def project(request, abstractid):
LogRequest(request, "project: " + str(abstractid))
try:
project = NSFProject.objects.get(awardID = abstractid)
except:
msg = "No project found for award ID: " + str(abstractid)
LogWarning(msg)
return render_to_response('error.html',
{'message': msg,
'menu': generate_error_menu(request),
},
context_instance=RequestContext(request))
pis = project.getPIs()
collabs = uniq([c.project2 for c in CollabProjects.objects.filter(project1 = project)])
collabpis = uniq([(p.investigator, collab)
for collab in collabs
for p in ProjectPIs.objects.filter(project=collab)])
collabpis.sort(key=lambda r: r[0].lastname)
amount = format_amount(project.amount)
return render_to_response(
'project.html',
{'project': project,
'menu': generate_menu(request),
'amount': amount,
'pis': pis, 'collabs': collabs, 'collabpis': collabpis},
context_instance=RequestContext(request)
)
def project(request, abstractid):
LogRequest(request, "project: " + str(abstractid))
try:
project = NSFProject.objects.get(awardID=abstractid)
except:
msg = "No project found for award ID: " + str(abstractid)
LogWarning(msg)
return render_to_response('error.html', {
'message': msg,
'menu': generate_error_menu(request),
},
context_instance=RequestContext(request))
pis = project.getPIs()
collabs = uniq(
[c.project2 for c in CollabProjects.objects.filter(project1=project)])
collabpis = uniq([(p.investigator, collab) for collab in collabs
for p in ProjectPIs.objects.filter(project=collab)])
collabpis.sort(key=lambda r: r[0].lastname)
amount = format_amount(project.amount)
return render_to_response('project.html', {
'project': project,
'menu': generate_menu(request),
'amount': amount,
'pis': pis,
'collabs': collabs,
'collabpis': collabpis
},
context_instance=RequestContext(request))
def write_mutatee_cmakelists(directory, info, platform):
cmakelists = open(directory + "/cmake-mutatees.txt", "w")
compilers = info['compilers']
mutatees = info['mutatees']
comps = utils.uniq(map(lambda m: m['compiler'], mutatees))
pname = os.environ.get('PLATFORM')
modules = utils.uniq(map(lambda t: t['module'], info['tests']))
print_src_lists(mutatees, platform, info, directory)
print_compiler_cmakefiles(mutatees, platform, info, cmakelists, directory)
def write_mutatee_cmakelists(directory, info, platform):
cmakelists = open(directory + "/cmake-mutatees.txt", "w")
compilers = info['compilers']
mutatees = info['mutatees']
comps = utils.uniq(map(lambda m: m['compiler'], mutatees))
pname = os.environ.get('PLATFORM')
modules = utils.uniq(map(lambda t: t['module'], info['tests']))
print_src_lists(mutatees, platform, info, directory)
print_compiler_cmakefiles(mutatees, platform, info, cmakelists, directory)
def home(request):
if not _is_logged_in(request):
return redirect(users.create_login_url('/'))
sites = all_sites()
logins = sorted(uniq([site.login for site in sites if site.login]))
passwords = sorted(uniq([site.password for site in sites if site.password]))
return render(request, 'passwords.html', {
'sites': sites,
'sites_json': json.dumps(_sites_dict(sites)),
'logins_json': json.dumps(logins),
'passwords_json': json.dumps(passwords),
'logout_url': users.create_logout_url('/'),
})
def _refresh_sites(request):
sites = all_sites()
sites_html = render(request, '_sites.html', {
'sites': sites
}).content
logins = sorted(uniq([site.login for site in sites if site.login]))
passwords = sorted(uniq([site.password for site in sites if site.password]))
return json.dumps({
'sites_html': sites_html,
'sites': _sites_dict(sites),
'logins': logins,
'passwords': passwords,
})
def gooddsspfilename(filename, dsspdirList=None):
# first check if pdbid is really a file
if os.path.exists(filename):
return filename
# extract pdbid from pdbid
if dsspdirList is None:
dsspdirList = _DSSP_DIR
if type(dsspdirList) == str:
dsspdirList = _DSSP_DIR.split(os.pathsep)
pdbid = pdbidFromFilename(filename)
pdbidl = pdbid.lower()
branch = pdbidl[1:3]
# generate filename variants
basenames = [
x % vars()
for x in ("%(filename)s", "%(pdbid)s", "%(pdbidl)s", "pdb%(pdbidl)s")
]
basenames = uniq(basenames)
extensions = ("", ".dssp", ".DSSP")
compressions = ("", ".gz", ".Z")
# generate subdirectory locations
subdirs = []
for dsspdir in dsspdirList:
innerSubdirs = [
x % vars()
for x in ("", "%(branch)s", "%(dsspdir)s",
os.path.join("%(dsspdir)s", "%(branch)s"),
os.path.join("%(dsspdir)s", "divided", "%(branch)s"),
os.path.join("%(dsspdir)s", "data", "structures",
"divided", "pdb", "%(branch)s"))
]
subdirs.extend(innerSubdirs)
subdirs = uniq(subdirs)
# search tree
for subdir in subdirs:
for cmp in compressions:
for base in basenames:
for ext in extensions:
filename = os.path.join(subdir,
"%(base)s%(ext)s%(cmp)s" % vars())
if os.path.exists(filename):
return filename
return None
def generateCollaborators(institution):
pis = NSFInvestigator.objects.filter(satc=True).extra(
select={
'lower_name': 'lower(lastname)'
}).order_by('lower_name', 'firstname').filter(attendee=True)
for pi in pis:
line = pi.email + ", "
piprojects = ProjectPIs.objects.filter(investigator=pi)
projects = sorted(uniq([p.project for p in piprojects if p.project]),
key=lambda proj: proj.startDate)
collaborators = sorted(uniq([
p.investigator for proj in projects
for p in ProjectPIs.objects.filter(project=proj)
] + [
p.investigator for proj in projects for collab in
[c.project2 for c in CollabProjects.objects.filter(project1=proj)]
for p in ProjectPIs.objects.filter(project=collab)
