def expand_videos(msid, video):
gc_data = metadata(msid) # cached on first hit
gc_id_str = ", ".join(gc_data.keys())
v_id = video['id']
ensure(v_id in gc_data,
"glencoe doesn't know %r, only %r" % (v_id, gc_id_str))
video_data = gc_data[v_id]
video_data = utils.subdict(video_data, ['jpg_href', 'width', 'height'])
video_data = utils.renkeys(video_data, [('jpg_href', 'image')])
func = lambda mtype: {
'mediaType': SOURCES[mtype],
'uri': gc_data[v_id][mtype + "_href"]
}
video_data['sources'] = lmap(func, SOURCES)
video.update(video_data)
del video['uri'] # returned by elife-tools, not part of spec
# Add placeholder, the video thumbnail image
video["placeholder"] = {}
video["placeholder"]["uri"] = video["image"].split('/')[-1]
video["placeholder"]["alt"] = ""
return video
def expand_location(path):
# if isinstance(path, file):
if is_file(path):
path = path.name
if path.startswith('https://s3-external-1.amazonaws.com/') or path.startswith('https://s3.amazonaws.com/'):
# it's being downloaded from a bucket, no worries
return path
# resolve any symlinks
# the backfill uses symlinks to the article-xml dir
path = os.path.abspath(os.path.realpath(path))
if re.match(r".*article-xml/articles/.+\.xml$", path):
# this article is coming from the local ./article-xml/ directory, which
# is almost certainly a git checkout. we want a location that looks like:
# https://raw.githubusercontent.com/elifesciences/elife-article-xml/5f1179c24c9b8a8b700c5f5bf3543d16a32fbe2f/articles/elife-00003-v1.xml
rc, rawsha = utils.run_script(["cat", "elife-article-xml.sha1"])
ensure(rc == 0, "failed to read the contents of './elife-article-xml.sha1'")
sha = rawsha.strip()
fname = os.path.basename(path)
return "https://raw.githubusercontent.com/elifesciences/elife-article-xml/%s/articles/%s" % (sha, fname)
# who knows what this path is ...
LOG.warn("scraping article content in a non-repeatable way. path %r not found in article-xml dir. please don't send the results to lax", path)
return path
def expand_location(path):
# if isinstance(path, file):
if is_file(path):
path = path.name
if path.startswith('https://s3-external-1.amazonaws.com/'
) or path.startswith('https://s3.amazonaws.com/'):
# it's being downloaded from a bucket, no worries
return path
# resolve any symlinks
# the backfill uses symlinks to the article-xml dir
path = os.path.abspath(os.path.realpath(path))
if re.match(r".*article-xml/articles/.+\.xml$", path):
# this article is coming from the local ./article-xml/ directory, which
# is almost certainly a git checkout. we want a location that looks like:
# https://raw.githubusercontent.com/elifesciences/elife-article-xml/5f1179c24c9b8a8b700c5f5bf3543d16a32fbe2f/articles/elife-00003-v1.xml
rc, rawsha = utils.run_script(["cat", "elife-article-xml.sha1"])
ensure(rc == 0,
"failed to read the contents of './elife-article-xml.sha1'")
sha = rawsha.strip()
fname = os.path.basename(path)
return "https://raw.githubusercontent.com/elifesciences/elife-article-xml/%s/articles/%s" % (
sha, fname)
