added migration tools

Author: dpfoose

common_scripts/get_collection.m

@@ -43,3 +43,4 @@
 h5_filename = sprintf('%s%d.h5', tempdir, collection_id);
 h5_filename = websave(h5_filename, url, omics_weboptions);
 collection = load_hdf5_collection(h5_filename);
+collection.x = collection.x'; % x is row vector here, but column vector on site

common_scripts/post_collection.m

@@ -38,7 +38,9 @@
 % file upload routes take multipart/form-data instead of JSON
 outdir = tempname;
 mkdir(outdir);
+collection.x = collection.x'; % row vector here, column vector on site
 filename = save_collection(outdir, suffix, collection);
+collection.x = collection.x'; % convert back to row vector
 fid = fopen(filename, 'r');
 data = fread(fid);
 fclose(fid);

migration_tools/get_old_collection.m

@@ -0,0 +1,72 @@
+function [collection,message] = get_old_collection(collection_id,username,password)
+% Gets the given collection from the birg website using the given username 
+% and password.  If called without any of the parameters, displays dialogs
+% to get them from the user.
+%
+% Returns the collection or {} on error.  If there is an error, message
+% contains an error message for the user.
+message = [];
+
+if ~exist('username','var') || ~exist('password','var')
+    [username,password] = logindlg;
+    if isempty(username) && isempty(password)
+        collection = {};
+        message = 'You must enter a username and password';
+        return;
+    end
+end
+
+if ~exist('collection_id','var') || isempty(collection_id)
+    prompt={'Collection ID:'};
+    name='Enter the collection ID from the website';
+    numlines=1;
+    defaultanswer={''};
+    answer=inputdlg(prompt,name,numlines,defaultanswer);
+    if isempty(answer)
+        message = 'You must enter a collection ID';
+        collection = {};
+        return;
+    end
+    collection_id = str2double(answer{1});
+    if isnan(collection_id) || length(collection_id) ~= 1
+        message = 'You must enter a number as the collection ID';
+        collection = {};
+        return;
+    end
+end
+
+url = sprintf('http://birg.cs.wright.edu/omics_analysis/collections/%d.xml',collection_id);
+try
+    if exist('proxy.conf','file')
+        load_proxy('proxy.conf');
+    end
+    %[xml, urlstatus] = webread(url, 'name', username, 'password', password);
+    [xml,urlstatus] = urlread(url, 'Timeout', 360, 'get',{'name',username,'password',password});
+    if ~isempty(regexp(xml,'password', 'once'))
+        message = 'Invalid password';
+        collection = {};
+        return;
+    end
+    if urlstatus == 0
+        error('urlread failed with status 0: %s',url); %#ok<SPERR>
+    end
+catch ME
+    disp(urlstatus);
+    throw(ME);
+end
+n = regexp(xml,'<data>(.*)</data>','tokens');
+data = n{1}{1};
+% file = tempname;
+% fid = fopen(file,'w');
+% fwrite(fid,xml);
+% %fprintf(fid,xml);
+% fclose(fid);
+% collection_xml = xml2struct(file);
+% data = collection_xml.Children(2).Children.Data;
+file = tempname;
+fid = fopen(file,'w');
+fwrite(fid,data);
+%fprintf(fid,data);
+fclose(fid);
+
+collection = load_collection(file,'');

migration_tools/migrate_collections.m

@@ -0,0 +1,10 @@
+function migrate_collections
+%MIGRATE_COLLECTIONS Summary of this function goes here
+%   Detailed explanation goes here
+collections = get_old_collections;
+for i = 1:length(collections)
+    collections{i}.('name') = sprintf('%s (from %s)', collections{i}.description, collections{i}.collection_id);
+end
+post_collections('', collections);
+end
+