]),
key=lambda pi: pi.lastname)
if institution:
institutions = pi.getInstitutions()
for institution in institutions:
pis = uniq([
ppi.investigator for ppi in ProjectPIs.objects.filter(
institution=institution)
])
pis = [icollab for icollab in pis if pi.attendee]
if pi in pis:
pis.remove(pi)
else:
pass # LogWarning("Not a self institution collaborator! " + pi.fullDisplay())
collaborators += pis
if pi in collaborators:
collaborators.remove(pi)
else:
pass # print "Not self-collaborator: " + pi.email
line += ', '.join([
collaborator.email for collaborator in collaborators
if collaborator.attendee
])
print line
def get_all_mutatee_sources(groupable, module, info): return utils.uniq(reduce(lambda a, b: set(a) | set(b), (map(lambda m: m['preprocessed_sources'], filter(lambda m: m['name'] != 'none' and is_valid_test(m) == 'true' and is_groupable(m, info) == groupable and get_module(m) == module, info['mutatees']))), []))
def institutions(request, max_page=MAX_PAGE):
title = 'Institutions'
projects, explanation = NSFProject.selectProjectsFromRequest(request)
institutions = uniq([project.institution for project in projects])
institutions.sort(key=lambda inst: inst.name)
explanation = str(len(institutions)) + " institutions hosting " + explanation
if max_page < len(institutions) < 1.85 * max_page:
max_page = 2 * max_page # don't paginate
paginator = Paginator(institutions, max_page)
page = request.GET.get('page')
if page == 'all':
showinstitutions = institutions
else:
try:
showinstitutions = paginator.page(page)
except PageNotAnInteger:
showinstitutions = paginator.page(1)
except EmptyPage:
showinstitutions = paginator.page(paginator.num_pages)
return render_to_response(
'institutions.html',
{'title': title,
'menu': generate_menu(request),
'explanation': explanation,
'paginate': len(institutions) > len(showinstitutions),
'institutions': showinstitutions },
context_instance=RequestContext(request))
def generate_institution_graph(projects):
edges = []
institutions = []
for project in projects:
cols = []
institution = project.institution
if not institution in institutions:
institutions.append(institution)
collabs = uniq([c.project2 for c in CollabProjects.objects.filter(project1 = project)])
for collab in collabs:
collabinst = collab.institution
if not collabinst in institutions:
institutions.append(collabinst)
cols.append(institutions.index(collabinst))
val = 1
val += int(project.amount / 1000000)
if project.satc:
val *= 2
edges += make_edges(cols, val)
edges = merge_edges(edges)
json_obj = {'nodes': [], 'links': []}
for institution in institutions:
desc = {'name': institution.showName(), 'group': 1, 'instid': institution.id }
json_obj['nodes'].append(desc)
for edge in edges:
desc = {"source": edge[0], "target": edge[1], "value": edge[2]}
json_obj['links'].append(desc)
json_str = json.dumps(json_obj)
return json_str
def group_textlines(self, laparams, lines):
plane = Plane(self.bbox)
plane.extend(lines)
boxes = {}
for line in lines:
neighbors = line.find_neighbors(plane, laparams.line_margin)
if line not in neighbors: continue
members = []
for obj1 in neighbors:
members.append(obj1)
if obj1 in boxes:
members.extend(boxes.pop(obj1))
if isinstance(line, LTTextLineHorizontal):
box = LTTextBoxHorizontal()
else:
box = LTTextBoxVertical()
for obj in uniq(members):
box.add(obj)
boxes[obj] = box
done = set()
for line in lines:
if line not in boxes: continue
box = boxes[line]
if box in done:
continue
done.add(box)
if not box.is_empty():
yield box
return
def get_textboxes(self, laparams, lines):
plane = Plane(lines)
boxes = {}
for line in lines:
neighbors = line.find_neighbors(plane, laparams.line_margin)
assert line in neighbors, line
members = []
for obj1 in neighbors:
members.append(obj1)
if obj1 in boxes:
members.extend(boxes.pop(obj1))
if isinstance(line, LTTextLineHorizontal):
box = LTTextBoxHorizontal()
else:
box = LTTextBoxVertical()
for obj in uniq(members):
box.add(obj)
boxes[obj] = box
done = set()
for line in lines:
box = boxes[line]
if box in done: continue
done.add(box)
if not box.is_empty():
yield box
return
def nomination_ids_for(congress, options={}):
nomination_ids = []
page = page_for(congress, options)
if not page:
logging.error("Couldn't download page for %d congress" % congress)
return None
# extract matching links
doc = html.document_fromstring(page)
raw_nomination_ids = doc.xpath('//div[@id="content"]/p[2]/a/text()')
nomination_ids = []
for raw_id in raw_nomination_ids:
pieces = raw_id.split(' ')
# ignore these
if raw_id in ["PDF", "Text", "split into two or more parts"]:
pass
elif len(pieces) < 2:
logging.error("Bad nomination ID detected: %s" % raw_id)
return None
else:
nomination_ids.append(pieces[1])
return utils.uniq(nomination_ids)
def get_textboxes(self, laparams, lines):
plane = Plane(lines)
boxes = {}
for line in lines:
neighbors = line.find_neighbors(plane, laparams.line_margin)
assert line in neighbors, line
members = []
for obj1 in neighbors:
members.append(obj1)
if obj1 in boxes:
members.extend(boxes.pop(obj1))
if isinstance(line, LTTextLineHorizontal):
box = LTTextBoxHorizontal()
else:
box = LTTextBoxVertical()
for obj in uniq(members):
box.add(obj)
boxes[obj] = box
done = set()
for line in lines:
box = boxes[line]
if box in done: continue
done.add(box)
yield box.analyze(laparams)
return
def edit_statements_page(title, csv_file, username, summary=None):
"""
Edit a wiki page of suggested statements.
