Mercurial > hg > ltpda

annotate m-toolbox/classes/@collection/fromRepository.m @ 7:1e91f84a4be8 database-connection-manager

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Make ltpda_up.retrieve work with java.sql.Connection objects
author Daniele Nicolodi <nicolodi@science.unitn.it>
date Mon, 05 Dec 2011 16:20:06 +0100
parents f0afece42f48
children b11e88004fca
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0
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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1 % Retrieve a ltpda_uo from a repository
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Daniele Nicolodi <nicolodi@science.unitn.it>
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2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Daniele Nicolodi <nicolodi@science.unitn.it>
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3 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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4 % FUNCTION: fromRepository
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Daniele Nicolodi <nicolodi@science.unitn.it>
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5 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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6 % DESCRIPTION: Retrieve a ltpda_uo from a repository
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Daniele Nicolodi <nicolodi@science.unitn.it>
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7 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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8 % CALL: obj = fromRepository(pl)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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9 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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10 % PARAMETER: pl: Parameter list object
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11 %
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12 % VERSION: $Id: fromRepository.m,v 1.8 2010/10/29 16:09:11 ingo Exp $
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13 %
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14 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Daniele Nicolodi <nicolodi@science.unitn.it>
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15 function coll = fromRepository(coll, pli)
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16
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17 VERSION = '$Id: fromRepository.m,v 1.8 2010/10/29 16:09:11 ingo Exp $';
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18
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Daniele Nicolodi <nicolodi@science.unitn.it>
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19 % get object info
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Daniele Nicolodi <nicolodi@science.unitn.it>
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20 ii = collection.getInfo('collection', 'From Repository');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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21 % Set the method version string in the minfo object
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Daniele Nicolodi <nicolodi@science.unitn.it>
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22 ii.setMversion([VERSION '-->' ii.mversion]);
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23
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Daniele Nicolodi <nicolodi@science.unitn.it>
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24 % Check if the user supplied a DB connection
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Daniele Nicolodi <nicolodi@science.unitn.it>
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25 conn = find(pli, 'conn');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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26
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Daniele Nicolodi <nicolodi@science.unitn.it>
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27 % Add default values if necessary
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Daniele Nicolodi <nicolodi@science.unitn.it>
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28 if isempty(conn)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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29 pl = combine(pli, ii.plists);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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30 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
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31 pl = pli;
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Daniele Nicolodi <nicolodi@science.unitn.it>
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32 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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33 plh = copy(pl, 1);
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34
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Daniele Nicolodi <nicolodi@science.unitn.it>
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35 % Get parameters
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Daniele Nicolodi <nicolodi@science.unitn.it>
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36 hostname = find(pl, 'hostname');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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37 database = find(pl, 'database');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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38 user = find(pl, 'user');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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39 passwd = find(pl, 'passwd');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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40 ids = find(pl, 'id');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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41 cids = find(pl, 'cid');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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42 bin = find(pl, 'binary');
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43
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Daniele Nicolodi <nicolodi@science.unitn.it>
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44 collFound = false;
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45
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Daniele Nicolodi <nicolodi@science.unitn.it>
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46 %%% check if using binary or not: 'yes'/'no' or true/false or
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Daniele Nicolodi <nicolodi@science.unitn.it>
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47 %%% 'true'/'false'
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Daniele Nicolodi <nicolodi@science.unitn.it>
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48 bin = utils.prog.yes2true(bin);
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49
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Daniele Nicolodi <nicolodi@science.unitn.it>
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50 % do we have a connection?
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Daniele Nicolodi <nicolodi@science.unitn.it>
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51 closeConn = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
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52 if isempty(conn)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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53 closeConn = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
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54 % Connect to repository
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Daniele Nicolodi <nicolodi@science.unitn.it>
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55 % Connect to repository
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Daniele Nicolodi <nicolodi@science.unitn.it>
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56 if ~isempty(user) && ~isempty(passwd)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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57 conn = utils.jmysql.connect(hostname, database, user, passwd);
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58 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
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59 conn = utils.jmysql.connect(hostname, database);
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60 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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61 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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62 if ~isa(conn, 'database') && ~isa(conn, 'mpipeline.repository.RepositoryConnection')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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63 error('### connection to the database failed.');
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64 end
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65
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66 if ~isempty(cids)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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67 for kk=1:numel(cids)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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68 cid = cids(kk);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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69 if isa(conn, 'database')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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70 % get the ids from the cid
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Daniele Nicolodi <nicolodi@science.unitn.it>
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71 ids = [ids utils.mysql.getObjIds(conn,cid)];
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Daniele Nicolodi <nicolodi@science.unitn.it>
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72 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
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73 c_ids = mpipeline.repository.MySQLUtils.getObjectIDsFromCollectionID(conn, cid);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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74 ids = [ids c_ids.'];
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75 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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76 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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77 end
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78
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Daniele Nicolodi <nicolodi@science.unitn.it>
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79 % Get each ID
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Daniele Nicolodi <nicolodi@science.unitn.it>
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80 Nids = length(ids);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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81 collObjs = {};
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Daniele Nicolodi <nicolodi@science.unitn.it>
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82
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Daniele Nicolodi <nicolodi@science.unitn.it>
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83 for kk=1:Nids
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84
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Daniele Nicolodi <nicolodi@science.unitn.it>
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85 %---- copy the input plist because each object should get an other plist
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Daniele Nicolodi <nicolodi@science.unitn.it>
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86 plh = copy(pl, 1);
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87
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Daniele Nicolodi <nicolodi@science.unitn.it>
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88 %---- This id
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Daniele Nicolodi <nicolodi@science.unitn.it>
