Changeset 2622 for branches


Ignore:
Timestamp:
Sep 5, 2006, 12:01:35 PM (17 years ago)
Author:
Nicklas Nordborg
Message:

References #332: Fix bugs in migration program

This should fix most of the discovered bugs. TEST TEST AND TEST!!!

Location:
branches/2.0
Files:
1 added
1 deleted
20 edited

Legend:

Unmodified
Added
Removed

  • branches/2.0/doc/specifications/migration/index.html

    r2614 r2622  
    4949    <li><a href="#Quota">Quota</a></li>
    5050    <li><a href="#Reporters">Reporters</a></li>
    51     <li><a href="#Roles">Roles</a><br/>
    52       <ol>
    53       <li><a href="#defaultBaseRoles">Default BASE Roles</a></li>
    54       <li><a href="#rolesPermissions">Role Permissions</a></li>
    55       <li><a href="RolesAndPermissions.html">Roles And Permissions</a></li>   
    56       </ol>
    57     </li>
     51    <li><a href="#Roles">Roles</a></li>
    5852    <li><a href="#SampleOrigins">Sample Origins</a></li>
    5953    <li><a href="base1Tables.html">BASE 1 tables description</a></li>
    … …  
    160154  <li>Each user is assigned one of <a href="../core/defaultdata.html#quota">default quotas</a>.</li>
    161155  <li>Quota assignment depends on the fileQuota in base 1 and the total usage in BASE 2.</li>
    162   <li>Groups are not assigned any quotas</li>
    163156  </ul>
    164157
    … …  
    180173  <h3>Default BASE Roles</h3>
    181174  </a>
     175 
     176  <p>
     177    Role assignment is done according to the following protocol:
     178  </p>
     179 
    182180  <ol>
    183 
    184   <li>A user shall be assigned to role <b>Guest</b> if the following roles apply:<br/>
     181  <li>If <i>Admin privileges &raquo; Superuser</i> is checked that user shall <b><u>only</u></b>
     182    be assigned to the BASE 2 role <b>Administrator</b>.<br/>
     183      <ul> 
     184      <li>No read restrictions shall be set on users assigned to this role.</li>
     185      </ul>
     186  </li>
     187 
     188  <li>If <i>Admin privileges &raquo; Complete read access</i> is checked that user shall be assigned
     189    to the BASE 2 role <b>Supervisor</b>.<br/>
    185190    <ul>
    186     <li>Hardware/Software Administrator</li>
    187     <li>Arrays/Plates Administrator</li>
    188     <li>Uploader</li>
    189     <li>Reporters Viewer</li>
    190     <li>Arrays/Plates Viewer</li>
     191    <li>No read restrictions shall be set on users assigned to this role.</li>
     192    <li>Additional roles may be assigned if the user has more permissions.</li>
    191193    </ul>
    192194  </li>
    193   <li>A user shall be assigned to role <b>User</b> if the following roles apply:<br/>
     195
     196  <li>A user shall be assigned to at most one of the BASE 2 roles <b>Guest</b>, <b>User</b> and
     197    <b>Power user</b>:<br/>
    194198    <ul>
    195     <li>All roles that are needed for role <b>Guest</b>.</li>
    196     <li>Reporter Administrator</li>
    197     <li>Biomaterials Administrator</li>
    198     <li>Hybridizations Administrator</li>
    199           </ul>
    200   </li>
    201   <li>A user shall be assigned to role <b>Power User</b> if the following roles apply:<br/>
    202     <ul>
    203     <li>All roles that are needed for role <b>User</b>.</li>
    204     <li>Protocols Administrator</li>
    205     <li>Annotation Types Administrator</li>
    206     </ul>
    207   </li>
    208  
    209   <li>If <i>Admin privileges &raquo; Complete read access</i> is checked that user shall be assigned to the role <b>Supervisor</b>.<br/>
    210     <ul>
    211     <li>No read restrictions shall be set on users assigned to this role.</li>
    212     </ul>
    213   </li>
    214   <li>If <i>Admin privileges &raquo; Superuser</i> is checked that user shall <b><u>only</u></b> be assigned to the role <b>Administrator</b>.<br/>
    215     <ul> 
    216     <li>No read restrictions shall be set on users assigned to this role.</li>
     199    <li>Guest: Upload files</li>
     200    <li>User: Guest + Add biomaterials, Add hybridizations, Create experiments
     201    <li>Power user: User + Add file formats, Add reporters, Add hardware/software,
     202      Add annotation types, Add arrays/plates, Add protocols
    217203    </ul>
    218204  </li>
    219205  </ol>
    220206
    221 
    222   <a name="additionalBaseRoles">
    223   <h3>Additional BASE Roles</h3>
    224   </a>
    225 
    226207  <p>
    227   All users except those assigned to role <b>Administrator</b> shall also be assigned additional role[s] if needed.
    228  
    229   <ul>
    230   <li>User Administrator              <br/>if <i>Admin privileges &raquo; Administer Users</i> is checked</li>
    231   <li>Plugin Administrator       <br/>if <i>Admin privileges &raquo; Add Plugins</i> is checked</li>
    232   <li>News Administrator              <br/>if <i>Admin privileges &raquo; Add News</i> is checked</li>
    233   <li>Protocols Administrator    <br/>if <i>Advanced rights &raquo; Add Protocols</i> is checked</li>
    234   <li>Arrays/Plates Administrator    <br/>if <i>Advanced rights &raquo; Add Arrays/Plates</i> is checked</li>
    235   <li>Annotation Types Administrator  <br/>if <i>Advanced rights &raquo; Add AnnotationTypes</i> is checked</li>
    236   <li>Hardware/Software Administrator <br/>if <i>Advanced rights &raquo; Add Hardware/Software</i> is checked</li>
    237   <li>Reporter Administrator          <br/>if <i>Advanced rights &raquo; Add Reporters</i> is checked</li>
    238   <li>File Formats Administrator     <br/>if <i>Advanced rights &raquo; Add File Formats</i> is checked</li>
    239   <li>Biomaterials Administrator     <br/>if <i>Basic editing &raquo; Add Biomaterials</i> is checked</li>
    240   <li>Hybridizations Administrator     <br/>if <i>Basic editing &raquo; Add Hybridization</i> is checked</li>
    241   <li>Uploader         <br/>if <i>Basic editing &raquo; Upload Files</i> is checked</li>
    242   <li>Arrays/Plates Viewer       <br/>if <i>Basic read access &raquo; Read Arrays/Plates</i> is checked</li>
    243   <li>Hybridizations Viewer    <br/>if <i>Basic read access &raquo; Read Hybridizations</i> is checked and <br/>Restricted Arrays/Plates <br/>if unchecked</li>
    244   <li>Reporters Viewer       <br/>if <i>Basic read access &raquo; Read Reporters</i> is checked and <br/>Restricted Hybridizations <br/>if unchecked</li>
    245   <li>Biomaterials Viewer      <br/>if <i>Basic read access &raquo; Read Biomaterials</i> is checked and <br/>Restricted Biomaterials <br/>if unchecked</li>
    246   <li><i>Admin privileges &raquo; Speak in left frame</i> value shall not be assigned to any role.</li>
    247   </ul>
     208    If the user after this assignment has more permissions that couldn't be matched to a
     209    predefined role, the user is assigned to one or more of the migration roles. The migration
     210    roles are created by the migration program and have the same name as the BASE 1 permission
     211    with the prefix "BASE 1:" added to it.
    248212  </p>
    249213
    250   <a name="rolesPermissions">
    251   <h3>Role permissions</h3>
    252   </a>
    253 
    254214  <p>
    255   CRUWD is short for CREATE, READ, UPDATE, WRITE and DELETE
     215    C = Create, R = Read, U = Use, W = Write, D = Delete
    256216  </p>
    257  
    258   <ul>
    259   <li>User Administrator role has
    260       <b>CRUWD</b> on User, Group, Role, Quota and
    261       <b>C</b> on Directory</li>
    262 
    263   <li>Plugin Administrator role has
    264       <b>C</b> on PluginDefinition, PluginConfiguration</li>
    265 
    266   <li>News Administrator role has
    267       <b>CRUWD</b> on News</li>
    268 
    269   <li>Protocols Administrator role has
    270       <b>C</b> on Protocols and
    271       <b>RU</b> to ProtocolType</li>
    272 
    273   <li>Arrays/Plates Administrator role has
    274       <b>RU</b> on PlateGeometry, ProtocolType and
    275       <b>C</b> on PlateType, Plate, PlateMapping, ArrayDesign, ArrayBatch, ArraySlide</li>
    276 
    277   <li>Annotation Types Administrator role has
    278       <b>C</b> on AnnotationType</li>
    279 
    280   <li>Hardware/Software Administrator role has
    281       <b>C</b> on Hardware, Software and
    282       <b>RU</b> on HardwareType, SoftwareType</li>
    283 
    284   <li>Reporter Administrator role has
    285       <b>CRUWD</b> on Reporter, ReporterType</li>
    286 
    287   <li>File Formats Administrator role has