"""
rows = csv.reader(csv_file)
(header, property) = next(rows)
assert header == "qid"
statements = []
for (qid, value) in rows:
statements.append((qid, property, value))
statements.sort()
statements = list(uniq(statements))
lines = []
for (entity, property, value) in statements:
lines.append("* {{Statement|" + entity + "|" + property + "|" +
str(value) + "}}")
if statements:
lines.append("")
lines.append(
wikitext.link("Add via QuickStatements",
quickstatements_url(statements)))
lines.append("")
text = "\n".join(lines)
return page.edit(title, text, username, summary)
def institutions(request, max_page=MAX_PAGE):
title = 'Institutions'
projects, explanation = NSFProject.selectProjectsFromRequest(request)
institutions = uniq([project.institution for project in projects])
institutions.sort(key=lambda inst: inst.name)
explanation = str(
len(institutions)) + " institutions hosting " + explanation
if max_page < len(institutions) < 1.85 * max_page:
max_page = 2 * max_page # don't paginate
paginator = Paginator(institutions, max_page)
page = request.GET.get('page')
if page == 'all':
showinstitutions = institutions
else:
try:
showinstitutions = paginator.page(page)
except PageNotAnInteger:
showinstitutions = paginator.page(1)
except EmptyPage:
showinstitutions = paginator.page(paginator.num_pages)
return render_to_response(
'institutions.html', {
'title': title,
'menu': generate_menu(request),
'explanation': explanation,
'paginate': len(institutions) > len(showinstitutions),
'institutions': showinstitutions
},
context_instance=RequestContext(request))
def index(options={}):
concordance = defaultdict(list)
files = [
x for x in os.listdir(os.getcwd() + "/data/")
if re.sub("\d+\.json", "", x) == ""
]
if options.get('limit', False):
files = files[:options.get('limit')]
for file in files:
sermon = json.load(open(os.getcwd() + "/data/" + file, 'r'))
words = uniq(
re.findall(r"\b[A-z]+\b", sermon['opening'].replace('\n',
' ').lower()))
'''
if options.get("uniques", False):
words = uniq(re.findall(r"\b[A-z]+\b", sermon['opening'].replace('\n', ' ').lower()))
else:
words = re.findall(r"\b[A-z]+\b", sermon['opening'].replace('\n', ' ').lower())
'''
for word in words:
if len(word) > 2:
concordance[word].append(file.replace('.json', ''))
write(json.dumps(concordance, sort_keys=True, indent=2),
os.getcwd() + "/src/data/index.json")
write(json.dumps(concordance, sort_keys=True),
os.getcwd() + "/src/data/index.min.json")
def get_all_mutatee_sources(groupable, module, info): return utils.uniq(reduce(lambda a, b: set(a) | set(b), (map(lambda m: m['preprocessed_sources'], filter(lambda m: m['name'] != 'none' and is_valid_test(m) == 'true' and is_groupable(m, info) == groupable and get_module(m) == module, info['mutatees']))), []))
def getCollaborators(projects):
collaborators = sorted(uniq([
p.investigator for proj in projects
for p in ProjectPIs.objects.filter(project=proj)
] + [
p.investigator for proj in projects for collab in
[c.project2 for c in CollabProjects.objects.filter(project1=proj)]
for p in ProjectPIs.objects.filter(project=collab)
]),
key=lambda pi: pi.lastname)
return collaborators
def getCollaborators(projects):
collaborators = sorted(uniq(
[p.investigator
for proj in projects
for p in ProjectPIs.objects.filter(project=proj)]
+
[p.investigator
for proj in projects
for collab in [c.project2 for c in CollabProjects.objects.filter(project1 = proj)]
for p in ProjectPIs.objects.filter(project=collab)]),
key = lambda pi: pi.lastname)
return collaborators
def generateCollaborators(institution):
pis = NSFInvestigator.objects.filter(satc=True).extra(select={'lower_name': 'lower(lastname)'}).order_by('lower_name', 'firstname').filter(attendee=True)
for pi in pis:
line = pi.email + ", "
piprojects = ProjectPIs.objects.filter(investigator=pi)
projects = sorted(uniq([p.project for p in piprojects if p.project]),
key=lambda proj: proj.startDate)
collaborators = sorted(uniq(
[p.investigator
for proj in projects
for p in ProjectPIs.objects.filter(project=proj)]
+
[p.investigator
for proj in projects
for collab in [c.project2 for c in CollabProjects.objects.filter(project1 = proj)]
for p in ProjectPIs.objects.filter(project=collab)]),
key = lambda pi: pi.lastname)
if institution:
institutions = pi.getInstitutions()
for institution in institutions:
pis = uniq([ppi.investigator for ppi in ProjectPIs.objects.filter(institution=institution)])
pis = [icollab for icollab in pis if pi.attendee]
if pi in pis:
pis.remove(pi)
else:
pass # LogWarning("Not a self institution collaborator! " + pi.fullDisplay())
collaborators += pis
if pi in collaborators:
collaborators.remove(pi)
else:
pass # print "Not self-collaborator: " + pi.email
line += ', '.join([collaborator.email for collaborator in collaborators if collaborator.attendee])
print line
def bill_ids_for(congress, options):
bill_ids = []
bill_type = options.get('bill_type', None)
if bill_type:
bill_types = [bill_type]
else:
bill_types = utils.thomas_types.keys()
for bill_type in bill_types:
# match only links to landing pages of this bill type
# it shouldn't catch stray links outside of the confines of the 100 on the page,
# but if it does, no big deal
link_pattern = "^\s*%s\d+\s*$" % utils.thomas_types[bill_type][1]
# loop through pages and collect the links on each page until
# we hit a page with < 100 results, or no results
offset = 0
while True:
# download page, find the matching links
page = utils.download(
page_for(congress, bill_type, offset),
page_cache_for(congress, bill_type, offset),