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89 id = ids(kk);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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90 utils.helper.msg(utils.const.msg.OPROC2, 'retrieving ID %d', id);
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91
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Daniele Nicolodi <nicolodi@science.unitn.it>
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92 try
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Daniele Nicolodi <nicolodi@science.unitn.it>
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93 %---- call database constructor
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Daniele Nicolodi <nicolodi@science.unitn.it>
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94 if bin
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Daniele Nicolodi <nicolodi@science.unitn.it>
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95 try
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Daniele Nicolodi <nicolodi@science.unitn.it>
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96 robj = ltpda_uo.retrieve(conn, 'binary', id);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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97 catch
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Daniele Nicolodi <nicolodi@science.unitn.it>
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98 warning('!!! Unable to do binary retrieval for object %d; trying to retrieve XML instead.', id);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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99 robj = ltpda_uo.retrieve(conn, id);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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100 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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101 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
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102 robj = ltpda_uo.retrieve(conn, id);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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103 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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104
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Daniele Nicolodi <nicolodi@science.unitn.it>
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105 % - remove connection object from plist first
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Daniele Nicolodi <nicolodi@science.unitn.it>
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106 if isempty(hostname) || isempty(database)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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107 txt = textscan(conn.URL, '%s', 'Delimiter', '/', 'CollectOutput', 1);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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108 plc = plist('hostname', txt{1}{3}, 'database', txt{1}{4});
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Daniele Nicolodi <nicolodi@science.unitn.it>
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109 plh = combine(pli, plc);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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110 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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111
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Daniele Nicolodi <nicolodi@science.unitn.it>
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112 %---- remove the connection from the history plist
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Daniele Nicolodi <nicolodi@science.unitn.it>
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113 if plh.isparam('conn')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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114 plh.remove('conn');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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115 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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116
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Daniele Nicolodi <nicolodi@science.unitn.it>
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117 %---- Set only the ID of the current object to the plist
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Daniele Nicolodi <nicolodi@science.unitn.it>
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118 plh.pset('ID', id);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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119
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Daniele Nicolodi <nicolodi@science.unitn.it>
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120 %---- Add history
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Daniele Nicolodi <nicolodi@science.unitn.it>
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121 robj.addHistoryWoChangingUUID(robj.getInfo(class(robj), 'From Repository'), plh, [], robj.hist);
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122
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Daniele Nicolodi <nicolodi@science.unitn.it>
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123 %---- Add to output array
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Daniele Nicolodi <nicolodi@science.unitn.it>
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124 if isa(robj, 'collection')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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125 if numel(ids) == 1
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Daniele Nicolodi <nicolodi@science.unitn.it>
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126 coll = robj;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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127 return
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Daniele Nicolodi <nicolodi@science.unitn.it>
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128 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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129
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Daniele Nicolodi <nicolodi@science.unitn.it>
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130 if numel(robj.objs)>0
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Daniele Nicolodi <nicolodi@science.unitn.it>
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131 collFound = true;
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Daniele Nicolodi <nicolodi@science.unitn.it>
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132 collObjs = [collObjs; robj.objs(:)];
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Daniele Nicolodi <nicolodi@science.unitn.it>
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133 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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134 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
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135 collObjs = [collObjs; {robj}];
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Daniele Nicolodi <nicolodi@science.unitn.it>
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136 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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137 catch Exception
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Daniele Nicolodi <nicolodi@science.unitn.it>
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138 if closeConn
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Daniele Nicolodi <nicolodi@science.unitn.it>
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139 close(conn);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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140 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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141 throw(Exception)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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142 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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143
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Daniele Nicolodi <nicolodi@science.unitn.it>
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144 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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145
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Daniele Nicolodi <nicolodi@science.unitn.it>
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146 % close connection
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Daniele Nicolodi <nicolodi@science.unitn.it>
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147 if closeConn
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Daniele Nicolodi <nicolodi@science.unitn.it>
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148 if isa(conn, 'database')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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149 close(conn);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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150 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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151 conn.closeConnection;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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152 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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153 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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154
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Daniele Nicolodi <nicolodi@science.unitn.it>
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155 if collFound
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Daniele Nicolodi <nicolodi@science.unitn.it>
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156 warning(sprintf(['!!! The output collection contains the contents of at least one retrieved collection.' ...
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Daniele Nicolodi <nicolodi@science.unitn.it>
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157 '\nThe history of those collection objects is discarded. The internal objects of those ' ...
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Daniele Nicolodi <nicolodi@science.unitn.it>
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158 'objects is retained.']));
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Daniele Nicolodi <nicolodi@science.unitn.it>
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159 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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160 if isempty(collObjs)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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161 warning('!!! No objects were retrieved from the ids %s and/or collection id %s', mat2str(ids), mat2str(cid));
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Daniele Nicolodi <nicolodi@science.unitn.it>
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162 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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163
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Daniele Nicolodi <nicolodi@science.unitn.it>
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164 % Define collection-plist for the history
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Daniele Nicolodi <nicolodi@science.unitn.it>
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165 plh.pset('id', pli.find('id'));
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Daniele Nicolodi <nicolodi@science.unitn.it>
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166 plh.pset('cid', pli.find('cid'));
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167
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168 % Set properties from the plist
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169 coll.setProperties(pl);
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170 coll.objs = collObjs;
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171 coll.addHistory(ii, plh, [], []);
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172
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173 end
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174