothing.pdf 
courseYYYYSSSprojNNNN
where YYYY
is the year, SSSS
is the semester (spr
or fal
) and NNNN
is zero
, one
, two
, and so on.
courseYYYYSSSprojzero
) will be a public repository so that those who are not members of the DataMechanics organization can see and fork it in the steps below, as that will be how the course staff obtain everyone's GitHub usernames.
BUlogin1
, BUlogin1_BUlogin2
, or BUlogin1_BUlogin2_BUlogin3
(depending on the number of members), where the login names BUloginN
are the official Boston University login names for the members, and they are ordered in ascending alphabetical order and separated by underscores. All changes constituting work on the project should be made within this subdirectory and nowhere else, unless otherwise specified in the posted project instructions.
master
branch will represent the group's submission. At some point before the project deadline, the group must submit a pull request to officially submit their work. Only the changes that were committed before the merge request is made will be accepted as submitted.mapReduce
operations: https://jira.mongodb.org/browse/SERVER2517 andeval()
and stored procedure capabilities: https://jira.mongodb.org/browse/SERVER17453.GEO2D
index using PyMongo, andprov
package:
optimize.linprog
module for solving linear optimization problems, and the library is relatively straightforward to install:
pip install numpy
and pip install scipy
should be sufficient.