# who knows what this path is ...
LOG.warn(
"scraping article content in a non-repeatable way. path %r not found in article-xml dir. please don't send the results to lax",
path)
return path
def add_connection(self, from_room, to_room):
ensure(from_room >= 0 and from_room < len(self.nodes),
'from_room out of bounds')
ensure(to_room >= 0 and to_room < len(self.nodes),
'to_room out of bounds')
self.connections[from_room, to_room] = distance.euclidean(
self.nodes[from_room].center, self.nodes[to_room].center)
def expand_videos(msid, video):
gc_data = metadata(msid) # cached on first hit
gc_id_str = ", ".join(gc_data.keys())
v_id = video['id']
ensure(gc_data, "glencoe doesn't know %r, it doesn't have any media")
ensure(v_id in gc_data, "glencoe doesn't know %r, only %r" % (v_id, gc_id_str))
video_data = gc_data[v_id]
video_data = utils.subdict(video_data, ['jpg_href', 'width', 'height'])
video_data = utils.renkeys(video_data, [('jpg_href', 'image')])
func = lambda mtype: OrderedDict([
('mediaType', SOURCES[mtype]),
('uri', gc_data[v_id][mtype + "_href"])
])
video_data['sources'] = lmap(func, SOURCES)
video.update(video_data)
del video['uri'] # returned by elife-tools, not part of spec
# Add placeholder, the video thumbnail image
video["placeholder"] = OrderedDict()
video["placeholder"]["uri"] = video["image"].split('/')[-1]
video["placeholder"]["alt"] = ""
return video
def triangulate(self):
ensure(
len(self.nodes) >= 4,
'Cannot triangulate with less than four rooms')
self.reset_connections()
points = []
self.lookup = []
i = 0
for id, n in enumerate(self.nodes):
if n.is_main:
points.append(n.center)
self.lookup.append(id)
i += 1
tri = Delaunay(points)
for simplex in tri.simplices:
self.add_connection(self.lookup[simplex[0]],
self.lookup[simplex[1]])
self.add_connection(self.lookup[simplex[1]],
self.lookup[simplex[2]])
self.add_connection(self.lookup[simplex[2]],
self.lookup[simplex[0]])
self.triangulation = tri
def file_handler(path):
ensure(
path.startswith(PROJECT_DIR),
"unsafe operation - refusing to read from a file location outside of project root. %r does not start with %r"
% (path, PROJECT_DIR))
xml = open(path, 'r').read()
# write cache?
return xml
def splitter(string):
if isinstance(string, list):
pair = string # already split into pairs, return what we have
return pair
ensure('|' in string, "override key and value must be seperated by a pipe '|'")
first, rest = string.split('|', 1)
ensure(rest.strip(), "a value must be provided. use 'null' without quotes to use an empty value")
return first, rest
def manual_overrides(ctx, data):
"replace top-level article keys with new values provided in ctx.override"
overrides = ctx.get('override', {})
ensure(isinstance(overrides, dict), "given mapping of overrides is not a dictionary")
# possibly add support for dotted paths in future?
for key, value in overrides.items():
data['article'][key] = value
return data
def test_divide():
l1 = ['/', 2, 2]
l2 = ['/', 30, 2, ['+', 1, 2]]
# log(Apply().divide(l1))
# log(Apply().divide(l2))
ensure(Apply().divide(l1) == 1, 'divide 测试1')
ensure(Apply().divide(l2) == 5, 'divide 测试2')
def validate_response(response):
utils.validate(response, conf.RESPONSE_SCHEMA)
max_size_in_bytes = 262144
response_size = len(serialise_response(response))
ensure(
response_size <= max_size_in_bytes,
"response size (%s) is too large: %s" %
(response_size, max_size_in_bytes), ValidationError)
def manual_overrides(ctx, data):
"replace top-level article keys with new values provided in ctx.override"
overrides = ctx.get('override', {})
ensure(isinstance(overrides, dict),
"given mapping of overrides is not a dictionary")
# possibly add support for dotted paths in future?
for key, value in overrides.items():
data['article'][key] = value
return data
def test_call_function():
d1 = [['def', 'f1', ['a', 'b'], [['if', ['<', 'a', 0], 3, 'b']]]]
apply = Apply()
apply.apply_trees(d1)
# print('func', self.func)
l1 = ['call', 'f1', [1, 2]]
# log('var', apply.var)
# log('func', apply.func)
# log('func result', apply.call_func(l1))
ensure(apply.call_func(l1) == 2, 'call_function 测试1')
def download(location):
"download file, convert and pipe content straight into lax + transparent cache"
ensure('://' in location[:10], 'no protocol found in %r, failing' % location)
protocol, path = location.split('://')
downloaderficationer = {
'https': lambda: http_download(location),
# load files relative to adaptor root
'file': partial(file_handler, path)
}
file_contents = downloaderficationer[protocol]()
return file_contents
def download(location):
"download file, convert and pipe content straight into lax + transparent cache"
ensure('://' in location[:10],
'no protocol found in %r, failing' % location)
