def main():
form = cgi.FieldStorage()
# CGI variables:
# key = project, lab, data, freeze, status
keyField = form.getvalue('key')
if not keyField:
keyField = 'project'
switch = {'project':0, 'lab':1, 'data':2, 'freeze':5, 'status':8 }
titleTag = {'project':"Project", 'lab':"Lab", 'data':"Data_Type",
'freeze':"Freeze", 'status':"Status" }
if keyField not in switch:
keyField = 'project'
keyIndex = switch[keyField]
reportFile, currentDate = encodeReportLib.getRecentReport()
matrix, labels = processReportFile(reportFile, keyIndex)
# Headers for the columns in the data matrix
description = [("Time", "string")]
for label in labels:
tmpDesc = [(label, 'number')]
description += tmpDesc
# Create the data table
data_table = gviz_api.DataTable(description)
data_table.LoadData(matrix)
# Convert to JavaScript code
jscode = data_table.ToJSCode("jscode_data")
# Set variables for HTML output
template_vars = {}
template_vars['jscode'] = jscode
template_vars['dateStamp'] = encodeReportLib.dateIntToDateStr(currentDate)
template_vars['title'] = "ENCODE Amount of Time Until Release by %s" % titleTag[keyField]
template_vars['packageName'] = 'columnchart'
template_vars['visClass'] = 'ColumnChart'
template_vars['style'] = ""
# Set the chart specific configuration options
chart_config = {}
chart_config['isStacked'] = 'true'
chart_config['legendFontSize'] = 16
chart_config['width'] = 1200
chart_config['height'] = 480
chart_config['legend'] = 'bottom'
chart_config['titleX'] = '# of Weeks'
chart_config['titleY'] = '# of Submissions'
chart_config['tooltipFontSize'] = 16
if (keyField == 'freeze'):
chart_config['colors'] = encodeReportLib.getColorArray(len(labels))
template_vars['chart_config'] = json.dumps(chart_config)
encodeReportLib.renderHtml(template_vars, 1, 0)
return
def main():
reportFile, currentDate = encodeReportLib.getRecentReport()
# Output the file as Google JSON Query Response
description = []
dataMatrix = []
line_idx = 0
hash = {}
f = open(reportFile, "r")
for line in f:
line = line.rstrip()
splitArray = line.split('\t')
project = splitArray[0]
freeze = splitArray[5]
assembly = splitArray[9]
if line.startswith('Project') and line_idx == 0:
pass
else:
# Parse the data
if assembly != 'hg19' or freeze != 'Jun-2010':
continue
if not project in hash:
hash[project] = 0
hash[project] += 1
data = line.split('\t')
line_idx += 1
f.close()
for key in hash.keys():
array = []
array.append(key)
array.append(hash[key])
dataMatrix.append(array)
projectHeader = ('Project', 'string')
countHeader = ('Count', 'number')
description.append(projectHeader)
description.append(countHeader)
data_table = gviz_api.DataTable(description)
data_table.LoadData(dataMatrix)
print "Content-type: text/plain"
print
print data_table.ToJSonResponse(req_id=1)
return
def main():
reportFile, currentDate = encodeReportLib.getRecentReport()
# Output the file as Google JSON Query Response
description = []
dataMatrix = []
line_idx = 0
hash = {}
f = open(reportFile, "r")
for line in f:
line = line.rstrip()
splitArray = line.split('\t')
project = splitArray[0]
freeze = splitArray[5]
assembly = splitArray[9]
if line.startswith('Project') and line_idx == 0:
pass
else:
# Parse the data
if assembly != 'hg19' or freeze != 'Jun-2010':
continue
if not project in hash:
hash[project] = 0
hash[project] += 1
data = line.split('\t')
line_idx += 1
f.close()
for key in hash.keys():
array = []
array.append(key)
array.append(hash[key])
dataMatrix.append(array)
projectHeader = ('Project', 'string')
countHeader = ('Count', 'number')
description.append(projectHeader)
description.append(countHeader)
data_table = gviz_api.DataTable(description)
data_table.LoadData(dataMatrix)
print "Content-type: text/plain"
print
print data_table.ToJSonResponse(req_id=1)