options.get('force', False))
if not page:
logging.error("Couldn't download page with offset %i, aborting" % offset)
return None
# extract matching links
doc = html.document_fromstring(page)
links = doc.xpath(
"//a[re:match(text(), '%s')]" % link_pattern,
namespaces={"re": "http://exslt.org/regular-expressions"})
# extract the bill ID from each link
for link in links:
code = link.text.lower().replace(".", "").replace(" ", "")
bill_ids.append("%s-%s" % (code, congress))
if len(links) < 100:
break
offset += 100
# sanity check, while True loops are dangerous
if offset > 100000:
break
return utils.uniq(bill_ids)
def mat_h2_plus_old(bond_length, bspline_set, l_list):
""" gives hamiltonian matrix and overlap matrix of hydrogem molecule ion
Parameters
----------
bond_length : Double
bond length of hydrogen molecular ion
bspline_set : BSplineSet
l_list: list of non negative integer
list of angular quauntum number to use
Returns
-------
h_mat : numpy.ndarray
hamiltonian matrix
s_mat : numpy.ndarray
overlap pmatrix
"""
# compute r1 matrix (B_i|O|B_j)
# (-1/2 d^2/dr^2, 1, 1/r^2, {s^L/g^{L+1} | L<-l_list})
rs = bspline_set.xs
d2_rmat = bspline_set.d2_mat()
r2_rmat = bspline_set.v_mat(1.0/(rs*rs))
s_rmat = bspline_set.s_mat()
tmp_L_list = uniq(flatten([ls_non_zero_YYY(L1, L2)
for L1 in l_list for L2 in l_list]))
en_r1mat_L = {}
for L in tmp_L_list:
en_r1mat_L[L] = bspline_set.en_mat(L, bond_length/2.0)
# compute r1Y matrix (B_iY_L1M1|O|B_jY_L2M2)
def one_block(L1, L2):
v = -2.0*sum([sqrt(4.0*pi/(2*L+1)) *
y1mat_Yqk((L1, 0), (L, 0), (L2, 0)) *
en_r1mat_L[L]
for L in ls_non_zero_YYY(L1, L2)])
if L1 == L2:
L = L1
t = -0.5 * d2_rmat + L*(L+1)*0.5*r2_rmat
return t+v
else:
return v
H_mat = bmat([[one_block(L1, L2)
for L1 in l_list]
for L2 in l_list])
S_mat = bmat([[s_rmat if L1 == L2 else None
for L1 in l_list]
for L2 in l_list])
return (H_mat, S_mat)
def getScopFamily(self, id, chainid=None, resnum=None):
if len(id) == 4:
families = []
for entry in self.entriesByPdbid.get(id, []):
if chainid is not None:
# check chainid
pass
if resnum is not None:
# check resnum
pass
families.append(entry.scopfamily)
families = sort(uniq(families))
return ';'.join(families)
return ''
def nomination_ids_for(congress, options={}):
nomination_ids = []
page = page_for(congress)
if not page:
logging.error("Couldn't download page for %d congress" % congress)
return None
# extract matching links
doc = html.document_fromstring(page)
nomination_ids = doc.xpath('//div[@id="content"]/p[2]/a/text()')
nomination_ids = [x.split(' ')[1] for x in nomination_ids]
return utils.uniq(nomination_ids)
def vote_ids_for_house(congress, session_year, options):
vote_ids = []
index_page = "http://clerk.house.gov/evs/%s/index.asp" % session_year
group_page = r"ROLL_(\d+)\.asp"
link_pattern = r"http://clerk.house.gov/cgi-bin/vote.asp\?year=%s&rollnumber=(\d+)" % session_year
# download index page, find the matching links to the paged listing of votes
page = utils.download(
index_page,
"%s/votes/%s/pages/house.html" % (congress, session_year),
options)
if not page:
logging.error("Couldn't download House vote index page, skipping")
return None
# extract matching links
doc = html.document_fromstring(page)
links = doc.xpath(
"//a[re:match(@href, '%s')]" % group_page,
namespaces={"re": "http://exslt.org/regular-expressions"})
for link in links:
# get some identifier for this inside page for caching
grp = re.match(group_page, link.get("href")).group(1)
# download inside page, find the matching links
page = utils.download(
urllib.parse.urljoin(index_page, link.get("href")),
"%s/votes/%s/pages/house_%s.html" % (congress, session_year, grp),
options)
if not page:
logging.error("Couldn't download House vote group page (%s), aborting" % grp)
continue
doc = html.document_fromstring(page)
votelinks = doc.xpath(
"//a[re:match(@href, '%s')]" % link_pattern,
namespaces={"re": "http://exslt.org/regular-expressions"})
for votelink in votelinks:
num = re.match(link_pattern, votelink.get("href")).group(1)
vote_id = "h" + num + "-" + str(congress) + "." + session_year
if not should_process(vote_id, options):
continue
vote_ids.append(vote_id)
return utils.uniq(vote_ids)
def nomination_ids_for(congress, options = {}):
nomination_ids = []
page = page_for(congress)
if not page:
logging.error("Couldn't download page for %d congress" % congress)
return None
# extract matching links
doc = html.document_fromstring(page)
nomination_ids = doc.xpath('//div[@id="content"]/p[2]/a/text()')
nomination_ids = [x.split(' ')[1] for x in nomination_ids]
return utils.uniq(nomination_ids)
def vote_ids_for_house(congress, session_year, options):
vote_ids = []
index_page = "http://clerk.house.gov/evs/%s/index.asp" % session_year
group_page = r"ROLL_(\d+)\.asp"
link_pattern = r"http://clerk.house.gov/cgi-bin/vote.asp\?year=%s&rollnumber=(\d+)" % session_year
# download index page, find the matching links to the paged listing of votes
page = utils.download(
index_page,
"%s/votes/%s/pages/house.html" % (congress, session_year),
options)
if not page:
logging.error("Couldn't download House vote index page, aborting")
return None
# extract matching links
doc = html.document_fromstring(page)
links = doc.xpath(
"//a[re:match(@href, '%s')]" % group_page,
namespaces={"re": "http://exslt.org/regular-expressions"})
for link in links:
# get some identifier for this inside page for caching
grp = re.match(group_page, link.get("href")).group(1)
# download inside page, find the matching links
page = utils.download(
urlparse.urljoin(index_page, link.get("href")),