protocol, path = location.split('://')
downloaderficationer = {
'https': lambda: http_download(location),
# load files relative to adaptor root
'file': partial(file_handler, path)
}
file_contents = downloaderficationer[protocol]()
return file_contents
def splitter(string):
if isinstance(string, list):
pair = string # already split into pairs, return what we have
return pair
ensure('|' in string,
"override key and value must be seperated by a pipe '|'")
first, rest = string.split('|', 1)
ensure(
rest.strip(),
"a value must be provided. use 'null' without quotes to use an empty value"
)
return first, rest
def validate_gc_data(gc_data):
# we've had one case like this
ensure(gc_data != {}, "glencoe returned successfully, but response is empty")
# we also can't guarantee all of the sources will always be present
known_sources = SOURCES.keys()
for v_id, v_data in gc_data.items():
available_sources = lfilter(lambda mtype: mtype + "_href" in v_data, known_sources)
# fail if we have partial data
msg = "number of available sources less than known sources for %r. missing: %s" % \
(v_id, ", ".join(set(known_sources) - set(available_sources)))
ensure(len(available_sources) == len(known_sources), msg)
def test_apply_trees(): # 这是最顶层的函数，传入抽象语法树
l1 = [['+', 1, 2, ['-', 2, 1]]]
l2 = [['-', 2, 2], ['-', 2, 1]]
l3 = [['var', 'a', ['-', 2, 1]]]
l4 = [['var', 'a', 1], ['var', 'b', ['+', 1, 1]],
['if', ['<', 'a', 0], 3, 'b']]
l5 = [['var', 'a', 3], ['var', 'b', 2],
['def', 'f1', ['a', 'b'], [['-', ['+', 'a', 2], 3, 'b']]],
['call', 'f1', ['a', 'b']]]
# ensure(Apply().apply_trees(l1) == 4, 'apply_trees 测试1')
# ensure(Apply().apply_trees(l2) == 1, 'apply_trees 测试2')
# ensure(Apply().apply_trees(l3) == 'N/A', 'apply_trees 测试3')
# ensure(Apply().apply_trees(l4) == 2, 'apply_trees 测试4')
ensure(Apply().apply_trees(l5) == 0, 'apply_trees 测试5')
def validate_gc_data(gc_data):
# we've had one case like this
ensure(gc_data != {},
"glencoe returned successfully, but response is empty")
# we also can't guarantee all of the sources will always be present
known_sources = SOURCES.keys()
for v_id, v_data in gc_data.items():
available_sources = lfilter(lambda mtype: mtype + "_href" in v_data,
known_sources)
# fail if we have partial data
msg = "number of available sources less than known sources for %r. missing: %s" % \
(v_id, ", ".join(set(known_sources) - set(available_sources)))
assert len(available_sources) == len(known_sources), msg
def test():
# test case,
arr1 = [2, 3, 1, 0, 2, 5, 3]
arr2 = [5, 4, 3, 2, 1, 0]
arr3 = [12, 3]
arr4 = []
ensure((True, 2) == duplicate(arr1), 'arr1')
ensure((False,) == duplicate(arr2), 'arr2')
ensure((False,) == duplicate(arr3), 'arr3')
ensure((False,) == duplicate(arr4), 'arr4')
def random_edges(self, percentage):
ensure(self.triangulation,
'You must triangulate before creating random edges')
s_count = len(self.triangulation.simplices)
rnd_count = int(s_count * 3 * percentage)
rnd = s_count * np.random.rand(rnd_count)
rnd = rnd.astype(int)
counter = 0
cur_try = 0
while counter < len(rnd) and cur_try < s_count:
cur_try += 1
rn = rnd[counter]
s = self.triangulation.simplices[rn]
ri = random.randint(0, 2)
i = s[ri]
j = s[ri + 1] if ri < 2 else s[0]
if not self.is_connected(self.lookup[i], self.lookup[j]):
self.add_connection(self.lookup[i], self.lookup[j])
counter += 1
def serialize(pair):
key, val = pair
ensure(isinstance(key, basestring), "key must be a string")
ensure('|' not in key, "key must not contain a pipe")
key = key.strip()
ensure(key, "key must not be empty")
return '|'.join([key, json.dumps(val)])
def serialize(pair):
key, val = pair
ensure(isinstance(key, basestring), "key must be a string")
ensure('|' not in key, "key must not contain a pipe")
key = key.strip()
ensure(key, "key must not be empty")
return '|'.join([key, json.dumps(val)])
def test():
# test case,
arr1 = [2, 3, 5, 4, 3, 2, 6, 7]
arr2 = [5, 4, 3, 2, 1, 0]
arr3 = [1, 2, 3, 4, 3]
arr4 = []
result1 = duplicate(arr1)
ensure(result1[0] == True and result1[1] in (2, 3), 'arr1')
result2 = duplicate(arr2)
ensure(result2[0] == False, 'arr2')
result3 = duplicate(arr3)
ensure(result3[0] == True and result3[1] in (3, ), 'arr3')
result4 = duplicate(arr4)
ensure(result4[0] == False, 'arr4')
def mkreq(path, **overrides):
ensure(not path.startswith('http://'), "no insecure requests, please")
# TODO: consider removing these two lines
if path.lstrip('/').startswith('article-xml/articles/'):
path = os.path.abspath(path)
path = 'file://' + path if not path.startswith('https://') else path
msid, ver = utils.version_from_path(path)
request = {
'action': conf.INGEST,
'location': path,
'id': msid,
'version': ver,
'force': True, # TODO: shouldn't this be False?