    288       <b>C</b> on PluginConfiguration and
    289       <span class="question">RU ? Standard import plugins</span></li>
    290 
    291   <li>Biomaterials Administrator role has
    292       <b>C</b> on BioSource, Sample, Extract, LabeledExtract, Label</li>
    293 
    294   <li>Hybridizations Administrator role has
    295       <b>C</b> on Hybridization, Scan, RawBioAssay</li>
    296 
    297   <li>Uploader role has
    298       <b>C</b> on File, Directory</li>
    299 
    300   <li>Arrays/Plates Viewer role has
    301       <b>R</b> on PlateGeometry, PlateType, Plate, PlateMapping, ProtocolType, ArrayDesign, ArrayBatch, ArraySlide</li>
    302 
    303   <li>Hybridizations Viewer role has
    304       <b>R</b> on Hybridization, Scan, RawBioAssay</li>
    305 
    306   <li>Reporters Viewer role has
    307       <b>RU</b> on Reporter and
    308       <b>R</b> on ReporterType</li>
    309 
    310   <li>Biomaterials Viewer role has
    311       <b>R</b> on BioSource, Sample, Extract, LabeledExtract, Label</li>
    312 
    313 
    314   <li>Restricted Arrays/Plates role has
    315       <b>DENIED</b> on PlateGeometry, PlateType, Plate, PlateMapping, ProtocolType, ArrayDesign, ArrayBatch, ArraySlide</li>
    316 
    317   <li>Restricted Hybridizations role has
    318       <b>DENIED</b> on Hybridization, Scan, RawBioAssay</li>
    319 
    320   <li>Restricted Biomaterials role has
    321       <b>DENIED</b> on BioSource, Sample, Extract, LabeledExtract, Label</li>
    322 
    323   </ul>
    324   </p>
    325 
     217
     218  <table style="border: 1px solid #000000" cellspacing="0" cellpadding="2" width="100%">
     219  <tr style="background: #E0E0E0">
     220    <th>BASE 1 permission</th>
     221    <th>BASE 2 Permissions</th>
     222  </tr>
     223 
     224  <tr valign="top">
     225    <td style="border-top: 1px solid #000000">Administer users</td>
     226    <td style="border-top: 1px solid #000000">
     227      USER (CRUWD), GROUP (CRUWD), ROLE (CRUWD), <br>
     228      QUOTA (CRUWD), QUOTATYPE (RU), DIRECTORY (C)
     229    </td>
     230  </tr>
     231 
     232  <tr valign="top">
     233    <td style="border-top: 1px solid #000000">Speak in left frame</td>
     234    <td style="border-top: 1px solid #000000">
     235      Not used by BASE 2.
     236    </td>
     237  </tr>
     238 
     239  <tr valign="top">
     240    <td style="border-top: 1px solid #000000">Add plug-ins</td>
     241    <td style="border-top: 1px solid #000000">PLUGINDEFINITION (C), PLUGINCONFIGURATION (C), PLUGINTYPE (RU)</td>
     242  </tr>
     243 
     244  <tr valign="top">
     245    <td style="border-top: 1px solid #000000">Add news</td>
     246    <td style="border-top: 1px solid #000000">NEWS (CRUWD)</td>
     247  </tr>
     248 
     249  <tr valign="top">
     250    <td style="border-top: 1px solid #000000">Add protocols</td>
     251    <td style="border-top: 1px solid #000000">PROTOCOL (CRUWD), PROTOCOLTYPE (RU)</td>
     252  </tr>
     253 
     254  <tr valign="top">
     255    <td style="border-top: 1px solid #000000">Add arrays/plates</td>
     256    <td style="border-top: 1px solid #000000">
     257      PLATEGEOMETRY (RU), PLATETYPE (C), PLATE (C), PLATEMAPPING (RU),<br>
     258      ARRAYDESIGN (C), ARRAYBATCH (C), ARRAYSLIDE (C), PROTOCOLTYPE (RU)
     259    </td>
     260  </tr>
     261 
     262  <tr valign="top">
     263    <td style="border-top: 1px solid #000000">Add annotation types</td>
     264    <td style="border-top: 1px solid #000000">
     265      ANNOTATIONTYPE (C), ANNOTATIONTYPECATEGORY (C)
     266    </td>
     267  </tr>
     268
     269  <tr valign="top">
     270    <td style="border-top: 1px solid #000000">Add hardware/software</td>
     271    <td style="border-top: 1px solid #000000">
     272      HARDWARE (C), HARDWARETYPE (RU), SOFTWARE (C), SOFTWARETYPE (RU)
     273    </td>
     274  </tr>
     275
     276  <tr valign="top">
     277    <td style="border-top: 1px solid #000000">Add reporters</td>
     278    <td style="border-top: 1px solid #000000">
     279      REPORTER (CRUWD), REPORERTYPE (CRUWD), REPORTERLIST (C)
     280    </td>
     281  </tr>
     282
     283  <tr valign="top">
     284    <td style="border-top: 1px solid #000000">Add file formats</td>
     285    <td style="border-top: 1px solid #000000">
     286      PLUGINCONFIGURATION (C)
     287    </td>
     288  </tr>
     289
     290  <tr valign="top">
     291    <td style="border-top: 1px solid #000000">Read more user info</td>
     292    <td style="border-top: 1px solid #000000">
     293      -
     294    </td>
     295  </tr>
     296
     297  <tr valign="top">
     298    <td style="border-top: 1px solid #000000">Read plugins (if missing)</td>
     299    <td style="border-top: 1px solid #000000">
     300      PLUGINDEFINITION (DENIED), PLUGINCONFIGURATION (DENIED)
     301    </td>
     302  </tr>
     303
     304  <tr valign="top">
     305    <td style="border-top: 1px solid #000000">Create MAGE-ML file</td>
     306    <td style="border-top: 1px solid #000000">
     307      -
     308    </td>
     309  </tr>
     310
     311  <tr valign="top">
     312    <td style="border-top: 1px solid #000000">Share with world</td>
     313    <td style="border-top: 1px solid #000000">
     314      SHARE_TO_EVERYONE
     315    </td>
     316  </tr>
     317
     318  <tr valign="top">
     319    <td style="border-top: 1px solid #000000">Add biomaterials</td>
     320    <td style="border-top: 1px solid #000000">
     321      BIOSOURCE (C), SAMPLE (C), EXTRACT (C), LABELEDEXTRACT (C), LABEL (C)
     322    </td>
     323  </tr>
     324
     325  <tr valign="top">
     326    <td style="border-top: 1px solid #000000">Add hybridization</td>
     327    <td style="border-top: 1px solid #000000">
     328      HYBRIDIZATION (C), SCAN (C), RAWBIOASSAY (C)
     329    </td>
     330  </tr>
     331
     332  <tr valign="top">
     333    <td style="border-top: 1px solid #000000">Create experiments</td>
     334    <td style="border-top: 1px solid #000000">
     335      EXPERIMENT (C)
     336    </td>
     337  </tr>
     338 
     339  <tr valign="top">
     340    <td style="border-top: 1px solid #000000">Edit experiments</td>
     341    <td style="border-top: 1px solid #000000">
     342      -
     343    </td>
     344  </tr>
     345
     346  <tr valign="top">
     347    <td style="border-top: 1px solid #000000">Upload files</td>
     348    <td style="border-top: 1px solid #000000">
     349      FILE (C), DIRECTORY (C)
     350    </td>
     351  </tr>
     352
     353  <tr valign="top">
     354    <td style="border-top: 1px solid #000000">Read arrays/plates (if missing)</td>
     355    <td style="border-top: 1px solid #000000">
     356      PLATEGEOMETRY (DENIED), PLATETYPE (DENIED), PLATE (DENIED), <br>
     357      PLATEMAPPING (DENIED), ARRAYDESIGN (DENIED),<br>
     358      ARRAYBATCH (DENIED), ARRAYSLIDE (DENIED)
     359    </td>
     360  </tr>
     361 
     362  <tr valign="top">
     363    <td style="border-top: 1px solid #000000">Read user info (if missing)</td>
     364    <td style="border-top: 1px solid #000000">
     365      USER (DENIED)
     366    </td>
     367  </tr>
     368 
     369  <tr valign="top">
     370    <td style="border-top: 1px solid #000000">Read biomaterials (if missing)</td>
     371    <td style="border-top: 1px solid #000000">
     372      BIOSOURCE (DENIED), SAMPLE (DENIED), EXTRACT (DENIED),<br>
     373      LABELEDEXTRACT (DENIED), LABEL (DENIED)
     374    </td>
     375  </tr>
     376 
     377  <tr valign="top">
     378    <td style="border-top: 1px solid #000000">Read hybridizations (if missing)</td>
     379    <td style="border-top: 1px solid #000000">
     380      HYBRIDIZATION (DENIED), SCAN (DENIED), RAWBIOASSAY (DENIED)
     381    </td>
     382  </tr>
     383 
     384  <tr valign="top">
     385    <td style="border-top: 1px solid #000000">Read experiments (if missing)</td>
     386    <td style="border-top: 1px solid #000000">
     387      EXPERIMENT (DENIED)
     388    </td>
     389  </tr>
     390 
     391  <tr valign="top">
     392    <td style="border-top: 1px solid #000000">Read reporters</td>
     393    <td style="border-top: 1px solid #000000">
     394      REPORTER (RU), REPORTERTYPE (RU)
     395    </td>
     396  </tr>
     397  </table>
    326398
    327399  <a name="SampleOrigins">

