def episodes(id_show, id_episode):
if id_show not in utils.AVAILABE_SHOWS:
section_template = "./templates/404.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=section_template,
sectionData={})
show = json.loads(utils.getJsonFromFile(id_show))
episodes = show['_embedded']['episodes']
try:
parsed_id_episode = int(id_episode)
for chapter in episodes:
if chapter['id'] == parsed_id_episode:
section_template = "./templates/episode.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=section_template,
sectionData=chapter)
except ValueError:
pass
section_template = "./templates/404.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=section_template,
sectionData={})
def episode(id, episode_id):
sectionData = utils.get_specific_episode_api(id, episode_id)
if not sectionData:
sectionTemplate = "./templates/404.tpl"
return template("./pages/index.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,
sectionData={})
else:
sectionTemplate = "./templates/episode.tpl"
return template("./pages/index.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,
sectionData=sectionData)
def show(id):
sectionData = utils.get_specific_show_api(id)
if not sectionData:
sectionTemplate = "./templates/404.tpl"
return template("./pages/index.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,
sectionData={})
else:
sectionTemplate = "./templates/show.tpl"
return template("./pages/index.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,
sectionData=sectionData)
def show_id(show_id):
sectionTemplate = "./templates/show.tpl"
sectionData = utils.show_info(show_id)
try:
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
query=sectionData)
except:
return template("./pages/index.html",
sectionTemplate="./templates/404.tpl",
version=utils.getVersion(),
sectionData={})
def episode_id(episode_id, show_id):
sectionTemplate = "./templates/episode.tpl"
sectionData = utils.get_episode_info(show_id, episode_id)
try:
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=sectionData)
except:
return template("./pages/index.html",
sectionTemplate="./templates/404.tpl",
version=utils.getVersion(),
sectionData={})
def browse():
result = utils.data_of_shows(utils.api_shows_address, utils.AVAILABE_SHOWS)
sectionTemplate = "./templates/browse.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=result)
def browse():
sectionTemplate = "./templates/browse.tpl"
sectionData = utils.getShows()
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=sectionData)
def search():
searchQuery = request.forms.get('q')
results = []
shows = [
json.loads(utils.getJsonFromFile(id)) for id in utils.AVAILABE_SHOWS
]
for show in shows:
for episode in show['_embedded']['episodes']:
if episode['name'] is None:
tmpName = ''
else:
tmpName = episode['name']
if episode['summary'] is None:
tmpSummary = ''
else:
tmpSummary = episode['summary']
if searchQuery in tmpName or searchQuery in tmpSummary:
res = {}
res['showid'] = show['id']
res['episodeid'] = episode['id']
res['text'] = show['name'] + ":" + episode['name']
results.append(res)
sectionTemplate = "./templates/search_result.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
query=searchQuery,
results=results,
sectionData={})
def show(show_id):
sectionTemplate = "./templates/show.tpl"
show_current = json.loads(utils.getJsonFromFile(show_id))
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=show_current)
def browse():
sectionTemplate = "./templates/browse.tpl"
result = utils.getShows()
return template(INDEX,
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=result)
def search():
sectionTemplate = "./templates/search_result.tpl"
search_input = request.forms.get('q')
shows_list = [
json.loads(utils.getJsonFromFile(elem))
for elem in utils.AVAILABE_SHOWS
]
search_output = []