"%s/votes/%s/pages/house_%s.html" % (congress, session_year, grp),
options)
if not page:
logging.error("Couldn't download House vote group page (%s), aborting" % grp)
continue
doc = html.document_fromstring(page)
votelinks = doc.xpath(
"//a[re:match(@href, '%s')]" % link_pattern,
namespaces={"re": "http://exslt.org/regular-expressions"})
for votelink in votelinks:
num = re.match(link_pattern, votelink.get("href")).group(1)
vote_id = "h" + num + "-" + str(congress) + "." + session_year
if not should_process(vote_id, options):
continue
vote_ids.append(vote_id)
return utils.uniq(vote_ids)
def mat_h2_plus(bond_length, bspline_set, l_list):
""" gives hamiltonian matrix and overlap matrix of hydrogem molecule ion
Parameters
----------
bond_length : Double
bond length of hydrogen molecular ion
bspline_set : BSplineSet
l_list: list of non negative integer
list of angular quauntum number to use
Returns
-------
h_mat : numpy.ndarray
hamiltonian matrix
s_mat : numpy.ndarray
overlap pmatrix
"""
# compute r1 matrix (B_i|O|B_j)
# (-1/2 d^2/dr^2, 1, 1/r^2, {s^L/g^{L+1} | L<-l_list})
rs = bspline_set.xs
d2_rmat = bspline_set.d2_mat()
r2_rmat = bspline_set.v_mat(1.0/(rs*rs))
s_rmat = bspline_set.s_mat()
tmp_L_list = uniq(flatten([ls_non_zero_YYY(L1, L2)
for L1 in l_list for L2 in l_list]))
en_r1mat_L = {}
for L in tmp_L_list:
en_r1mat_L[L] = bspline_set.en_mat(L, bond_length/2.0)
# compute y1 matrix (Y_L1|P_L(w_A)|Y_L2)
en_y1mat_L = {}
for L in tmp_L_list:
en_y1mat_L[L] = coo_matrix([[np.sqrt(4.0*np.pi/(2*L+1)) *
y1mat_Yqk((L1, 0), (L, 0), (L2, 0))
for L1 in l_list]
for L2 in l_list])
LL_y1mat = coo_matrix(np.diag([1.0*L*(L+1) for L in l_list]))
diag_y1mat = coo_matrix(np.diag([1 for L in l_list]))
# compute r1y1 matrix
h_r1y1mat = (synthesis_mat(-0.5*d2_rmat, diag_y1mat) +
synthesis_mat(+0.5*r2_rmat, LL_y1mat) - 2.0 *
sum([synthesis_mat(en_r1mat_L[L], en_y1mat_L[L])
for L in tmp_L_list]))
s_r1y1mat = synthesis_mat(s_rmat, diag_y1mat)
return (h_r1y1mat, s_r1y1mat)
def generate_institution_graph(projects):
edges = []
institutions = []
for project in projects:
cols = []
institution = project.institution
if not institution in institutions:
institutions.append(institution)
collabs = uniq([
c.project2 for c in CollabProjects.objects.filter(project1=project)
])
for collab in collabs:
collabinst = collab.institution
if not collabinst in institutions:
institutions.append(collabinst)
cols.append(institutions.index(collabinst))
val = 1
val += int(project.amount / 1000000)
if project.satc:
val *= 2
edges += make_edges(cols, val)
edges = merge_edges(edges)
json_obj = {'nodes': [], 'links': []}
for institution in institutions:
desc = {
'name': institution.showName(),
'group': 1,
'instid': institution.id
}
json_obj['nodes'].append(desc)
for edge in edges:
desc = {"source": edge[0], "target": edge[1], "value": edge[2]}
json_obj['links'].append(desc)
json_str = json.dumps(json_obj)
return json_str
def index(options = {}):
concordance = defaultdict(list)
files = [x for x in os.listdir(os.getcwd() + "/data/") if re.sub("\d+\.json", "", x) == ""]
if options.get('limit', False):
files = files[:options.get('limit')]
for file in files:
sermon = json.load(open(os.getcwd() + "/data/" + file, 'r'))
words = uniq(re.findall(r"\b[A-z]+\b", sermon['opening'].replace('\n', ' ').lower()))
'''
if options.get("uniques", False):
words = uniq(re.findall(r"\b[A-z]+\b", sermon['opening'].replace('\n', ' ').lower()))
else:
words = re.findall(r"\b[A-z]+\b", sermon['opening'].replace('\n', ' ').lower())
'''
for word in words:
if len(word) > 2:
concordance[word].append(file.replace('.json', ''))
write(json.dumps(concordance, sort_keys=True, indent=2), os.getcwd() + "/src/data/index.json")
write(json.dumps(concordance, sort_keys=True), os.getcwd() + "/src/data/index.min.json")
def displayPI(request, pi):
piprojects = ProjectPIs.objects.filter(investigator=pi)
projects = sorted(uniq([p.project for p in piprojects if p.project]),
key=lambda proj: proj.startDate)
totalawarded = format_amount(sum([project.amount for project in projects]))
collaborators = getCollaborators(projects)
try:
collaborators.remove(pi)
except:
LogWarning("Not a self-collaborator: " + pi.fullDisplay())
institutions = pi.getInstitutions()
return render_to_response('pi.html', {
'pi': pi,
'menu': generate_menu(request),
'totalawarded': totalawarded,
'institutions': institutions,
'projects': projects,
'collaborators': collaborators
},
context_instance=RequestContext(request))
def displayPI(request, pi):
piprojects = ProjectPIs.objects.filter(investigator=pi)
projects = sorted(uniq([p.project for p in piprojects if p.project]), key=lambda proj: proj.startDate)
totalawarded = format_amount(sum([project.amount for project in projects]))
collaborators = getCollaborators(projects)
try:
collaborators.remove(pi)
except:
LogWarning("Not a self-collaborator: " + pi.fullDisplay())
institutions = pi.getInstitutions()
return render_to_response(
'pi.html',
{'pi': pi,
'menu': generate_menu(request),
'totalawarded': totalawarded,
'institutions': institutions,
'projects': projects,
'collaborators': collaborators},
context_instance=RequestContext(request)
)
def bill_ids_for(congress, options, bill_states={}):
# override if we're actually using this method to get amendments
doing_amendments = options.get('amendments', False)
bill_ids = []
bill_type = options.get(
'amendment_type' if doing_amendments else 'bill_type', None)
if bill_type:
bill_types = [bill_type]
else:
bill_types = utils.thomas_types.keys()
for bill_type in bill_types:
# This sub is re-used for pulling amendment IDs too.
if (bill_type in ('samdt', 'hamdt', 'supamdt')) != doing_amendments:
continue
# match only links to landing pages of this bill type
# it shouldn't catch stray links outside of the confines of the 100 on the page,
# but if it does, no big deal
link_pattern = "^\s*%s\d+\s*$" % utils.thomas_types[bill_type][1]
# loop through pages and collect the links on each page until
# we hit a page with < 100 results, or no results
offset = 0
while True:
# download page, find the matching links
page = utils.download(page_for(congress, bill_type, offset),
page_cache_for(congress, bill_type, offset),
options)
if not page:
logging.error(
"Couldn't download page with offset %i, aborting" % offset)
return None
# extract matching links
doc = html.document_fromstring(page)
links = doc.xpath(
"//a[re:match(text(), '%s')]" % link_pattern,
namespaces={"re": "http://exslt.org/regular-expressions"})
# extract the bill ID from each link
for link in links:
code = link.text.lower().replace(".", "").replace(" ", "")
bill_id = "%s-%s" % (code, congress)
if options.get("fast", False):
fast_cache_path = utils.cache_dir(
) + "/" + bill_info.bill_cache_for(bill_id,
"search_result.html")
old_state = utils.read(fast_cache_path)
# Compare all of the output in the search result's <p> tag, which
# has last major action, number of cosponsors, etc. to a cache on
# disk to see if any major information about the bill changed.
parent_node = link.getparent(
) # the <p> tag containing the whole search hit
parent_node.remove(
parent_node.xpath("b")[0]
) # remove the <b>###.</b> node that isn't relevant for comparison
new_state = etree.tostring(
parent_node) # serialize this tag
if old_state == new_state:
logging.info("No change in search result listing: %s" %
bill_id)
continue
bill_states[bill_id] = new_state
bill_ids.append(bill_id)
if len(links) < 100:
break
offset += 100
# sanity check, while True loops are dangerous
if offset > 100000:
break
return utils.uniq(bill_ids)
def print_mutators_list(out, mutator_dict, test_dict, info, platform):
LibSuffix = platform['filename_conventions']['library_suffix']
ObjSuffix = platform['filename_conventions']['object_suffix']
out.write(
"######################################################################\n"
)
out.write("# A list of all the mutators to be compiled\n")
out.write(
"######################################################################\n\n"
)
module_list = []
for t in test_dict:
module_list.append(t['module'])
module_set = set(module_list)
for m in module_set:
out.write("\n")
out.write("include_directories (\"..src/%s\")\n" % m)
out.write("set (%s_MUTATORS\n" % (m))
module_tests = filter(lambda t: m == t['module'], test_dict)
module_mutators = map(lambda t: t['mutator'], module_tests)
for t in utils.uniq(module_mutators):
out.write("\t%s\n" % (t))
out.write(")\n\n")
out.write("set (%s_OBJS_ALL_MUTATORS\n" % (m))
for t in utils.uniq(module_mutators):
out.write("\t%s%s\n" % (t, ObjSuffix))
out.write(")\n\n")
# We're doing this cmake list style, so we need multiple iterations
# since cmake doesn't support structs
# Iteration 1: print the list of libraries
out.write("set (MUTATOR_NAME_LIST\n")
for m in mutator_dict:
out.write("\t%s\n" % m['name'])
out.write("\t)\n\n")
# Iteration 2: The appropriate module library for each mutator
out.write("set (MUTATOR_MODULE_LIB_LIST\n")
for m in mutator_dict:
# Module info is stored with the "test" dictionary, not the
# "mutator" dictionary
tests = filter(lambda t: t['mutator'] == m['name'], test_dict)
modules = map(lambda t: t['module'], tests)
if (len(utils.uniq(modules)) != 1):
print "ERROR: multiple modules for test " + m['name']
raise
module = modules.pop()
out.write("\ttest%s\n" % module)
# Keep this so we can provide source directories
m['module'] = module
out.write("\t)\n\n")
# Iteration 3: print the list of sources for these libraries. Sources
# must be singular (so, really, 'source')
out.write("set (SRC src)\n")
out.write("set (MUTATOR_SOURCE_LIST\n")
for m in mutator_dict:
if (len(m['sources']) != 1):
print "ERROR: multiple sources for test " + m['name']
raise
out.write("\t${SRC}/%s/%s\n" % (m['module'], m['sources'][0]))
out.write("\t)\n\n")
# Now, iterate over these lists in parallel with a CMake foreach
# statement to build the add_library directive
out.write("foreach (val RANGE %d)\n" % (len(mutator_dict) - 1))
out.write("\tlist (GET MUTATOR_NAME_LIST ${val} lib)\n")
out.write("\tlist (GET MUTATOR_SOURCE_LIST ${val} source)\n")
out.write("\tlist (GET MUTATOR_MODULE_LIB_LIST ${val} comp_dep)\n")
out.write("\tset(SKIP FALSE)\n")
out.write("\tforeach (dep ${comp_dep})\n")
out.write("\t\tif(NOT TARGET ${dep})\n")
out.write("\t\t\tset(SKIP TRUE)\n")
out.write("\t\tendif()\n")
out.write("\tendforeach()\n")
out.write("\tif(NOT SKIP)\n")
out.write("\t\tadd_library (${lib} ${source})\n")
out.write(
"\t\ttarget_link_libraries (${lib} ${comp_dep} ${LIBTESTSUITE})\n")
out.write("\t\tinstall (TARGETS ${lib} \n")
out.write("\t\t RUNTIME DESTINATION ${INSTALL_DIR}\n")
out.write("\t\t LIBRARY DESTINATION ${INSTALL_DIR})\n")
out.write("\tendif()\n")
out.write("endforeach()\n\n")
def project_pis(projects):
return sorted(uniq([ppi.investigator for ppi in itertools.chain.from_iterable([project.getPIs() for project in projects])]),key=lambda r: r.lastname + ' ' + r.firstname)
def project_pis(projects):
return sorted(uniq([
ppi.investigator for ppi in itertools.chain.from_iterable(
[project.getPIs() for project in projects])
]),
key=lambda r: r.lastname + ' ' + r.firstname)
import time
from glob import iglob
import mailbox
# procmail-py - Email content and spam filtering
# MIT License
# © 2012 Noah K. Tilton <*****@*****.**>
from config import BASE_MAILDIR, MY_DOMAINS, addresses, mark_read
from spam import spamc, blacklisted
from utils import mv, spammy_spamc, mark_as_read, uniq
INBOXDIR = os.path.join(BASE_MAILDIR, "INBOX")
maildirs_on_disk = [os.path.basename(dir) for dir in iglob(os.path.join(BASE_MAILDIR, "*"))]
maildirs_in_file = addresses.values() # <- some of these may not exist
maildirs = uniq(maildirs_on_disk + maildirs_in_file)
mailboxes = dict((d, mailbox.Maildir(os.path.join(BASE_MAILDIR, d), create=True)) for d in maildirs)