  • branches/2.0/src/clients/migrate/migrate.properties.in

    r2614 r2622  
    2525db1.user =
    2626db1.password =
    27 db1.url = jdbc:mysql://localhost:3306/base
     27db1.url = jdbc:mysql://localhost:3306/base?zeroDateTimeBehavior=convertToNull
    2828db1.driver = com.mysql.jdbc.Driver
    2929# Number of items to handle in one batch or query
    … …  
    6565#
    6666
     67includeQuota          = yes
    6768includeRole           = yes
    6869includeReporter       = yes

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTransfer.java

    r2614 r2622  
    7676  public void start()
    7777  {
    78     startProgress(getInt("countSampleAnnotations"));
     78    int count = getInt("countSampleAnnotations");
     79    initIdMap(count);
     80    startProgress(count);
    7981    runUnBatched(
    8082        prepareStatementFromFile("selectSampleAnnotations"), 0, getBatchSize());

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/GroupTransfer.java

    r2614 r2622  
    2727import net.sf.basedb.core.DbControl;
    2828import net.sf.basedb.core.Group;
     29import net.sf.basedb.core.Quota;
    2930import net.sf.basedb.core.User;
    3031import java.sql.PreparedStatement;
    … …  
    5455   */
    5556  private UserTransfer userT = null;
     57  private QuotaTransfer quotaT = null;
    5658
    5759  /**
    5860  @param userT Depends on a finnished UserTransfer.
    5961   */
    60   GroupTransfer(UserTransfer userT)
     62  GroupTransfer(UserTransfer userT, QuotaTransfer quotaT)
    6163  {
    62     if (userT.isDone())
     64    if (userT.isDone() && quotaT.isDone())
    6365    {
    6466      this.userT = userT;
     67      this.quotaT = quotaT;
    6568    }
    6669    else
    … …  
    106109    group.setDescription(rs.getString(3));
    107110    group.setRemoved(rs.getBoolean(4));
     111    long byteQuota = rs.getLong(6);
     112    if (rs.wasNull()) byteQuota = Quota.UNLIMITED;
     113    group.setQuota(quotaT.getQuotaForTotal(dc, byteQuota));
     114   
    108115    // Add users to this group
    109116    PreparedStatement usersSql = prepareStatementFromFile("selectUsersByGroup");

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/HybridizationTransfer.java

    r2614 r2622  
    2626import net.sf.basedb.core.ArraySlide;
    2727import net.sf.basedb.core.BaseException;
     28import net.sf.basedb.core.BioMaterialEvent;
    2829import net.sf.basedb.core.CommonItem;
    2930import net.sf.basedb.core.DbControl;
    3031import net.sf.basedb.core.Hybridization;
     32import net.sf.basedb.core.LabeledExtract;
     33
     34import java.sql.PreparedStatement;
    3135import java.sql.ResultSet;
    3236import java.sql.SQLException;
    … …  
    5054public class HybridizationTransfer extends CommonItemTransfer
    5155{
    52   ArraySlideTransfer arraySlideT = null;
     56  private ArraySlideTransfer arraySlideT = null;
     57  private LabeledExtractTransfer labeledExtractT = null;
     58  private ProtocolTransfer protocolT = null;
    5359
    5460  /**
    … …  
    6066   */
    6167  HybridizationTransfer(UserTransfer userT, GroupTransfer groupT,
    62       ArraySlideTransfer arraySlideT)
     68      ArraySlideTransfer arraySlideT, LabeledExtractTransfer labeledExtractT, ProtocolTransfer protocolT)
    6369  {
    6470    super(userT, groupT);
    65     if (arraySlideT.isDone())
     71    if (arraySlideT.isDone() && labeledExtractT.isDone() && protocolT.isDone())
    6672    {
    6773      this.arraySlideT = arraySlideT;
     74      this.labeledExtractT = labeledExtractT;
     75      this.protocolT = protocolT;
    6876    }
    6977    else
    … …  
    98106    Hybridization hybridization = Hybridization.getNew(dc);
    99107    setCommonItemData(dc, (CommonItem) hybridization, rs);
    100     int slideId = rs.getInt(10);
     108    int slideId = rs.getInt(11);
    101109    if (slideId != 0)
    102110    {
    … …  
    111119      }
    112120    }
     121    BioMaterialEvent creationEvent = hybridization.getCreationEvent();
     122    creationEvent.setEventDate(rs.getDate(9));
     123    creationEvent.setProtocol(protocolT.getProtocolById(dc, rs.getInt(10)));
     124    connectToLabeledExtracts(dc, hybridization, rs.getInt(ID));
    113125    return hybridization;
    114126  }
    115127
    116128  /**
    117   Returns an Hybridization from the given base 1 slide id.
     129  Connects labled extracts to a hybridization
     130 
     131  @param dc <code>DbControl</code>
     132  @param hybridization The hybridization
     133  @param base1Id The corresponding base 1 id for this hybridization
     134   */
     135  private void connectToLabeledExtracts(DbControl dc, Hybridization hybridization,
     136      int base1HybridizationId)
     137  {
     138    ResultSet rs = null;
     139    try
     140    {
     141      PreparedStatement ps = prepareStatementFromFile("selectLabeledExtractsByHybridization");
     142      ps.setInt(1, base1HybridizationId);
     143      rs = ps.executeQuery();
     144      BioMaterialEvent creationEvent = hybridization.getCreationEvent();
     145      while (rs.next())
     146      {
     147        LabeledExtract le = labeledExtractT.getLabeledExtractById(dc, rs.getInt(1));
     148        if (le != null)
     149        {
     150          creationEvent.addSource(le, rs.getFloat(2));
     151        }
     152      }
     153    }
     154    catch (Exception e)
     155    {
     156      stop("connectReportersToWells", e, rs);
     157    }
     158  }
     159 
     160 
     161  /**
     162  Returns a Hybridization from the given base 1 slide id.
    118163 
    119164  @param dc {@link DbControl} used to get this hybridization.

