# 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])