for shows in range(len(shows_list) - 1):
for episodes in range(
len(shows_list[shows]['_embedded']['episodes']) - 1):
show_current = shows_list[shows]
if search_input in str(show_current['name']) \
or search_input in str(show_current['_embedded']['episodes'][episodes]['name']) \
or search_input in str(show_current['_embedded']['episodes'][episodes]['summary']):
search_match = {
"showid":
shows_list[shows]['id'],
"episodeid":
shows_list[shows]['_embedded']['episodes'][episodes]['id'],
"text":
(shows_list[shows]['name'] + ": " + shows_list[shows]
['_embedded']['episodes'][episodes]['name'])
}
search_output.append(search_match)
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=search_output,
query=search_input)
def get_show(id):
sectionTemplate = "./templates/show.tpl"
result = utils.getShow(id)
return template(INDEX,
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=result)
def show(number):
selected_show = json.loads(utils.getJsonFromFile(number))
show_template = "./templates/show.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=show_template,
sectionData=selected_show)
def get_episode(show_id, episode_id):
sectionTemplate = "./templates/episode.tpl"
episode = utils.getEpisode(show_id, episode_id)
return template(INDEX,
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=episode)
def routing(name):
sectionTemplate = "./templates/show.tpl"
sectionData = json.loads(utils.getJsonFromFile(name))
return template(sectionTemplate,
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
result=sectionData)
def show(name):
sectionTemplate = "./templates/show.tpl"
sectionData = json.loads(utils.getJsonFromFile(name))
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=sectionData)
def episode(number, ep_number):
show = json.loads(utils.getJsonFromFile(number))
for episode in show["_embedded"]["episodes"]:
if int(ep_number) == episode["id"]:
return template("./templates/episode.tpl",
version=utils.getVersion(),
result=episode)
return
def signin():
if request.method == 'POST':
return handleLogin(request)
else:
context = {'err_msg': ''}
sectionTemplate = "./templates/login.tpl"
return template("./pages/index.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,**context,
sectionData={})
def search():
sectionTemplate = "./templates/seaerch_result.tpl"
query = request.forms.get('q')
return template("./pages/index.html",
version=getVersion(),
sectionData={},
sectionTemplate=sectionTemplate,
query=query,
results=search(query))
def display_show(showname):
sectionTemplate = "./templates/show.tpl"
sectionData = utils.displayShow(showname)
if sectionData == 'error':
return error(error)
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=sectionData)
def browse():
shows = []
for show in utils.AVAILABE_SHOWS:
shows.append(json.loads(utils.getJsonFromFile(show)))
browse_template = "./templates/browse.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=browse_template,
sectionData=shows)
def browse():
with connection.cursor() as cursor:
sql = "SELECT * FROM categories"
cursor.execute(sql)
result = cursor.fetchall()
sectionTemplate = "./templates/store1.tpl"
sectionData = result
return template("./pages/logged.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,
sectionData=sectionData)
def display_episode(showname, episodenum):
sectionTemplate = "./templates/episode.tpl"
sectionData = utils.displayEp(showname, episodenum)
if sectionData == 'error':
return error(error)
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData={sectionData})
def show(number):
with connection.cursor() as cursor:
sql = "SELECT id_product,pr.product_name, pr.product_image, price, sup.supermarket_name, sup.supermarket_image, cat.id as category_id FROM prices as p1 inner join supermarkets as sup on p1.id_supermarket = sup.id inner join products as pr on p1.id_product = pr.id inner join categories as cat on pr.id_category = cat.id group by id_product,pr.product_name, pr.product_image, price, sup.supermarket_name, sup.supermarket_image having price <= (select min(p2.price) from prices as p2 where p2.id_product = p1.id_product group by p2.id_product) and category_id ={} order by price;".format(number)
cursor.execute(sql)
result = cursor.fetchall()
print(result)
sectionTemplate = "./templates/store2.tpl"
return template("./pages/logged.html", version=utils.getVersion(), sectionTemplate=sectionTemplate,
sectionData=result)
def index():
sectionTemplate = "./templates/browse.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=[
json.loads(utils.getJsonFromFile(movie))
for movie in utils.AVAILABLE_SHOWS
])
def browse():
sectionTemplate = "./templates/browse.tpl"
sectionData = [
json.loads(utils.getJsonFromFile(id)) for id in utils.AVAILABE_SHOWS
]
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData=sectionData)
def handleLogin(request):
email = request.forms.get("email")
password = request.forms.get("password")
userVerified = verifyUser(email, password)
if userVerified:
redirect('/store')
else:
context = {"err_msg": "Wrong nickname or password"}
return template("./pages/logged.html",version=utils.getVersion(), sectionTemplate="./templates/login.tpl", **context, sectionData={})
def episode(showId, episodeId):
sectionData = json.loads(utils.getJsonFromFile(showId))
for ep in sectionData['_embedded']['episodes']:
if ep['id'] == int(episodeId):
sectionData = ep
break
return template("./templates/episode.tpl",
version=utils.getVersion(),
result=sectionData)
def search_result():
query = request.forms.get('q')
sectionTemplate = "./templates/search_result.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
query=query,
results=utils.search(query),
sectionData={})
def search_shows():
q = request.POST.get("q")
search_results = utils.search_shows(q)
sectionTemplate = "./templates/search_result.tpl"
return template("./pages/index.html",
version=utils.getVersion(),
sectionTemplate=sectionTemplate,
sectionData={},
results=search_results,
query=q)
def logException_internal(exClass, exValue, stack):
import linecache, time
log = logging.getLogger('exception')
counter = 0
log.critical('Exception occured: %s' % time.strftime("%Y-%m-%d %H:%M:%S"))
try:
import utils
log.critical('grid-control: %s' % utils.getVersion())
except:
log.critical('grid-control: Unknown version')
log.critical('')
while stack:
counter += 1
code = stack.tb_frame.f_code
# Output relevant code fragment
linecache.checkcache(code.co_filename)
log.critical('Stack #%s [%s:%d] %s', counter, code.co_filename, stack.tb_lineno, code.co_name)
fmtLine = lambda line: linecache.getline(code.co_filename, line).rstrip().replace('\t', ' ')
log.critical('\t | %s', fmtLine(stack.tb_lineno - 1))
log.critical('\t=>| %s', fmtLine(stack.tb_lineno + 0))
log.critical('\t | %s', fmtLine(stack.tb_lineno + 1))
log.critical('')
# Output local and class variables
def safeRepr(obj):
try:
value = repr(obj)
if log.isEnabledFor(logging.INFO1) or (len(value) < 500):
return value
return value[:500] + " ... [length:%d]" % len(value)
except:
return 'unable to display!'
def display(keys, varDict, varPrefix = ''):
maxlen = max(map(len, tmp.keys()) + [0])
for var in sorted(keys):
value = safeRepr(varDict[var])
if 'password' in var:
value = '<redacted>'
log.critical('\t\t%s%s = %s', varPrefix, var.ljust(maxlen), value)
tmp = dict(stack.tb_frame.f_locals)
log.critical('\tLocal variables:')
display(filter(lambda v: v != 'self', tmp), tmp)
try:
log.critical('\tClass variables (%s):' % safeRepr(tmp['self']))
display(tmp['self'].__dict__, tmp['self'].__dict__, 'self.')