# N.B.: the order of the following filters matters. note the return
# statements. this short-circuiting is desirable, but has to be done
# carefully to avoid double-booking mails.
def filter(args):
try:
key, message = args
# BLACKLISTED WORDS/PHRASES
if not message.is_multipart():
# Can't run blacklist logic against multipart messages
# because random phrases such as "gucci" may show up in
# base64-encoded strings ... and I'm too lazy to write a
def numberOfPrimeFactors(n):
return len(uniq(primeFactors(n)))
import mailbox
# procmail-py - Email content and spam filtering
# MIT License
# © 2014 Noah K. Tilton <*****@*****.**>
from config import BASE_MAILDIR, MY_DOMAINS, addresses, mark_read
from spam import spamc, blacklisted
from utils import file, spammy_spamc, mark_as_read, uniq
INBOXDIR = os.path.join(BASE_MAILDIR, "INBOX")
maildirs_on_disk = [
os.path.basename(dir) for dir in iglob(os.path.join(BASE_MAILDIR, "*"))
]
maildirs_in_file = addresses.values() # <- some of these may not exist
maildirs = uniq(maildirs_on_disk + maildirs_in_file)
mailboxes = dict(
(d, mailbox.Maildir(os.path.join(BASE_MAILDIR, d), create=True))
for d in maildirs)
# N.B.: the order of the following filters matters. note the return
# statements. this short-circuiting is desirable, but has to be done
# carefully to avoid double-booking mails.
def mfilter(args):
try:
key, message = args
# BLACKLISTED WORDS/PHRASES
if not message.is_multipart():
# Can't run blacklist logic against multipart messages
def bill_ids_for(congress, options, bill_states={}):
# override if we're actually using this method to get amendments
doing_amendments = options.get('amendments', False)
bill_ids = []
bill_type = options.get('amendment_type' if doing_amendments else 'bill_type', None)
if bill_type:
bill_types = [bill_type]
else:
bill_types = utils.thomas_types.keys()
for bill_type in bill_types:
# This sub is re-used for pulling amendment IDs too.
if (bill_type in ('samdt', 'hamdt', 'supamdt')) != doing_amendments:
continue
# match only links to landing pages of this bill type
# it shouldn't catch stray links outside of the confines of the 100 on the page,
# but if it does, no big deal
link_pattern = "^\s*%s\d+\s*$" % utils.thomas_types[bill_type][1]
# loop through pages and collect the links on each page until
# we hit a page with < 100 results, or no results
offset = 0
while True:
# download page, find the matching links
page = utils.download(
page_for(congress, bill_type, offset),
page_cache_for(congress, bill_type, offset),
options)
if not page:
logging.error("Couldn't download page with offset %i, aborting" % offset)
return None
# extract matching links
doc = html.document_fromstring(page)
links = doc.xpath(
"//a[re:match(text(), '%s')]" % link_pattern,
namespaces={"re": "http://exslt.org/regular-expressions"})
# extract the bill ID from each link
for link in links:
code = link.text.lower().replace(".", "").replace(" ", "")
bill_id = "%s-%s" % (code, congress)
if options.get("fast", False):
fast_cache_path = utils.cache_dir() + "/" + bill_info.bill_cache_for(bill_id, "search_result.html")
old_state = utils.read(fast_cache_path)
# Compare all of the output in the search result's <p> tag, which
# has last major action, number of cosponsors, etc. to a cache on
# disk to see if any major information about the bill changed.
parent_node = link.getparent() # the <p> tag containing the whole search hit
parent_node.remove(parent_node.xpath("b")[0]) # remove the <b>###.</b> node that isn't relevant for comparison
new_state = etree.tostring(parent_node) # serialize this tag
if old_state == new_state:
logging.info("No change in search result listing: %s" % bill_id)
continue
bill_states[bill_id] = new_state
bill_ids.append(bill_id)
if len(links) < 100:
break
offset += 100
# sanity check, while True loops are dangerous
if offset > 100000:
break
return utils.uniq(bill_ids)
def print_mutators_list(out, mutator_dict, test_dict, info, platform):
LibSuffix = platform['filename_conventions']['library_suffix']
ObjSuffix = platform['filename_conventions']['object_suffix']
out.write("######################################################################\n")
out.write("# A list of all the mutators to be compiled\n")
out.write("######################################################################\n\n")
module_list = []
for t in test_dict:
module_list.append(t['module'])
module_set = set(module_list)
for m in module_set:
out.write("\n")
out.write("include_directories (\"..src/%s\")\n" % m)
out.write("set (%s_MUTATORS " % (m))
module_tests = filter(lambda t: m == t['module'], test_dict)
module_mutators = map(lambda t: t['mutator'], module_tests)
for t in utils.uniq(module_mutators):
out.write("%s " % (t))
out.write(")\n\n")
out.write("set (%s_OBJS_ALL_MUTATORS " % (m))
for t in utils.uniq(module_mutators):
out.write("%s%s " % (t, ObjSuffix))
out.write(")\n\n")
# We're doing this cmake list style, so we need multiple iterations
# since cmake doesn't support structs
# Iteration 1: print the list of libraries
out.write("set (MUTATOR_NAME_LIST\n")
for m in mutator_dict:
out.write("\t%s\n" % m['name'])
out.write("\t)\n\n")
# Iteration 2: The appropriate module library for each mutator
out.write("set (MUTATOR_MODULE_LIB_LIST\n")
for m in mutator_dict:
# Module info is stored with the "test" dictionary, not the
# "mutator" dictionary
tests = filter(lambda t: t['mutator'] == m['name'], test_dict)
modules = map(lambda t: t['module'], tests)
if (len(utils.uniq(modules)) != 1):
print "ERROR: multiple modules for test " + m['name']
raise
module = modules.pop()
