def get_onefile(self, table, kwargs):
"""Print the raw data (csv format) into a single file for the user to download
table(string) - name of table to pull the vars from
kwargs - optional query info
"""
u = cherrypy.user.name
datatable = "%s_%s" % (table, u)
dm = mt.MongoAdmin("datamaster")
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(datatable, sids=True)
q = parseQuery(kwargs)
# put the headers together
headers = [sid, trial] + IVs + DVs
sort = [sid, trial]
if run:
headers.insert(3, run)
sort = [sid, run, trial]
if outlier:
headers += [outlier]
# write that biznass out
name = dm.write(datatable, q, headers=headers, sort=sort)
name = os.path.basename(name)
name += ".csv"
up = mt.MongoAdmin("datamaster").db["user_files"].posts
if not up.find_one({"user": u, "fname": name}):
up.insert({"user": u, "fname": name})
common.activity_log("download", "download single raw", table, kwargs)
output = getAlert(
"Your file is ready. <a href='%s/output/%s'>Click here to download.</a>" % (domain, name), "good"
)
return output
def make_prts(self, table):
"""make prt interface
"""
datatable = "%s_%s" % (table, cherrypy.user.name)
sid, trial, IVs, DVs, sids, run, outlier = common.getVariables(datatable, sids=False)
output = "<p>Let's make some PRTs (files for BrainVoyager).</p>"
form = "<label>Experiment Onset Delay (ms):</label>"
form += '<input type="number" name="prt_onset" value=0>'
form += "<label>Stimulus Onset:</label>" + getOptions(IVs, ID="prt_stim_onset")
form += '<label>Stimulus Offset (ms):</label><input type="number" name="prt_offset" value=2000>'
form += "<hr>"
form += "<label>Condition:</label>" + getOptions(IVs, ID="prt_cond")
form += "<label>Specify IV levels(e.g., <em>level1, level2</em> - leave blank to simply use levels present in run):</label>"
form += "<input type ='text' name='prt_con_names'/></input><br/>"
form += "<hr>"
form += "<label>Check Accuracy?</label>" + getRadios(["yes", "no"], name="check_error")
form += "<label>Accuracy listed in...</label>" + getOptions(DVs, ID="prt_ACC")
form += "<label>Reaction time listed in...:</label>" + getOptions(DVs, ID="prt_RT")
form += "<hr>"
output += getForm(form, download_url)
return output
def index(self, **kwargs):
u = cherrypy.user.name
output = ""
t = common.getCookie('datamaster_table')
#select any tables
if kwargs.has_key('select_table'):
t = kwargs['select_table']
common.setCookie('datamaster_table', t)
if t:
table = "%s_%s" % (t, u)
var_table = "%s_%s_vars" % (t, u)
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(table, sids=True)
posts = mt.MongoAdmin("datamaster").db[var_table].posts
if kwargs.has_key('set_op'):
output += self.query(table, kwargs)
if kwargs.has_key('new_var'):
output += self.create(table, kwargs)
if kwargs.has_key('merge_var'):
output += self.merge(table, kwargs)
if kwargs.has_key('op-outlier-recurse-field'):
output += self.outlier(table, kwargs)
keys = posts.find().distinct('name')
condition = getCondition(var_options=keys, label='If (optional)')
setter = getSetter(var_options=keys, label='Set (required)')
modify = getForm(condition + setter, modify_url, legend='transform a variable')
create = getForm(template.get_def("create_column").render(var_options=keys), modify_url)
merge = getForm(template.get_def("merge_column").render(var_options=keys), modify_url)
preview = common.preview(table, kwargs, modify_url)
outliers = common.outlierReport(mt.MongoAdmin("datamaster").db[table].posts) + getForm(template.get_def("mark_outliers").render(DVs=DVs), modify_url)
else:
modify = no_table
create = no_table
merge = no_table
preview = no_table
outliers = no_table
items = [['select table', select_table(modify_url, t)], ['create', create], ['merge', merge], ['modify', modify], ['detect outliers', outliers], ['preview', preview]]
output += getAccordion(items, contentID='modify-small')
return getPage(output, "modify", "modify")
def prts(self, table, kwargs):
"""make prts function
"""
datatable = "%s_%s" % (table, cherrypy.user.name)
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(datatable, sids=False)
# get the values
onset_start = int(kwargs["prt_onset"])
stim_onset = kwargs["op-prt_stim_onset"]
stim_offset = int(kwargs["prt_offset"])
if kwargs["check_error"] == "no":
check_errors = False
else:
check_errors = True
ACC = kwargs["op-prt_ACC"]
RT = kwargs["op-prt_RT"]
conditions = []
if kwargs["prt_con_names"]:
for con in kwargs["prt_con_names"].split(","):