'validate-only': False,
'token': 'pants-party'
}
request.update(overrides)
# don't ever generate an invalid request
utils.validate(request, conf.REQUEST_SCHEMA)
return request
def test_greater_than():
l1 = ['>', 2, 1]
l2 = ['>', 1, 2]
l3 = ['>', 1, ['+', 1, 1]]
ensure(Apply().greater_than(l1), 'more 测试1')
ensure(not Apply().greater_than(l2), 'more 测试2')
ensure(not Apply().greater_than(l3), 'more 测试3')
def test_apply():
l1 = ['+', 1, 2, ['-', 2, 1]]
l2 = ['if', ['>', 1, 2], 1, 2]
l3 = ['if', ['<', 1, 2], 1, 2]
l4 = ['if', ['=', 1, 2], 1, 2]
# print(apply(l1))
# print(apply(l2))
# print(apply(l3))
# print(apply(l4))
ensure(Apply().apply(l1) == 4, 'apply 测试1')
ensure(Apply().apply(l2) == 2, 'apply 测试2')
ensure(Apply().apply(l3) == 1, 'apply 测试3')
ensure(Apply().apply(l4) == 2, 'apply 测试4')
def test_less_than():
l1 = ['<', 2, 1]
l2 = ['<', 1, 2]
l3 = ['<', 1, ['+', 1, 1]]
ensure(not Apply().less_than(l1), 'less 测试1')
ensure(Apply().less_than(l2), 'less 测试2')
ensure(Apply().less_than(l3), 'less 测试3')
def test_judge_cmp():
l1 = ['if', ['>', 3, 4], 1, 2]
l2 = ['if', False, 2, ['+', 1, 2]]
l3 = ['if', False, 2, ['if', True, 1, 2]]
ensure(Apply().judge(l1) == 2, 'judge 测试1')
ensure(Apply().judge(l2) == 3, 'judge 测试2')
ensure(Apply().judge(l3) == 1, 'judge 测试3')
def test_equal():
l1 = ['=', 2, 1]
l2 = ['=', 2, 2]
l3 = ['=', 2, ['+', 1, 1]]
ensure(not Apply().equal(l1), 'equal 测试1')
ensure(Apply().equal(l2), 'equal 测试2')
ensure(Apply().equal(l3), 'equal 测试3')
def _subdesc(desc, path):
"""a path looks like: <type>.<target>
for example: `file./opt/thing/` or `mysql-database.mydb1"""
bits = path.split('.', 1)
ensure(len(bits) == 2, "expecting just two bits, got %s bits: %s" % (len(bits), path), ValueError)
toplevel, target = bits
ensure(toplevel in desc, "descriptor has no %r key" % toplevel, ValueError)
ensure(target in desc[toplevel], "given descriptor has no path %r" % path, ValueError)
return {toplevel: [target]}
def test():
# test case,
# 此方法有缺陷，不能找出所有的重复的数字，
# 因为在1~2的范围里有1和2两个数字，这个范围的数字也出现两次，
# 不能确定是每个数字各出现一次还是某个数字出现了两次
arr1 = [2, 3, 5, 4, 3, 2, 6, 7]
arr2 = [5, 4, 3, 2, 1, 0]
arr3 = [1, 2, 3, 4, 4]
arr4 = []
result1 = duplicate(arr1)
ensure(result1[0] == True and result1[1] in (2, 3), 'arr1')
result2 = duplicate(arr2)
ensure(result2[0] == False, 'arr2')
result3 = duplicate(arr3)
ensure(result3[0] == True and result3[1] in (4, ), 'arr3')
result4 = duplicate(arr4)
ensure(result4[0] == False, 'arr4')
def make_inf_list(params,steps, make_string):
l=[make_string(day,steps) for day in params['days']]
return l
# specify params for synth data
# params are also needed to construct inference prog / ripl
params_name = 'easy_d4_s33_bi4_be10'
#featurefunctions__maxDay_size_num_birds_softmaxbeta
params = get_params(params_name, 'onebird')
gtruth_params = params.copy()
infer_params = params.copy()
gtruth_params['name'] = 'gtruth'
infer_params['name'] = 'infer'
ensure(params_name)
directory = params_name +'/'
generate_save_synthetic_data(gtruth_params,directory)