return
def main():
# Headers for the columns in the data matrix
description = [ ("date", "date"), ("release", "number"),
("release_cumul", "number"), ("submit", "number"),
("submit_cumul", "number"), ("events", "string") ]
# Create the data table
data_table = gviz_api.DataTable(description)
currentFile, currentDate = encodeReportLib.getRecentReport()
# Create and load the matrix
matrix = processReportFile(currentFile, currentDate)
data_table.LoadData(matrix)
# Convert to JavaScript code
jscode = data_table.ToJSCode("jscode_data")
# Set variables for HTML output
template_vars = {}
template_vars['jscode'] = jscode
template_vars['dateStamp'] = encodeReportLib.dateIntToDateStr(currentDate)
template_vars['title'] = "ENCODE Cumulative Release and Submit Timeline"
template_vars['packageName'] = 'annotatedtimeline'
template_vars['visClass'] = 'AnnotatedTimeLine'
template_vars['style'] = 'style="width:854px; height:480px"'
# Set the chart specific configuration options
chart_config = {}
chart_config['annotationsWidth'] = 15
chart_config['displayAnnotations'] = 'true'
chart_config['displayAnnotationsFilter'] = 'true'
chart_config['fill'] = 25
chart_config['thickness'] = 3
chart_config['width'] = 854
chart_config['height'] = 480
template_vars['chart_config'] = json.dumps(chart_config)
encodeReportLib.renderHtml(template_vars, 0, 0)
return
def main():
# Headers for the columns in the data matrix
description = [("date", "date"), ("release", "number"),
("release_cumul", "number"), ("submit", "number"),
("submit_cumul", "number"), ("events", "string")]
# Create the data table
data_table = gviz_api.DataTable(description)
currentFile, currentDate = encodeReportLib.getRecentReport()
# Create and load the matrix
matrix = processReportFile(currentFile, currentDate)
data_table.LoadData(matrix)
# Convert to JavaScript code
jscode = data_table.ToJSCode("jscode_data")
# Set variables for HTML output
template_vars = {}
template_vars['jscode'] = jscode
template_vars['dateStamp'] = encodeReportLib.dateIntToDateStr(currentDate)
template_vars['title'] = "ENCODE Cumulative Release and Submit Timeline"
template_vars['packageName'] = 'annotatedtimeline'
template_vars['visClass'] = 'AnnotatedTimeLine'
template_vars['style'] = 'style="width:854px; height:480px"'
# Set the chart specific configuration options
chart_config = {}
chart_config['annotationsWidth'] = 15
chart_config['displayAnnotations'] = 'true'
chart_config['displayAnnotationsFilter'] = 'true'
chart_config['fill'] = 25
chart_config['thickness'] = 3
chart_config['width'] = 854
chart_config['height'] = 480
template_vars['chart_config'] = json.dumps(chart_config)
encodeReportLib.renderHtml(template_vars, 0, 0)
return
def main():
form = cgi.FieldStorage()
# CGI variables:
# key = project, lab, data, freeze, or status
# value = values based on "key"
# status = loaded, displayed, approved, reviewing, released or all
# species = human, mouse or all
# norelease = 0 or 1
keyField = form.getvalue('key')
keyValue = form.getvalue('value')
if not keyField or not keyValue:
printErrorMsg("Error: Must specify both key and value variables")
return
# Convert from standard freeze value to non-standard for "post" case
pattern = re.compile("post (.{3})\-(\d{4})")
m = pattern.match(keyValue)
if m:
month = m.group(1)
year = m.group(2)
if month == 'Jun':
# Adjust for June
month = 'June'
keyValue = "post ENCODE %s %s Freeze" % (month, year)
status = form.getvalue('status')
if not status:
status = 'released'
species = form.getvalue('species')
if not species:
species = 'all'
norelease = form.getvalue('norelease')
if not norelease:
norelease = 0
norelease = int(norelease)
freeze = form.getvalue('freeze')
if not freeze:
freeze = 'all'
switch = {'project': 0, 'lab': 1, 'data': 2, 'freeze': 5, 'status': 8}