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/LabeledExtractTransfer.java

    r2614 r2622  
    3030import net.sf.basedb.core.LabeledExtract;
    3131import net.sf.basedb.core.MeasuredBioMaterial;
     32
    3233import java.sql.ResultSet;
    3334import java.sql.SQLException;
    … …  
    7879  public void start()
    7980  {
    80     startProgress(getInt("countLabeledExtracts"));
     81    int count = getInt("countLabeledExtracts");
     82    initIdMap(count);
     83    startProgress(count);
    8184    run(prepareStatementFromFile("selectLabeledExtracts"), 0, 1000);
    8285    done();
    … …  
    118121    return null;
    119122  }
     123 
     124  /**
     125  Returns a Labeled extract from a base1 id.
     126 
     127  @param dbc DbControl
     128  @param base1LabeledExtractId Base1 labeled extract id
     129   */
     130  public LabeledExtract getLabeledExtractById(DbControl dbc, int base1LabeledExtractId)
     131  {
     132    try
     133    {
     134      Integer id = getBase2Id(base1LabeledExtractId);
     135      return id == null ? null : LabeledExtract.getById(dbc, id);
     136    }
     137    catch (BaseException e)
     138    {
     139      log("getLabeledExtractById", e);
     140    }
     141    return null;
     142  }
     143 
    120144}

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java

    r2614 r2622  
    8383      RoleTransfer roleT = new RoleTransfer();
    8484      startTransfer(roleT, "Role");
    85       UserTransfer userT = new UserTransfer(roleT);
     85      QuotaTransfer quotaT = new QuotaTransfer();
     86      startTransfer(quotaT, "Quota");
     87      UserTransfer userT = new UserTransfer(roleT, quotaT);
    8688      startTransfer(userT, "User");
    87       GroupTransfer groupT = new GroupTransfer(userT);
     89      GroupTransfer groupT = new GroupTransfer(userT, quotaT);
    8890      startTransfer(groupT, "Group");
    8991      WizzzardTransfer wizzzardT = new WizzzardTransfer(userT, groupT);
    … …  
    156158      startTransfer(arraySlideT, "ArraySlide");
    157159      HybridizationTransfer hybridizationT = new HybridizationTransfer(
    158           userT, groupT, arraySlideT);
     160          userT, groupT, arraySlideT, labeledExtractT, protocolT);
    159161      startTransfer(hybridizationT, "Hybridization");
    160162      ScanTransfer scanT = new ScanTransfer(userT, groupT,
    … …  
    165167      startTransfer(imageFT, "Image");
    166168      RawBioAssayTransfer rawBioAssayT = new RawBioAssayTransfer(userT,
    167           groupT, scanT, arrayTypeT, uploadFT);
     169          groupT, scanT, arrayTypeT, uploadFT, softwareT);
    168170      startTransfer(rawBioAssayT, "RawBioAssay");
    169171      RawBioAssayDataTransfer rawBioAssayDataT = new RawBioAssayDataTransfer(
    … …  
    173175          groupT, rawBioAssayT);
    174176      startTransfer(experimentT, "Experiment");
     177      userT.finalizeQuota();
    175178      print("END MIGRATION");
    176179      log("END MIGRATION");
    … …  
    444447    System.err.println("NOTE!!! We have found that the migration program has some serious bugs.");
    445448    System.err.println("We do not recommend using the migration program except for testing.");
     449    System.err.println("-----------------------------------------------------------------------");
    446450
    447451    if (args == null || args.length == 0 || !"debug".equals(args[0]))
    448452    {
    449453      System.err.println("Use: \"./migrate_from_1.2.sh debug\" to start the program");
    450       System.err.println("-----------------------------------------------------------------------");
    451454      System.exit(0);
    452455    }
    … …  
    455458      System.err.println("Debug switch found, press ENTER to continue with migration...");
    456459      waitForEnter();
    457       System.err.println("-----------------------------------------------------------------------");
    458460    }
    459461   

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/NewsTransfer.java

    r2304 r2622  
    6262  public void start()
    6363  {
    64     startProgress(getInt("countNews"));
     64    int count = getInt("countNews");
     65    initIdMap(count);
     66    startProgress(count);
    6567    run(prepareStatementFromFile("selectNews"));
    6668    done();

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTransfer.java

    r2614 r2622  
    7272  public void start()
    7373  {
    74     startProgress(getInt("countPlateEvents"));
     74    int count = getInt("countPlateEvents");
     75    initIdMap(count);
     76    startProgress(count);
    7577    run(prepareStatementFromFile("selectPlateEvents"));
    7678    done();

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTransfer.java

    r2614 r2622  
    5959  {
    6060    super(userT, groupT);
    61     if (uploadFT.isDone() && protocolTypeT.isDone())
     61    if (protocolTypeT.isDone())
    6262    {
    6363      this.uploadFT = uploadFT;
    … …  
    137137    return null;
    138138  }
     139 
     140  /**
     141  Returns a Protocol by the given base 1 protocol id.
     142 
     143  @param dbc <code>DbControl</code> used to get the Protocol.
     144  @param base1ProtocolId
     145  @return <code>Protocol</code> or null if the given protocol id does not exsist.
     146   */
     147  public Protocol getProtocolById(DbControl dbc, int base1ProtocolId)
     148  {
     149    try
     150    {
     151      Integer base2Id = getBase2Id(base1ProtocolId);
     152      return base2Id == null ? null : Protocol.getById(dbc, base2Id);
     153    }
     154    catch (BaseException e)
     155    {
     156      log("getProtocolById", e);
     157    }
     158    return null;
     159  }
     160 
    139161}

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java

    r2614 r2622  
    8585  public void start()
    8686  {
    87     startProgress(getInt("countRawBioAssayData"));
     87    int count = getInt("countRawBioAssayData");
     88    startProgress(count);
    8889    runUnBatched(
    8990        prepareStatementFromFile("selectRawBioAssaysWithSpotData"), 0,

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java

    r2614 r2622  
    4646  private ArrayTypeTransfer arrayTypeT = null;
    4747  private UploadFileTransfer uploadFT = null;
     48  private SoftwareTransfer softwareT = null;
    4849
    4950  /**
    … …  
    5556  RawBioAssayTransfer(UserTransfer userT, GroupTransfer groupT,
    5657      ScanTransfer scanT, ArrayTypeTransfer arrayTypeT,
    57       UploadFileTransfer uploadFT)
     58      UploadFileTransfer uploadFT, SoftwareTransfer softwareT)
    5859  {
    5960    super(userT, groupT);
    … …  
    6465      this.scanT = scanT;
    6566      this.arrayTypeT = arrayTypeT;
     67      this.softwareT = softwareT;
    6668    }
    6769    else
    … …  
    100102    Scan scan = scanT.getScanById(dc, rs.getInt(9));
    101103    rawBioAssay.setScan(scan);
     104    rawBioAssay.setSoftware(softwareT.getSoftwareById(dc, rs.getInt(11)));
    102105    // rawBioAssay.setFile(file);
    103106    ArrayDesign ad = arrayTypeT.getArrayDesignById(dc, rs.getInt(20));

