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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
import httplib
from dbFunction import webqtlDatabaseFunction
import SharingBody
#########################################
# Sharing Info
#########################################
class SharingInfo:
def __init__(self, GN_AccessionId, InfoPageName):
self.GN_AccessionId = GN_AccessionId
self.InfoPageName = InfoPageName
def getInfo(self):
cursor = webqtlDatabaseFunction.getCursor()
if (not cursor):
return
sql = "select Id, GEO_Series, Status, Title, Organism, Experiment_Type, Summary, Overall_Design, Contributor, Citation, Submission_Date, Contact_Name, Emails, Phone, URL, Organization_Name, Department, Laboratory, Street, City, State, ZIP, Country, Platforms, Samples, Species, Normalization, InbredSet, InfoPageName, DB_Name, Organism_Id, InfoPageTitle, GN_AccesionId, Tissue, AuthorizedUsers, About_Cases, About_Tissue, About_Download, About_Array_Platform, About_Data_Values_Processing, Data_Source_Acknowledge, Progreso from InfoFiles where "
if(self.GN_AccessionId):
sql += "GN_AccesionId = %s"
cursor.execute(sql, self.GN_AccessionId)
elif (self.InfoPageName):
sql += "InfoPageName = %s"
cursor.execute(sql, self.InfoPageName)
else:
raise 'No correct parameter found'
info = cursor.fetchone()
# fetch datasets file list
try:
conn = httplib.HTTPConnection("atlas.uthsc.edu")
conn.request("GET", "/scandatasets.php?GN_AccesionId=%s" % (info[32]))
response = conn.getresponse()
data = response.read()
filelist = data.split()
conn.close()
except Exception:
filelist = []
return info, filelist
def getBody(self, infoupdate=""):
info, filelist = self.getInfo()
if filelist:
htmlfilelist = '<ul style="line-height:160%;">\n'
for i in range(len(filelist)):
if i%2==0:
filename = filelist[i]
filesize = filelist[i+1]
htmlfilelist += "<li>"
htmlfilelist += '<a href="ftp://atlas.uthsc.edu/users/shared/Genenetwork/GN%s/%s">%s</a>' % (self.GN_AccessionId, filename, filename)
htmlfilelist += ' '
#r=re.compile(r'(?<=\d)(?=(\d\d\d)+(?!\d))')
#htmlfilelist += '[%s B]' % r.sub(r',',filesize)
if 12<len(filesize):
filesize=filesize[0:-12]
filesize += ' T'
elif 9<len(filesize):
filesize=filesize[0:-9]
filesize += ' G'
elif 6<len(filesize):
filesize=filesize[0:-6]
filesize += ' M'
elif 3<len(filesize):
filesize=filesize[0:-3]
filesize += ' K'
htmlfilelist += '[%sB]' % filesize
htmlfilelist += "</li>\n"
htmlfilelist += "</ul>"
else:
htmlfilelist = "Data sets are not available or are not public yet."
return SharingBody.sharinginfo_body_string % (info[31], info[32], infoupdate, info[32], info[1], info[3], info[30], info[4], info[27], info[33], info[2], info[23], info[26], info[11], info[15], info[16], info[18], info[19], info[20], info[21], info[22], info[13], info[12], info[14], info[14], htmlfilelist, info[6], info[35], info[36], info[37], info[38], info[39], info[40], info[5], info[7], info[8], info[9], info[10], info[17], info[24])
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