From 243a0ff8a0926f9653d8196613d55fe8abdba871 Mon Sep 17 00:00:00 2001 From: Sam Ockman Date: Fri, 29 Jun 2012 18:24:50 -0400 Subject: removed some previously deleted files --- wqflask/dataSharing/SharingBody.py | 290 -------------------------- wqflask/dataSharing/SharingInfo.py | 98 --------- wqflask/dataSharing/SharingInfoAddPage.py | 47 ----- wqflask/dataSharing/SharingInfoDeletePage.py | 55 ----- wqflask/dataSharing/SharingInfoEditPage.py | 51 ----- wqflask/dataSharing/SharingInfoPage.py | 52 ----- wqflask/dataSharing/SharingInfoUpdatePage.py | 109 ---------- wqflask/dataSharing/SharingListDataSetPage.py | 99 --------- wqflask/dataSharing/SharingPage.py | 40 ---- wqflask/dataSharing/__init__.py | 0 10 files changed, 841 deletions(-) delete mode 100755 wqflask/dataSharing/SharingBody.py delete mode 100755 wqflask/dataSharing/SharingInfo.py delete mode 100755 wqflask/dataSharing/SharingInfoAddPage.py delete mode 100755 wqflask/dataSharing/SharingInfoDeletePage.py delete mode 100755 wqflask/dataSharing/SharingInfoEditPage.py delete mode 100755 wqflask/dataSharing/SharingInfoPage.py delete mode 100755 wqflask/dataSharing/SharingInfoUpdatePage.py delete mode 100755 wqflask/dataSharing/SharingListDataSetPage.py delete mode 100755 wqflask/dataSharing/SharingPage.py delete mode 100755 wqflask/dataSharing/__init__.py diff --git a/wqflask/dataSharing/SharingBody.py b/wqflask/dataSharing/SharingBody.py deleted file mode 100755 index 4445e0d1..00000000 --- a/wqflask/dataSharing/SharingBody.py +++ /dev/null @@ -1,290 +0,0 @@ -# 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 - -sharing_body_string = """ - - -

Data Set Download

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Species: - - - -
- Group: - - - -
- Type: - - - -
- Database: - - - -
-     -
- - -
- -

GeneNetwork Accession Number

-
- - - - - - - - - - - - -
GN:  E.g. 112
-     -
-
- - -""" - -sharinginfo_body_string = """ -List of DataSets
-

%s -modify this page -%s -

- - - - - -
- - - - - - - - - - - -
GN Accession: GN%s
GEO Series: %s
Title: %s
Organism: %s
Group: %s
Tissue: %s
Dataset Status: %s
Platforms: %s
Normalization: %s
- See Contact Information
-
-		 - - - - - - - -
Download datasets and supplementary data files
%s
-
-
-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Summary:
%s

About the cases used to generate this set of data:
%s

About the tissue used to generate this set of data:
%s

About downloading this data set:
%s

About the array platform:
%s

About data values and data processing:
%s

Data source acknowledgment:
%s

Experiment Type:
%s

Overall Design:
%s

Contributor:
%s

Citation:
%s

Submission Date:
%s

Laboratory:
%s

Samples:
%s

-

- -""" - -sharinginfoedit_body_string = """ -

%s

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Principal Investigator

Contact Name:
Emails:
Phone:
URL:
Organization Name:
Department:
Laboratory:
Address:
City:
State:
ZIP:
Country:

Summary

Summary:

Biology

Experiment Design:
About the cases used to
generate this set of data:
About the tissue used to
generate this set of data:

Technique

About downloading this data set:
About the array platform:

Bioinformatics

About data values and
data processing:
Overall Design:

Misc

Contributor:
Citation:
Data source acknowledgment:

Administrator ONLY

GN Accesion Id:
DB Title in GN:
GEO Series:
Status:
Title:
Organism_Id (Taxonomy ID):
Organism:
Submission Date:
Platforms:
Species:
Tissue:
Normalization:
Inbred Set:
Info Page Name:
Samples:
Authorized Users:
Progress:
-""" diff --git a/wqflask/dataSharing/SharingInfo.py b/wqflask/dataSharing/SharingInfo.py deleted file mode 100755 index 10abcefa..00000000 --- a/wqflask/dataSharing/SharingInfo.py +++ /dev/null @@ -1,98 +0,0 @@ -# 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 = '