diff options
Diffstat (limited to 'web/webqtl/dataSharing/SharingInfo.py')
| -rwxr-xr-x | web/webqtl/dataSharing/SharingInfo.py | 98 |
1 files changed, 98 insertions, 0 deletions
diff --git a/web/webqtl/dataSharing/SharingInfo.py b/web/webqtl/dataSharing/SharingInfo.py new file mode 100755 index 00000000..10abcefa --- /dev/null +++ b/web/webqtl/dataSharing/SharingInfo.py @@ -0,0 +1,98 @@ +# 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]) |