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/ReporterTransfer.java

    r2614 r2622  
    8484  {
    8585    int count = getInt("countReporters");
    86     startProgress(count*2);
     86    startProgress(count*2); // First pass creates reporters, second one reads in the new ID:s
    8787    PreparedStatement ps = QUICK_TRANSFER ? prepareStatementFromFile("selectMinimumReporters")
    8888        : prepareStatementFromFile("selectReporters");

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/RoleTransfer.java

    r2581 r2622  
    2424package net.sf.basedb.clients.migrate;
    2525
     26import net.sf.basedb.core.BaseException;
    2627import net.sf.basedb.core.DbControl;
    2728import net.sf.basedb.core.Item;
    … …  
    3031import net.sf.basedb.core.RoleKey;
    3132import net.sf.basedb.core.SystemItems;
    32 import java.util.ArrayList;
     33
     34import java.util.EnumSet;
    3335import java.util.HashMap;
    3436import java.util.HashSet;
    3537import java.util.Map;
     38import java.util.Set;
    3639
    3740/**
    … …  
    4245public class RoleTransfer extends Transfer
    4346{
    44   // BASE 1 description
     47  // BASE 1 access masks
    4548  private final int SUPERUSER = (1 << 0); // Almighty
    4649  private final int SUPERREADER = (1 << 30); // Full read access
    4750  private final int SHARE_WORLD = (1 << 25); // Share with 'world'
    4851  private final int ADMIN_USER = (1 << 1); // Edit users
    49 //  private final int USER_READ = (1 << 2); // Read user list
     52  private final int USER_READ = (1 << 2); // Read user list
    5053  private final int NEWS_EDIT = (1 << 3); // Edit site news
    51 //  private final int USER_READ_MORE = (1 << 4); // Read more user info
     54  private final int USER_READ_MORE = (1 << 4); // Read more user info
    5255  private final int ARRAY_READ = (1 << 6); // Read array and plate info
    5356  private final int ARRAY_EDIT = (1 << 7); // Edit arrays and plates
    … …  
    5760  private final int BIO_READ = (1 << 11); // Read sample/extract/label
    5861  private final int BIO_EDIT = (1 << 12); // Edit sample/extract/label
    59 //  private final int BIO_TISSUE = (1 << 13); // Edit sample origins
     62  private final int BIO_TISSUE = (1 << 13); // Edit sample origins
    6063  private final int BIO_ANNOT = (1 << 14); // Edit sample annotation types
    6164  private final int PROGRAM_READ = (1 << 15); // Read plugins
    … …  
    6366  private final int HYB_EDIT = (1 << 17); // Edit hybridizations
    6467  private final int UPLOAD = (1 << 18); // Upload files
    65 //  private final int WIZZZARD_EDIT = (1 << 19); // Edit file formats
    66 //  private final int EXPER_READ = (1 << 20); // Read experiments
    67 //  private final int EXPER_EDIT = (1 << 21); // Edit experiments
    68 //  private final int EXPER_CREATE = (1 << 22); // Create experiments
    69 //  private final int EXPER_MAGEML = (1 << 23); // Create MAGE-ML for
     68  private final int WIZZZARD_EDIT = (1 << 19); // Edit file formats
     69  private final int EXPER_READ = (1 << 20); // Read experiments
     70  private final int EXPER_EDIT = (1 << 21); // Edit experiments
     71  private final int EXPER_CREATE = (1 << 22); // Create experiments
     72  private final int EXPER_MAGEML = (1 << 23); // Create MAGE-ML for
    7073                        // experiments
    71 //  private final int BROADCAST = (1 << 24); // Chat in left frame
     74  private final int BROADCAST = (1 << 24); // Chat in left frame
    7275  private final int REPORTER_READ = (1 << 26); // Read reporters
    7376  private final int REPORTER_EDIT = (1 << 27); // Edit reporters
    74   private final int RESTRICTED_ARRAY_READ = -1 * ARRAY_READ;
    75   private final int RESTRICTED_HYB_READ = -1 * HYB_READ;
    76   private final int RESTRICTED_BIO_READ = -1 * BIO_READ;
    77   // BASE 2 roles and their corresponding base 1 permissions
    78   private final int GUEST = (UPLOAD | ARRAY_EDIT | WARE_EDIT | REPORTER_READ | ARRAY_READ);
    79   private final int USER = (GUEST | HYB_EDIT | BIO_EDIT | REPORTER_EDIT);
    80   private final int POWER_USER = (USER | PROTOCOL_EDIT | BIO_ANNOT);
     77
     78  // The access masks corresponding to BASE 2 predefined roles
     79  private final int GUEST = UPLOAD | REPORTER_READ;
     80  private final int USER = GUEST | BIO_EDIT | HYB_EDIT | EXPER_CREATE;
     81  private final int POWER_USER = USER | WIZZZARD_EDIT | REPORTER_EDIT | WARE_EDIT | BIO_ANNOT | ARRAY_EDIT | PROTOCOL_EDIT;
    8182  private final int SUPERVISOR = SUPERREADER;
    8283  private final int ADMINISTRATOR = SUPERUSER;
    83   // Map role id to
    84   private Map<Integer, Integer> roleIdMaskMap = new HashMap<Integer, Integer>();
    85   private Map<Integer, Integer> systemRoleIds = new HashMap<Integer, Integer>();
    86   private int ADMINISTRATOR_ID;
    87   private int SUPERVISOR_ID;
    88   private int POWER_USER_ID;
    89   private int USER_ID;
    90   private int GUEST_ID;
    91   private int RESTRICTED_ARRAY_READ_ID;
    92 
     84
     85  // The meaningless access masks are not used in BASE 2
     86  private final int MEANINGLESS = BROADCAST | BIO_TISSUE | EXPER_EDIT | EXPER_MAGEML | USER_READ_MORE;
     87
     88  // Access masks that corresponds to a DENIED permission in BASE 2 if missing
     89  private final int DENIED = PROGRAM_READ | ARRAY_READ | USER_READ | BIO_READ | HYB_READ | EXPER_READ;
     90 
     91  // Maps access mask to roles (for the new roles only)
     92  private Map<Integer, Role> maskMap = null;
     93 
    9394  RoleTransfer()
    9495  {}
    … …  
    9798  {
    9899    // The number of roles created is static
    99     startProgress(19);
     100    startProgress(21);
    100101    log("start", "Administrator has mask " + ADMINISTRATOR);
    101102    log("start", "Supervisor has mask " + SUPERVISOR);
    … …  
    103104    log("start", "User has mask " + USER);
    104105    log("start", "Guest has mask" + GUEST);
     106    maskMap = new HashMap<Integer, Role>();
     107    DbControl dc = newDbControl();
    105108    try
    106109    {
    107       setDefaultRoleIds();
    108       createRole(
    109           "User Administrator", ADMIN_USER, "CREATE,READ,DELETE",
    110           "USER,GROUP,ROLE,QUOTA");
    111       createRole(
    112           "Plugin Administrator", PROGRAM_EDIT, "CREATE,READ",
    113           "PLUGINDEFINITION,PLUGINCONFIGURATION");
    114       createRole(
    115           "News Administrator", NEWS_EDIT, "CREATE,READ,DELETE",
    116           "NEWS");
    117       createRole(
    118           "Protocols Administrator", PROTOCOL_EDIT, "CREATE,READ",
    119           "PROTOCOL");
    120       Role role = createRole("Arrays/Plates Administrator", ARRAY_EDIT);
    121       addPermission(role, "READ,USE", "PLATEGEOMETRY,PROTOCOLTYPE");
    122       addPermission(
    123           role, "CREATE,READ",
    124           "PLATETYPE,PLATE,PLATEMAPPING,ARRAYBATCH,ARRAYDESIGN,ARRAYSLIDE");
    125       createRole(
    126           "Annotation Types Administrator", BIO_ANNOT, "CREATE,READ",
    127           "ANNOTATIONTYPE");
    128       role = createRole("Hardware/Software Administrator", WARE_EDIT);
    129       addPermission(role, "CREATE,READ", "HARDWARE,SOFTWARE");
    130       addPermission(role, "READ,USE", "HARDWARETYPE,SOFTWARETYPE");
    131       // "0x00002000","Sample Origins Administrator" ,"",
    132       createRole(
    133           "Reporter Administrator", REPORTER_EDIT,
    134           "CREATE,READ,DELETE", "REPORTER,REPORTERTYPE");
    135       createRole( "File Formats Administrator", PROGRAM_READ,