conditions.append(con.strip())
output = ""
myCond = kwargs["op-prt_cond"]
settings = settings = (
"""FileVersion: 2\n\nResolutionOfTime: msec\n\nExperiment: %s\n\nBackgroundColor: 0 0 0\nTextColor: 255 255 255\nTimeCourseColor: 255 255 255\nTimeCourseThick: 3\nReferenceFuncColor: 0 0 80\nReferenceFuncThick: 3\n\n"""
% (table)
)
prt_maker = makePRTs.prtFile(
"datamaster", datatable, sid, run, settings, onset_start, stim_offset, check_errors
)
prt_maker.make(myCond, conditions, stim_onset, ACC, RT, trial, balance=False)
files = prt_maker.fileList
zipname = "%s_%s_prts" % (datatable, myCond)
zippath = os.path.join("output", "%s.zip" % zipname)
z = zipfile.ZipFile(zippath, "w")
for f in files:
z.write(f)
os.system("rm %s" % f)
z.close()
up = mt.MongoAdmin("datamaster").db["user_files"].posts
if not up.find_one({"user": cherrypy.user.name, "fname": zipname + ".zip"}):
up.insert({"user": cherrypy.user.name, "fname": zipname + ".zip"})
common.activity_log("download", "download prts", table, kwargs)
output += getAlert(
"Your files are ready. <a href='%s/%s'>Click here to download.</a>" % (domain, zippath), "good"
)
return output
def raw(self, table):
"""Raw data interface
table(string)
"""
datatable = "%s_%s" % (table, cherrypy.user.name)
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(datatable, sids=False)
form = ""
form += getCondition([trial] + IVs + DVs, "Include only data where:")
output = "<p>You will get one file for each subject you have.</p>"
output += getForm(form, download_url, hidden=["dl", "raw"])
return output
def get_raw(self, table, kwargs):
"""Print the raw data (csv format) and put data in a zip file for download
table(string) - name of table to pull the vars from
kwargs - optional query info
"""
u = cherrypy.user.name
datatable = "%s_%s" % (table, u)
dm = mt.MongoAdmin("datamaster")
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(datatable, sids=True)
q = parseQuery(kwargs)
files = []
for sub in sids:
headers = [sid, trial] + IVs + DVs
sort = trial
if run:
headers.insert(3, run)
sort = [run, trial]
if outlier:
headers += [outlier]
name = dm.write(datatable, dict(q, **{sid: sub}), headers=headers, sort=sort)
files.append(name)
zipname = datatable
zipname = os.path.join("output", zipname + ".zip")
z = zipfile.ZipFile(zipname, "w")
for f in files:
z.write(f + ".csv")
os.system("rm %s.csv" % f)
z.close()
up = mt.MongoAdmin("datamaster").db["user_files"].posts
if not up.find_one({"user": u, "fname": datatable + ".zip"}):
up.insert({"user": u, "fname": datatable + ".zip"})
common.activity_log("download", "download raw", table, kwargs)
output = getAlert(
"Your files are ready. <a href='%s/%s'>Click here to download.</a>" % (domain, zipname), "good"
)
return output
def aggregate(self, table, kwargs):
u = cherrypy.user.name
datatable = "%s_%s" % (table, u)
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(datatable, sids=False)
output = ""
ivs = []
dvs = []
for k in kwargs.keys():
if kwargs[k] == "on":
if k in IVs:
ivs.append(k)
elif k in DVs:
dvs.append(k)
q = parseQuery(kwargs)
w = mt.WriteTable(dvs, ivs, q, "datamaster", datatable, subject=sid)
w.Compute()
w.WriteForSPSS()
w.WriteForR()
spss_name = w.name + ".csv"
r_name = w.name + ".dat"
up = mt.MongoAdmin("datamaster").db["user_files"].posts
if not up.find_one({"user": u, "fname": spss_name}):
up.insert({"user": u, "fname": spss_name})
if not up.find_one({"user": u, "fname": r_name}):
up.insert({"user": u, "fname": r_name})
common.activity_log("download", "aggregate", table, kwargs)
output += (
"<p>Your data is ready. <a href='%s/output/%s'>Click here for SPSS format</a> or <a href='%s/output/%s'>click here for R format.</p>"
% (domain, spss_name, domain, r_name)
)
return output
def agg(self, table):
"""aggregate interface
table(string)
"""
datatable = "%s_%s" % (table, cherrypy.user.name)
sid, trial, IVs, DVs, run, outlier, sids = common.getVariables(datatable, sids=False)
check_vars = common.checkVariables(datatable, ["subject", "trial", "IV", "DV"])
if check_vars:
output = check_vars
else:
form = ""
form += getCheckbox(IVs)
form += getCheckbox(DVs)
form += getCondition(IVs + DVs + [trial], "Include only data where:")
output = "<p>Here are the variables you have labelled. Select the ones you want to combine into your new file. You will get a single file with each subject's average DV(s) for each IV(s).</p>"
output += getForm(form, download_url, hidden=["dl", "agg"])
return output