titleTag = {
'project': "Project",
'lab': "Lab",
'data': "Data_Type",
'freeze': "Freeze",
'status': "Status"
}
keyIndex = switch[keyField]
reportFile, date = encodeReportLib.getRecentReport()
try:
f = open(reportFile, "r")
except:
print >> sys.stderr, "Error: Can't open file '%s'" % f
sys.exit(-1)
print "Content-type: text/plain"
print
rowCount = 0
for line in f:
line = line.rstrip()
splitArray = line.split('\t')
assembly = splitArray[9]
if splitArray[8] == 'revoked' or status == 'replaced':
continue
if norelease == 1 and status == 'released':
continue
if species == 'all':
pass
else:
if species == 'human' and assembly.startswith('hg'):
pass
elif species == 'mouse' and assembly.startswith('mm'):
pass
elif species == assembly:
pass
else:
continue
if splitArray[keyIndex] == keyValue:
if status == 'all' or splitArray[8] == status:
pass
else:
continue
if freeze == 'all' or splitArray[5] == freeze:
pass
else:
continue
print line
rowCount += 1
f.close()
print
print "%d rows" % rowCount
print "key = %s, value = %s, status = %s, species = %s, norelease = %d" % (
keyField, keyValue, status, species, norelease)
def main():
form = cgi.FieldStorage()
# CGI variables:
# key = project, lab, data, freeze, or status
# value = values based on "key"
# status = loaded, displayed, approved, reviewing, released or all
# species = human, mouse or all
# norelease = 0 or 1
keyField = form.getvalue('key')
keyValue = form.getvalue('value')
if not keyField or not keyValue:
printErrorMsg("Error: Must specify both key and value variables")
return
# Convert from standard freeze value to non-standard for "post" case
pattern = re.compile("post (.{3})\-(\d{4})")
m = pattern.match(keyValue)
if m:
month = m.group(1)
year = m.group(2)
if month == 'Jun':
# Adjust for June
month = 'June'
keyValue = "post ENCODE %s %s Freeze" % (month, year)
status = form.getvalue('status')
if not status:
status = 'released'
species = form.getvalue('species')
if not species:
species = 'all'
norelease = form.getvalue('norelease')
if not norelease:
norelease = 0
norelease = int(norelease)
freeze = form.getvalue('freeze')
if not freeze:
freeze = 'all'
switch = {'project':0, 'lab':1, 'data':2, 'freeze':5, 'status':8}
titleTag = {'project':"Project", 'lab':"Lab", 'data':"Data_Type",
'freeze':"Freeze", 'status':"Status"}
keyIndex = switch[keyField]
reportFile, date = encodeReportLib.getRecentReport()
try:
f = open(reportFile, "r")
except:
print >> sys.stderr, "Error: Can't open file '%s'" % f
sys.exit(-1)
print "Content-type: text/plain"
print
rowCount = 0
for line in f:
line = line.rstrip()
splitArray = line.split('\t')
assembly = splitArray[9]
if splitArray[8] == 'revoked' or status == 'replaced':
continue
if norelease == 1 and status == 'released':
continue
if species == 'all':
pass
else:
if species == 'human' and assembly.startswith('hg'):
pass
elif species == 'mouse' and assembly.startswith('mm'):
pass
elif species == assembly:
pass
else:
continue
if splitArray[keyIndex] == keyValue:
if status == 'all' or splitArray[8] == status:
pass
else:
continue
if freeze == 'all' or splitArray[5] == freeze:
pass
else:
continue
print line
rowCount += 1
f.close()
print
print "%d rows" % rowCount
print "key = %s, value = %s, status = %s, species = %s, norelease = %d" % (keyField, keyValue, status, species, norelease)
def main():
form = cgi.FieldStorage()
# CGI Variables
# key = project, lab, data, freeze, or species
# Display data based on the key variable
# norelease = 0 or 1
# 0 = Output all data
# 1 = Output only unreleased data
# species = human, mouse, all
# human = Output only human data
# mouse = Output only mouse data
# all = Output all data
keyField = form.getvalue('key')
if keyField == None:
keyField = 'project'