out.write("\ttest%s\n" % module)
# Keep this so we can provide source directories
m['module'] = module
out.write("\t)\n\n")
# Iteration 3: print the list of sources for these libraries. Sources
# must be singular (so, really, 'source')
out.write("set (SRC src)\n")
out.write("set (MUTATOR_SOURCE_LIST\n")
for m in mutator_dict:
if (len(m['sources']) != 1):
print "ERROR: multiple sources for test " + m['name']
raise
out.write("\t${SRC}/%s/%s\n" % (m['module'], m['sources'][0]))
out.write("\t)\n\n")
# Now, iterate over these lists in parallel with a CMake foreach
# statement to build the add_library directive
out.write("foreach (val RANGE %d)\n" % (len(mutator_dict) - 1))
out.write("\tlist (GET MUTATOR_NAME_LIST ${val} lib)\n")
out.write("\tlist (GET MUTATOR_SOURCE_LIST ${val} source)\n")
out.write("\tlist (GET MUTATOR_MODULE_LIB_LIST ${val} comp_dep)\n")
out.write("\tset(SKIP FALSE)\n")
out.write("\tforeach (dep ${comp_dep})\n")
out.write("\t\tif(NOT TARGET ${dep})\n")
out.write("\t\t\tset(SKIP TRUE)\n")
out.write("\t\tendif()\n")
out.write("\tendforeach()\n")
out.write("\tif(NOT SKIP)\n")
out.write("\t\tadd_library (${lib} ${source})\n")
out.write("\t\ttarget_link_libraries (${lib} ${comp_dep} ${LIBTESTSUITE})\n")
out.write("\t\tinstall (TARGETS ${lib} \n")
out.write("\t\t RUNTIME DESTINATION ${INSTALL_DIR}\n")
out.write("\t\t LIBRARY DESTINATION ${INSTALL_DIR})\n")
out.write("\tendif()\n")
out.write("endforeach()\n\n")
#!/usr/bin/python
# ADIC client program
#
# usage is the same as for "adiC" with additional
# required option "--username", e.g.:
# adic_client.py --username=nobody -vd gradient f.c
#
import sys, glob, socket
from ADIC import ADIC_Client
from utils import uniq, get_username, include_files, get_server, string
adic = ADIC_Client()
username, args = get_username(sys.argv[1:])
options,files = adic.check_options(args)
reduce(lambda x, y: x+y,map(glob.glob, files),[]) # expand unix wildcards
files = uniq(include_files(files,adic.LanguageClass)) # add include files
try:
host,port = get_server("r_adic")
except socket.error:
sys.exit(1)
else:
print adic.submit_request(host,port,username,string.join(options),files)
#!/usr/bin/python
# ADIC client program
#
# usage is the same as for "adiC" with additional
# required option "--username", e.g.:
# adic_client.py --username=nobody -vd gradient f.c
#
import sys, glob, socket
from ADIC import ADIC_Client
from utils import uniq, get_username, include_files, get_server, string
adic = ADIC_Client()
username, args = get_username(sys.argv[1:])
options, files = adic.check_options(args)
reduce(lambda x, y: x + y, map(glob.glob, files), []) # expand unix wildcards
files = uniq(include_files(files, adic.LanguageClass)) # add include files
try:
host, port = get_server("r_adic")
except socket.error:
sys.exit(1)
else:
print adic.submit_request(host, port, username, string.join(options),
files)
def collect(options = {}):
#landing page with links to all guest prayers
page = fromstring(download('http://chaplain.house.gov/chaplaincy/guest_chaplains.html'))
links = uniq(page.xpath("//td/a/@href"))
limit = options.get("limit", False)
if limit:
links = links[:limit]
for link in links:
try:
uid = link.split('id=')[1]
except Exception, e:
print e
continue
html = fromstring(download('http://chaplain.house.gov/chaplaincy/' + link, uid + '.html'))
info = {}
info['name'] = html.xpath("//h2/text()")[0]
#get h3 pairings, guess whether a church is listed based on number of hits
hs = html.xpath("//h3/text()")
if len(hs) > 1:
info['church'] = hs[0].strip()
info['location'] = hs[1].strip()
else:
info['location'] = hs[0].strip()
# get boldface pairings
for pair in html.xpath('//strong'):
if pair.tail:
label, data = pair.text.replace(':', '').strip(), pair.tail.strip()
info[label.lower().split(" ")[0]] = data
elif pair.getnext().tag == 'a':
label, data = pair.text.replace(':', '').strip(), pair.getnext().xpath("text()")[0].strip()
info[label.lower().split(" ")[0]] = data
# add h4/p pairings
for pair in html.xpath('//h4'):
if pair.getnext().tag == 'p':
label, data = pair.text.replace(':', '').strip(), '\n'.join([x.strip() for x in pair.getnext().xpath("text()")])
info[label.lower().split(" ")[0]] = data
if "one" in info:
info["introduction"] = info["one"]
info.pop("one")
#sessions
info["session"] = int(math.floor((int(info["date"].split("/")[-1]) - 1789) / 2) + 1)
info['uid'] = uid
info['member'] = {}
#get bioguide match for sponsor
if 'sponsor' in info:
#fix a recurring typo on House Chaplain website
info['member'] = {}
info['sponsor'] = info['sponsor'].replace("Rep. Rep.", "Rep.")
pieces = re.search("\s(.+?), \(([A-Z])-([A-Z]{2})\)", info['sponsor']).groups()
info['member']['name'] = pieces[0]
info['member']['party'] = pieces[1]
info['member']['state'] = pieces[2]
member_info = lookup(info['member']['name'], info['session'], info['member']['state'], 'house')
if member_info['status'] == 'Found':
#use name info from API instead since it's more canonical
if not member_info['middle_name']:
member_info['middle_name'] = ''
info['member']['name'] = member_info["first_name"] + " " + member_info['middle_name'] + " " + member_info['last_name']
info['member']['name'] = info['member']['name'].replace(" ", " ")
info['member']['state'] = member_info["state"]
info['member']['bioguide'] = member_info['id']
else:
print member_info['status'], info['member']['name']
print "Unable to find %s (%d) in the NYT API" % (info['sponsor'], info['session'])
info['member']['bioguide'] = None
info.pop("sponsor")
write(json.dumps(info, indent=2), os.getcwd() + "/data/" + uid + ".json")