    136       "CREATE,READ", "PLUGINCONFIGURATION" );
    137       //READ,USE:STANDARD INPUT
    138       // PLUGIN
    139       createRole(
    140           "Biomaterials Administrator", BIO_EDIT,
    141           "CREATE,READ,DELETE",
    142           "EXTRACT,LABEL,LABELEDEXTRACT,SAMPLE,BIOSOURCE");
    143       createRole(
    144           "Hybridizations Administrator", HYB_EDIT, "CREATE,READ",
    145           "HYBRIDIZATION,SCAN,RAWBIOASSAY");
    146       createRole("Uploader", UPLOAD, "CREATE,READ", "FILE,DIRECTORY");
    147       createRole(
    148           "Arrays/Plates Viewer",
    149           ARRAY_READ,
    150           "READ",
    151           "ARRAYBATCH,ARRAYDESIGN,ARRAYSLIDE,PLATEGEOMETRY,PLATETYPE,PLATE,PLATEMAPPING,PROTOCOLTYPE");
    152       createRole(
    153           "Hybridizations Viewer", HYB_READ, "READ",
    154           "HYBRIDIZATION,SCAN,RAWBIOASSAY");
    155       role = createRole("Reporters Viewer", REPORTER_READ);
    156       addPermission(role, "READ,USE", "REPORTER");
    157       addPermission(role, "READ", "REPORTERTYPE");
    158       createRole(
    159           "Biomaterials Viewer", BIO_READ, "READ",
    160           "BIOSOURCE,EXTRACT,LABEL,LABELEDEXTRACT,SAMPLE");
    161       createRole(
    162           "Share With World", SHARE_WORLD, "SHARE_TO_EVERYONE",
    163           "SYSTEM");
    164       role = createRole(
    165           "Restricted Arrays/Plates",
    166           RESTRICTED_ARRAY_READ,
    167           "DENIED",
    168           "ARRAYBATCH,ARRAYDESIGN,ARRAYSLIDE,PLATEGEOMETRY,PLATETYPE,PLATE,PLATEMAPPING,PROTOCOLTYPE");
    169       // This role is specific to the Guest user
    170       RESTRICTED_ARRAY_READ_ID = role.getId();
    171       createRole(
    172           "Restricted Hybridizations", RESTRICTED_HYB_READ, "DENIED",
    173           "HYBRIDIZATION,SCAN,RAWBIOASSAY");
    174       createRole(
    175           "Restricted Biomaterials", RESTRICTED_BIO_READ, "DENIED",
    176           "BIOSOURCE,EXTRACT,LABEL,LABELEDEXTRACT,SAMPLE");
     110      // Permissions that are used for the new roles
     111      Set<Permission> create = EnumSet.of(Permission.CREATE);
     112      Set<Permission> admin = EnumSet.of(Permission.CREATE, Permission.READ, Permission.USE, Permission.WRITE, Permission.DELETE);
     113      Set<Permission> denied = EnumSet.of(Permission.DENIED);
     114      Set<Permission> use = EnumSet.of(Permission.READ, Permission.USE);
     115
     116      String migrationInfo = "This role was created by the migration tool and corresponds to the BASE 1 ";
     117      createRole(dc, "Administer users",  migrationInfo + "\"Administer users\" permission.",
     118        ADMIN_USER,
     119        new ItemPermission[]
     120        {
     121          new ItemPermission(Item.USER, admin),
     122          new ItemPermission(Item.GROUP, admin),
     123          new ItemPermission(Item.ROLE, admin),
     124          new ItemPermission(Item.QUOTA, admin),
     125          new ItemPermission(Item.QUOTATYPE, use),
     126          new ItemPermission(Item.DIRECTORY, create)
     127        }
     128      );
     129     
     130      createRole(dc, "Add plugins",  migrationInfo + "\"Add plug-ins\" permission.",
     131        PROGRAM_EDIT,
     132        new ItemPermission[]
     133          {
     134            new ItemPermission(Item.PLUGINDEFINITION, create),
     135            new ItemPermission(Item.PLUGINCONFIGURATION, create),
     136            new ItemPermission(Item.PLUGINTYPE, admin)
     137          }
     138        );
     139     
     140      createRole(dc, "News administrator",  migrationInfo + "\"Add news\" permission.",
     141        NEWS_EDIT,
     142        new ItemPermission[]
     143        {
     144          new ItemPermission(Item.NEWS, admin)
     145        }
     146      );
     147
     148      createRole(dc, "Add protocols",  migrationInfo + "\"Add protocols\" permission.",
     149        PROTOCOL_EDIT,
     150        new ItemPermission[]
     151        {
     152          new ItemPermission(Item.PROTOCOL, create),
     153          new ItemPermission(Item.PROTOCOLTYPE, use)
     154        }
     155      );
     156
     157      createRole(dc, "Add arrays/plates",  migrationInfo + "\"Add arrays/plates\" permission.",
     158        ARRAY_EDIT,
     159        new ItemPermission[]
     160        {
     161          new ItemPermission(Item.PLATETYPE, create),
     162          new ItemPermission(Item.PLATEGEOMETRY, use),
     163          new ItemPermission(Item.PLATE, create),
     164          new ItemPermission(Item.PLATEMAPPING, use),
     165          new ItemPermission(Item.ARRAYDESIGN, create),
     166          new ItemPermission(Item.ARRAYBATCH, create),
     167          new ItemPermission(Item.ARRAYSLIDE, create),
     168          new ItemPermission(Item.PROTOCOLTYPE, use)
     169        }
     170      );
     171     
     172      createRole(dc, "Add annotation types",  migrationInfo + "\"Add annotation types\" permission.",
     173        BIO_ANNOT,
     174        new ItemPermission[]
     175        {
     176          new ItemPermission(Item.ANNOTATIONTYPE, create),
     177          new ItemPermission(Item.ANNOTATIONTYPECATEGORY, create)
     178        }
     179      );
     180
     181      createRole(dc, "Add hardware/software",  migrationInfo + "\"Add hardware/software\" permission.",
     182        WARE_EDIT,
     183        new ItemPermission[]
     184        {
     185          new ItemPermission(Item.HARDWARE, create),
     186          new ItemPermission(Item.HARDWARETYPE, use),
     187          new ItemPermission(Item.SOFTWARE, create),
     188          new ItemPermission(Item.SOFTWARETYPE, use)
     189        }
     190      );
     191     
     192      createRole(dc, "Add reporters",  migrationInfo + "\"Add reporters\" permission.",
     193        REPORTER_EDIT,
     194        new ItemPermission[]
     195        {
     196          new ItemPermission(Item.REPORTER, admin),
     197          new ItemPermission(Item.REPORTERTYPE, admin),
     198          new ItemPermission(Item.REPORTERLIST, create)
     199        }
     200      );
     201     
     202      createRole(dc, "Add file formats",  migrationInfo + "\"Add file formats\" permission.",
     203        WIZZZARD_EDIT,
     204        new ItemPermission[]
     205        {
     206          new ItemPermission(Item.PLUGINCONFIGURATION, create)
     207        }
     208      );
     209     
     210      createRole(dc, "Denied plugins",  migrationInfo + "\"Read plugins\" permission.",
     211        PROGRAM_READ,
     212        new ItemPermission[]
     213        {
     214          new ItemPermission(Item.PLUGINCONFIGURATION, denied),
     215          new ItemPermission(Item.PLUGINDEFINITION, denied)
     216        }
     217      );
     218     
     219      createRole(dc, "Share with world",  migrationInfo + "\"Share with world\" permission.",
     220        SHARE_WORLD,
     221        new ItemPermission[]
     222        {
     223          new ItemPermission(Item.SYSTEM, EnumSet.of(Permission.SHARE_TO_EVERYONE))
     224        }
     225      );
     226     
     227      createRole(dc, "Add biomaterials",  migrationInfo + "\"Add biomaterials\" permission.",
     228        BIO_EDIT,
     229        new ItemPermission[]
     230        {
     231          new ItemPermission(Item.BIOSOURCE, create),
     232          new ItemPermission(Item.SAMPLE, create),
     233          new ItemPermission(Item.EXTRACT, create),