except:
pass
log.critical('')
stack = stack.tb_next
if exClass:
exMessage = '%s: %s' % (exClass.__name__, str.join(' ', map(str, exValue.args)))
log.critical(exMessage)
del stack
return exMessage + '\n'
id = os.path.abspath(timestamp)
libs = {}
frags = []
cf = ""
format ="fastq"
inserts = []
maxreadlen = 250
innie = True
readlibs = []
SFFLinkerType = "titanium"
contigs = dict()
lastLib = 0
libs = ""
for o, a in opts:
if o in ("-V", "--version"):
print "metAMOS Version %s"%(utils.getVersion())
sys.exit()
elif o in ("-W", "--workflow"):
if a.lower() not in availableWorkflows.keys():
print "Error: unknown wofkflow %s specified. Please choose one of %s."%(a.lower(), ",".join(availableWorkflows.keys()))
sys.exit(1)
wf = availableWorkflows[a.lower()]
# process any requested contigs/libs
for lib in wf.readlibs:
nlib = readLib(lib.format, lib.f1.path, "" if lib.interleaved or not lib.mated else lib.f2.path, lib.innie, lib.linkerType, lib.mated, lib.interleaved)
readlibs.append(nlib)
inserts.append([lib.mmin, lib.mmax])
for contig in wf.asmcontigs:
contigs[os.path.basename(contig)] = contig
selectedWorkflow = wf.name
def printConfiguration(fileName=None):
configurationText = []
configurationText.append("metAMOS configuration summary:\n")
configurationText.append("metAMOS Version:\t%s\n"%(utils.getVersion()))
configurationText.append("Time and Date:\t\t%s\n"%(str(datetime.date.today())))
configurationText.append("Working directory:\t%s\n"%(utils.Settings.rundir))
configurationText.append("Prefix:\t\t\t%s\n"%(utils.Settings.PREFIX))
configurationText.append("K-Mer:\t\t\t%s\n"%(utils.Settings.kmer))
configurationText.append("Threads:\t\t%d\n"%(utils.Settings.threads))
configurationText.append("Taxonomic level:\t%s\n"%(utils.Settings.taxa_level))
configurationText.append("Verbose:\t\t%s\n"%(utils.Settings.VERBOSE))
configurationText.append("Steps to skip:\t\t%s\n"%(", ".join(skipsteps)))
configurationText.append("Steps to force:\t\t%s\n"%(", ".join(forcesteps)))
# get metamos citations
configurationText.append("\n")
configurationText.append("[citation]\n")
(progName, citation) = utils.getProgramCitations(settings, "metamos")
configurationText.append(progName + "\n")
configurationText.append("\t" + citation + "\n\n")
if isolate_genome == True:
(progName, citation) = utils.getProgramCitations(settings, "metamos_isolate")
configurationText.append(progName + "\n")
configurationText.append("\t" + citation + "\n\n")
configurationText.append("\n")
configurationText.append("Step-specific configuration:\n")
for type in selected_programs.keys():
progs = set(selected_programs[type].split(","))
configurationText.append("[" + type + "]\n")
for prog in progs:
# special case for validation, orf is a reference to selected orf finder, n50 is nothing
if type == "validate" and prog == "n50":
continue
if type == "validate" and prog == "orf":
prog = selected_programs["findorfs"]
if type == "preprocess" and prog == "none":
configurationText.append(prog.upper() + "\n\tN/A\n\n")
continue
if type == "preprocess" and prog == "metamos":
configurationText.append("metAMOS built-in filtering\n\tN/A\n\n")
continue
if prog == None or prog == "none":
configurationText.append("None\n\n")
else:
(progName, citation) = utils.getProgramCitations(settings, prog)
if progName == "":
configurationText.append(prog + "\n")
else:
configurationText.append(progName + "\n")
try:
configurationText.append("\t" + eval("utils.Settings.%s"%(prog.replace("-", "_").upper()))+"\n")
except AttributeError:
try:
configurationText.append("\t" + generic.getLocation(utils.STEP_NAMES.mapping[type.upper()], prog) + "\n")
except KeyError:
configurationText.append("UNKNOWN")
if citation != "":
configurationText.append("\t" + citation + "\n\n")
# add step-indepent citations that are always run
configurationText.append("[other]\n")
for prog in always_run_programs:
if prog == None or prog == "none":
configurationText.append("None\n\n")
else:
(progName, citation) = utils.getProgramCitations(settings, prog)
configurationText.append(progName + "\n")
try:
configurationText.append("\t" + eval("utils.Settings.%s"%(prog.upper()))+"\n")
except AttributeError:
configurationText.append("\tUNKNOWN\n")
configurationText.append("\t" + citation + "\n\n")
if fileName == "" or fileName == None:
print ''.join(configurationText)
else:
conf = open(fileName, 'w')
conf.write(''.join(configurationText))
conf.close()