## specifying an inference prog:
# need list of inference strings or single one (filter/batch)
# for list, need num_days from params
exp_seed1=dict( type = 'seq_block_mh',
steps = 50,
make_inf_string = seq_block_mh_make_inf_string)
exp_seed2 = exp_seed1.copy()
exp_seed3=dict( type = 'seq_block_pgibbs',
steps = 50,
def find_lax():
ensure(os.path.exists(conf.PATH_TO_LAX), "could not find lax")
script = join(conf.PATH_TO_LAX, "manage.sh")
ensure(os.path.exists(script), "could not find lax's manage.sh script")
return script
def is_connected(self, from_room, to_room):
ensure(from_room >= 0 and from_room < len(self.nodes),
'from_room out of bounds')
ensure(to_room >= 0 and to_room < len(self.nodes),
'to_room out of bounds')
return self.connections[from_room, to_room] != 0
except BaseException as err:
strbuffer.write("failed (%s)" % err)
finally:
log = conf.multiprocess_log('generation.log', __name__)
log.info(strbuffer.getvalue())
def main(xml_dir, json_output_dir, num=None):
paths = lmap(lambda fname: join(xml_dir, fname), os.listdir(xml_dir))
paths = lfilter(lambda path: path.lower().endswith('.xml'), paths)
paths = sorted(paths, reverse=True)
if num:
paths = paths[:num] # only scrape first n articles
num_processes = -1
Parallel(n_jobs=num_processes)(delayed(render)(path, json_output_dir) for path in paths)
print('see scrape.log for errors')
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('xml-dir', nargs='?', default=conf.XML_DIR)
parser.add_argument('output-dir', nargs='?', default=conf.JSON_DIR)
parser.add_argument('--num', type=int, nargs='?')
args = vars(parser.parse_args())
indir, outdir = [os.path.abspath(args[key]) for key in ['xml-dir', 'output-dir']]
ensure(os.path.exists(indir), "the path %r doesn't exist" % indir)
ensure(os.path.exists(outdir), "the path %r doesn't exist" % outdir)
main(indir, outdir, args['num'])
def test_11():
ensure(applyCompare(['>', 2, 1]) == True, 'test_11 >')
def wrap(v):
ensure(v, "%s cannot be blank/empty/None" % label)
return v
def test_12():
arr = ['+', 1, 2, 3]
ensure(apply_ops(['>', 2, 1]) == True, 'test_12 >')
ensure(apply_ops(arr) == 6, 'test_12 +')
def wrap(v):
ensure(v, "%s cannot be blank/empty/None" % label)
return v
def find_lax():
ensure(os.path.exists(conf.PATH_TO_LAX), "could not find lax")
script = join(conf.PATH_TO_LAX, "manage.sh")
ensure(os.path.exists(script), "could not find lax's manage.sh script")
return script
def file_handler(path):
ensure(path.startswith(PROJECT_DIR),
"unsafe operation - refusing to read from a file location outside of project root. %r does not start with %r" % (path, PROJECT_DIR))
xml = open(path, 'r').read()
# write cache?
return xml
def test():
arr1 = [2, 3, 1, 0, 2, 5, 3]
ensure((True, 2) == duplicate(arr1), 'arr1')
def validate_response(response):
utils.validate(response, conf.RESPONSE_SCHEMA)
max_size_in_bytes = 262144
response_size = len(serialise_response(response))
ensure(response_size <= max_size_in_bytes, "response size (%s) is too large: %s" % (response_size, max_size_in_bytes), ValidationError)