     234          new ItemPermission(Item.LABELEDEXTRACT, create),
     235          new ItemPermission(Item.LABEL, create)
     236        }
     237      );
     238
     239      createRole(dc, "Add hybridizations",  migrationInfo + "\"Add hybridizations\" permission.",
     240        HYB_EDIT,
     241        new ItemPermission[]
     242        {
     243          new ItemPermission(Item.HYBRIDIZATION, create),
     244          new ItemPermission(Item.SCAN, create),
     245          new ItemPermission(Item.RAWBIOASSAY, create)
     246        }
     247      );
     248     
     249      createRole(dc, "Create experiments",  migrationInfo + "\"Create experiments\" permission.",
     250        EXPER_CREATE,
     251        new ItemPermission[]
     252        {
     253          new ItemPermission(Item.EXPERIMENT, create)
     254        }
     255      );
     256
     257      createRole(dc, "Upload files",  migrationInfo + "\"Upload files\" permission.",
     258        UPLOAD,
     259        new ItemPermission[]
     260        {
     261          new ItemPermission(Item.FILE, create),
     262          new ItemPermission(Item.FILETYPE, use),
     263          new ItemPermission(Item.DIRECTORY, create)
     264        }
     265      );
     266     
     267      createRole(dc, "Denied arrays/plates",  migrationInfo + "\"Read arrays/plates\" permission.",
     268        ARRAY_READ,
     269        new ItemPermission[]
     270        {
     271          new ItemPermission(Item.PLATETYPE, denied),
     272          new ItemPermission(Item.PLATEGEOMETRY, denied),
     273          new ItemPermission(Item.PLATEMAPPING, denied),
     274          new ItemPermission(Item.PLATE, denied),
     275          new ItemPermission(Item.ARRAYDESIGN, denied),
     276          new ItemPermission(Item.ARRAYBATCH, denied),
     277          new ItemPermission(Item.ARRAYSLIDE, denied)
     278        }
     279      );
     280     
     281      createRole(dc, "Denied users",  migrationInfo + "\"Read user info\" permission.",
     282        USER_READ,
     283        new ItemPermission[]
     284        {
     285          new ItemPermission(Item.USER, denied)
     286        }
     287      );
     288     
     289      createRole(dc, "Denied biomaterials",  migrationInfo + "\"Read biomaterials\" permission.",
     290        BIO_READ,
     291        new ItemPermission[]
     292        {
     293          new ItemPermission(Item.BIOSOURCE, denied),
     294          new ItemPermission(Item.SAMPLE, denied),
     295          new ItemPermission(Item.EXTRACT, denied),
     296          new ItemPermission(Item.LABELEDEXTRACT, denied),
     297          new ItemPermission(Item.LABEL, denied)
     298        }
     299      );
     300     
     301      createRole(dc, "Denied hybridizations",  migrationInfo + "\"Read hybridizations\" permission.",
     302        HYB_READ,
     303        new ItemPermission[]
     304        {
     305          new ItemPermission(Item.HYBRIDIZATION, denied),
     306          new ItemPermission(Item.SCAN, denied),
     307          new ItemPermission(Item.RAWBIOASSAY, denied)
     308        }
     309      );
     310
     311      createRole(dc, "Denied experiments",  migrationInfo + "\"Read experiments\" permission.",
     312        EXPER_READ,
     313        new ItemPermission[]
     314        {
     315          new ItemPermission(Item.EXPERIMENT, denied)
     316        }
     317      );
     318     
     319      createRole(dc, "Read reporters",  migrationInfo + "\"Read reporters\" permission.",
     320        REPORTER_READ,
     321        new ItemPermission[]
     322        {
     323          new ItemPermission(Item.REPORTER, use),
     324          new ItemPermission(Item.REPORTERTYPE, use)
     325        }
     326      );
     327      dc.commit();
    177328      progress.stop();
    178329    }
    … …  
    190341  @return A list of roles matching a given base 1 accessMask
    191342   */
    192   public ArrayList<Integer> getRoleIds(Integer accessMask)
     343  public Set<Integer> getRoleIds(Integer accessMask)
    193344  {
    194345    int mask = accessMask.intValue();
    195346    log("getRoleIds", "" + mask);
    196     ArrayList<Integer> roleIds = new ArrayList<Integer>();
     347   
     348    Set<Integer> roleIds = new HashSet<Integer>();
     349
     350    // Check if BASE1 superuser
    197351    if ((mask & ADMINISTRATOR) == ADMINISTRATOR)
    198352    {
    199       roleIds.add(ADMINISTRATOR_ID);
     353      roleIds.add(SystemItems.getId(Role.ADMINISTRATOR));
    200354      return roleIds;
    201355    }
    202     /* Predefinde roles have a combination of permissions see above. */
    203     int systemRoleMask = 0;
    204     boolean isSupervisor = false;
    205     boolean hasRestrictedArrayRead = false;
     356
     357    // Remove BASE 1 permission that have no meaining in BASE 2
     358    mask &= ~MEANINGLESS;
     359   
     360    // All "Read Item X" permissions are converted to DENIED permissions
     361    mask ^= DENIED;
     362   
    206363    if ((mask & SUPERVISOR) == SUPERVISOR)
    207364    {
    208       roleIds.add(SUPERVISOR_ID);
    209       isSupervisor = true;
    210       systemRoleMask = (systemRoleIds.get(SUPERVISOR_ID)).intValue();
    211     }
    212     else
    213     {
    214       if (matchRole(mask, RESTRICTED_ARRAY_READ, true))
     365      roleIds.add(SystemItems.getId(Role.SUPERVISOR));
     366      mask &= ~SUPERVISOR;
     367      mask &= ~DENIED;
     368    }
     369   
     370    // We use either POWER_USER, USER or GUEST as the basis for
     371    if ((mask & POWER_USER) == POWER_USER)
     372    {
     373      roleIds.add(SystemItems.getId(Role.POWER_USER));
     374      mask &= ~POWER_USER;
     375    }
     376    else if ((mask & USER) == USER)
     377    {
     378      roleIds.add(SystemItems.getId(Role.USER));
     379      mask &= ~USER;
     380    }
     381    else if ((mask & GUEST) == GUEST)
     382    {
     383      roleIds.add(SystemItems.getId(Role.GUEST));
     384      mask &= ~GUEST;
     385    }
     386   
     387    if (mask != 0)
     388    {
     389      // The remaining bits in the access mask didn't fit the predefined roles
     390      // Use the newly created roles to map the last bits
     391      for (Map.Entry<Integer, Role> entry : maskMap.entrySet())
    215392      {
    216         log("getRoleIds", mask + " matches Restricted Arrays/Plates");
    217         mask = (mask | ARRAY_READ);
    218         hasRestrictedArrayRead = true;
     393        int roleMask = entry.getKey();
     394        if ((mask & roleMask) == roleMask)
     395        {
     396          roleIds.add(entry.getValue().getId());
     397          mask &= ~roleMask;
     398        }
    219399      }
    220400    }
    221     if ((mask & POWER_USER) == POWER_USER)
    222     {
    223       roleIds.add(POWER_USER_ID);
    224       systemRoleMask = (systemRoleMask | POWER_USER);
    225     }
    226     else
    227     {
    228       if ((mask & USER) == USER)
    229       {
    230         roleIds.add(USER_ID);
    231         systemRoleMask = (systemRoleMask | USER);
    232       }
    233       else
    234       {
    235         if ((mask & GUEST) == GUEST)
    236         {
    237           systemRoleMask = (systemRoleMask | GUEST);
    238           roleIds.add(GUEST_ID);
    239         }
    240       }
    241     }
    242     if (hasRestrictedArrayRead)
    243     {
    244       if (systemRoleMask != 0)
    245       {
    246         roleIds.add(RESTRICTED_ARRAY_READ_ID);