norelease = form.getvalue('norelease')
if norelease == None:
norelease = 0
norelease = int(norelease)
species = form.getvalue('species')
if species == None:
species = 'all'
switch = {'project':0, 'lab':1, 'data':2, 'freeze':5, 'status':8}
titleTag = {'project':"Project", 'lab':"Lab", 'data':"Data_Type",
'freeze':"Freeze", 'status':"Status"}
if keyField not in switch:
keyField = 'project'
keyIndex = switch[keyField]
# Headers for the columns in the data matrix
description = [(titleTag[keyField], "string")]
fullLabel = ['released', 'reviewing', 'approved', 'displayed', 'downloads', 'loaded']
statusLabel = []
for label in fullLabel:
if label == 'released' and norelease == 1:
continue
tmpDesc = [(label, 'number')]
description += tmpDesc
statusLabel.append(label)
reportFile, currentDate = encodeReportLib.getRecentReport()
matrix = processReportFile(reportFile, statusLabel, keyIndex, norelease,
species)
# Create the data table
data_table = gviz_api.DataTable(description)
data_table.LoadData(matrix)
# Convert to JavaScript code
jscode = data_table.ToJSCode("jscode_data")
# Set variables for HTML output
template_vars = {}
template_vars['jscode'] = jscode
template_vars['dateStamp'] = encodeReportLib.dateIntToDateStr(currentDate)
template_vars['title'] = "ENCODE (%s) Status by %s" % (species,
titleTag[keyField])
template_vars['packageName'] = 'columnchart'
template_vars['visClass'] = 'ColumnChart'
template_vars['style'] = ""
template_vars['species'] = species
template_vars['keyField'] = keyField
template_vars['norelease']= norelease
# Set the chart specific configuration options
chart_config = {}
chart_config['isStacked'] = 'true'
chart_config['legendFontSize'] = 16
chart_config['width'] = 854
chart_config['height'] = 480
chart_config['titleX'] = titleTag[keyField]
chart_config['titleY'] = "# of Submissions"
chart_config['tooltipFontSize'] = 16
chart_config['enableTooltip'] = 'true'
colors = encodeReportLib.getColorArray(len(statusLabel))
colors.reverse()
chart_config['colors'] = colors
template_vars['chart_config'] = json.dumps(chart_config)
encodeReportLib.renderHtml(template_vars, 0, 1)
return
def main():
form = cgi.FieldStorage()
# CGI variables:
# format = raw or pretty or google
# raw = Output file as plain text
# pretty = Output file as Google Visualization Table
# google = Google Data Source Protocol
# reportDate = 0, 1
# returns a JSON object of the latest date of the report file
format = form.getvalue('format')
if format == None:
format = 'pretty'
if format != 'pretty' and format != 'raw' and format != 'google':
format = 'pretty'
reportDate = form.getvalue('reportDate')
if not reportDate:
reportDate = 0
reportDate = int(reportDate)
callback = form.getvalue('callback')
reportFile, currentDate = encodeReportLib.getRecentReport()
if reportDate:
jsonDate = {}
jsonDate['currentDate'] = encodeReportLib.dateIntToDateStr(currentDate)
print "Content-Type: application/json"
print
if not callback:
outString = json.dumps(jsonDate)
else:
outString = callback + "(" + json.dumps(jsonDate) + ")"
print outString
return
try:
f = open(reportFile, "r")
except:
print >> sys.stderr, "Error: Can't open file '%s'" % f
sys.exit(-1)
if format == 'raw':
# Output the file as raw text
print "Content-Type: text/plain"
print
for line in f:
line = line.rstrip()
print line
f.close()
return
elif format == 'pretty' or format == 'google':
# Output the file as Google Visualization Table
description = []
dataMatrix = []
line_idx = 0
for line in f:
line = line.rstrip()
if line.startswith('Project') and line_idx == 0:
# Parse the header line
headers = line.split('\t')
for header in headers:
tmpDesc = (header, 'string')
if header.endswith('Date'):
tmpDesc = (header, 'date')
description.append(tmpDesc)
else:
# Parse the data
data = line.split('\t')
data[6] = encodeReportLib.convertToDate(data[6])
data[7] = encodeReportLib.convertToDate(data[7])
dataMatrix.append(data)
line_idx += 1
f.close()
data_table = gviz_api.DataTable(description)
data_table.LoadData(dataMatrix)
if format == 'google':
print "Content-type: text/plain"
print
print data_table.ToJSonResponse(req_id=1)
return
jscode = data_table.ToJSCode("jscode_data")
# Set variables for HTML output
template_vars = {}
template_vars['jscode'] = jscode
template_vars['dateStamp'] = encodeReportLib.dateIntToDateStr(
currentDate)
template_vars['title'] = "ENCODE Report"
template_vars['packageName'] = 'table'
template_vars['visClass'] = 'Table'
template_vars['style'] = ''
# Set the chart specific configuration options
chart_config = {}
chart_config['page'] = 'enable'
chart_config['pageSize'] = 15
chart_config['pagingSymbols'] = {
'prev': 'prev',
'next': 'next'
}
chart_config['showRowNumber'] = 'true'
template_vars['chart_config'] = json.dumps(chart_config)
encodeReportLib.renderHtml(template_vars, 0, 0)
return
def main():
form = cgi.FieldStorage()
# CGI variables:
# format = raw or pretty or google
# raw = Output file as plain text
# pretty = Output file as Google Visualization Table
# google = Google Data Source Protocol
# reportDate = 0, 1
# returns a JSON object of the latest date of the report file
format = form.getvalue('format')
if format == None:
format = 'pretty'
if format != 'pretty' and format != 'raw' and format != 'google':
format = 'pretty'
reportDate = form.getvalue('reportDate')
if not reportDate:
reportDate = 0
reportDate = int(reportDate)
callback = form.getvalue('callback')
reportFile, currentDate = encodeReportLib.getRecentReport()
if reportDate:
jsonDate = {}
jsonDate['currentDate'] = encodeReportLib.dateIntToDateStr(currentDate)
print "Content-Type: application/json"
print
if not callback:
outString = json.dumps(jsonDate)
else:
outString = callback + "(" + json.dumps(jsonDate) + ")"
print outString
return
try:
f = open(reportFile, "r")
except:
print >> sys.stderr, "Error: Can't open file '%s'" % f
sys.exit(-1)
if format == 'raw':
# Output the file as raw text
print "Content-Type: text/plain"
print
for line in f:
line = line.rstrip()
print line
f.close()
return
elif format == 'pretty' or format == 'google':
# Output the file as Google Visualization Table
description = []
dataMatrix = []
line_idx = 0
for line in f:
line = line.rstrip()
if line.startswith('Project') and line_idx == 0:
# Parse the header line
headers = line.split('\t')
for header in headers:
tmpDesc = (header, 'string')
if header.endswith('Date'):
tmpDesc = (header, 'date')
description.append(tmpDesc)
else:
# Parse the data
data = line.split('\t')
data[6] = encodeReportLib.convertToDate(data[6])
data[7] = encodeReportLib.convertToDate(data[7])
dataMatrix.append(data)
line_idx += 1
f.close()
data_table = gviz_api.DataTable(description)
data_table.LoadData(dataMatrix)
if format == 'google':
print "Content-type: text/plain"
print
print data_table.ToJSonResponse(req_id=1)
return
jscode = data_table.ToJSCode("jscode_data")
# Set variables for HTML output
template_vars = {}
template_vars['jscode'] = jscode
template_vars['dateStamp'] = encodeReportLib.dateIntToDateStr(currentDate)
template_vars['title'] = "ENCODE Report"
template_vars['packageName'] = 'table'
template_vars['visClass'] = 'Table'
template_vars['style'] = ''
# Set the chart specific configuration options
chart_config = {}
chart_config['page'] = 'enable'
chart_config['pageSize'] = 15
chart_config['pagingSymbols'] = {'prev': 'prev', 'next': 'next'};
chart_config['showRowNumber'] = 'true'
template_vars['chart_config'] = json.dumps(chart_config)
encodeReportLib.renderHtml(template_vars, 0, 0)
return