    247         roleIdMaskMap.put(RESTRICTED_ARRAY_READ_ID, 0);
    248         log("getRoleIds", "Adding Arrays/Plates Viewer to "
    249             + systemRoleMask);
    250       }
    251       else
    252       {
    253         // If the user doesn't belong to any of the above system roles
    254         // we remove the added array_read bit which we added before
    255         mask = mask ^ ARRAY_READ;
    256       }
    257     }
    258     // Add additional roles
    259     for (Map.Entry<Integer, Integer> entry : roleIdMaskMap.entrySet())
    260     {
    261       int roleMask = entry.getValue();
    262       int roleId = entry.getKey();
    263       boolean matchRestrictiveRoles = true;
    264       if (isSupervisor)
    265       {
    266         matchRestrictiveRoles = false;
    267       }
    268       if ((systemRoleMask == 0 || !matchRole(
    269           systemRoleMask, roleMask, matchRestrictiveRoles))
    270           && matchRole(mask, roleMask, matchRestrictiveRoles))
    271       {
    272         roleIds.add(roleId);
    273       }
     401   
     402    // If there are more bits in the mask it is a bug
     403    // We must either map or ignore (see MEANINGLESS) all bits
     404    if (mask != 0)
     405    {
     406      throw new BaseException("Access mask could not be completely converted to roles: " +
     407        "original mask=" + accessMask + "; end mask="+mask+"; assigned roles=" + roleIds.toString());
    274408    }
    275409    return roleIds;
    276410  }
    277411
    278   /**
    279   @param mask Permission mask which we want to match
    280   @param roleMask The mask that specifies a role.
    281   @param matchRestrictiveRoles Some roles should match if a given mask is
    282          missing.
    283    */
    284   private boolean matchRole(int mask, int roleMask,
    285       boolean matchRestrictiveRoles)
     412  private Role createRole(DbControl dc, String name, String description, int base1Mask, ItemPermission[] permissions)
    286413  {
    287     if (roleMask > 0 && ((roleMask & mask) == roleMask))
    288     {
    289       return true;
    290     }
    291     else if (matchRestrictiveRoles
    292         && (roleMask < 0 && (-roleMask & ~mask) == -roleMask))
    293     {
    294       return true;
    295     }
    296     return false;
    297   }
    298 
    299   /**
    300   Creates a Role with the given permissions.
    301  
    302   @param name Role name
    303   @param mask Mask that represents this role
    304   @param permissions A string of comma seperated permissions e.g.
    305          READ,WRITE,USE
    306   @param items A string of comma seperated items that the permissions apply
    307          to e.g. LABEL,EXTRACT
    308    */
    309   private Role createRole(String name, int mask, String permissions,
    310       String items)
    311   {
    312     Role role = createRole(name, mask);
    313     log("createRole", name + " has mask " + mask);
    314     addPermission(role, permissions, items);
     414    Role role = Role.getNew(dc);
     415    role.setName("BASE 1.2: " + name);
     416    role.setDescription(description);
     417    for (ItemPermission ip : permissions)
     418    {
     419      RoleKey key = RoleKey.getByItemType(dc, ip.getItem());
     420      key.setPermissions(role, ip.getPermissions());
     421    }
     422    maskMap.put(base1Mask, role);
     423    dc.saveItem(role);
    315424    return role;
    316425  }
    317 
    318   /**
    319   Creates a role without setting any permissions.
    320426 
    321   @param name Role name
    322   @param mask Mask that represents this role
    323   @see #addPermission(Role, String, String)
    324    */
    325   private Role createRole(String name, int mask)
     427  static class ItemPermission
    326428  {
    327     try
    328     {
    329       DbControl dc = newDbControl();
    330       Role role = Role.getNew(dc);
    331       role.setName(name);
    332       dc.saveItem(role);
    333       commit(dc);
    334       roleIdMaskMap.put(role.getId(), mask);
    335       progress.increase();
    336       return role;
    337     }
    338     catch (Exception e)
    339     {
    340       stop("createRole", e);
    341     }
    342     return null;
     429    private final Item item;
     430    private final Set<Permission> permissions;
     431   
     432    ItemPermission(Item item, Set<Permission> permissions)
     433    {
     434      this.item = item;
     435      this.permissions = permissions;
     436    }
     437   
     438    public Item getItem()
     439    {
     440      return item;
     441    }
     442   
     443    public Set<Permission> getPermissions()
     444    {
     445      return permissions;
     446    }
     447   
    343448  }
    344 
    345   /**
    346   Adds permission to a given role
    347449 
    348   @param role Role
    349   @param permissionsString A string of comma seperated permissions e.g.
    350          READ,WRITE,USE
    351   @param items A string of comma seperated items that the permissions apply
    352          to e.g. LABEL,EXTRACT
    353    */
    354   private void addPermission(Role role, String permissionsString, String items)
    355   {
    356     DbControl dc = newDbControl();
    357     dc.reattachItem(role);
    358     Item logitem = null;
    359     try
    360     {
    361       HashSet<Permission> permissions = new HashSet<Permission>();
    362       for (String permission : permissionsString.split(","))
    363       {
    364         permissions.add(Permission.valueOf(permission));
    365       }
    366       for (String itemstr : items.split(","))
    367       {
    368         Item item = Item.valueOf(itemstr);
    369         logitem = item;
    370         RoleKey rk = RoleKey.getById(dc, SystemItems.getRoleKeyId(item));
    371         rk.setPermissions(role, permissions);
    372       }
    373     }
    374     catch (Exception e)
    375     {
    376       // This should only happend until BASE 2 is complete
    377       warn("addPermission() for " + logitem.toString() + " : "
    378           + e.getMessage());
    379     }
    380     dc.commit();
    381   }
    382 
    383   /**
    384   Sets the BASE 2 ids for the default roles.
    385    */
    386   private void setDefaultRoleIds()
    387   {
    388     try
    389     {
    390       ADMINISTRATOR_ID = SystemItems.getId(Role.ADMINISTRATOR);
    391       systemRoleIds.put(ADMINISTRATOR_ID, ADMINISTRATOR);
    392       SUPERVISOR_ID = SystemItems.getId(Role.SUPERVISOR);
    393       systemRoleIds.put(SUPERVISOR_ID, SUPERVISOR);
    394       POWER_USER_ID = SystemItems.getId(Role.POWER_USER);
    395       systemRoleIds.put(POWER_USER_ID, POWER_USER);
    396       USER_ID = SystemItems.getId(Role.USER);
    397       systemRoleIds.put(USER_ID, USER);
    398       GUEST_ID = SystemItems.getId(Role.GUEST);
    399       systemRoleIds.put(GUEST_ID, GUEST);
    400     }
    401     catch (Exception e)
    402     {
    403       stop("setDefaultRoleIds", e);
    404     }
    405   }
    406450}

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/SampleTissueTransfer.java

    r2614 r2622  
    5050  public void start()
    5151  {
    52     startProgress(getInt("countSampleTissues"));
     52    int count = getInt("countSampleTissues");
     53    initIdMap(count);
     54    startProgress(count);
    5355    run(prepareStatementFromFile("selectSampleTissues"), 0, getBatchSize());
    5456    done();

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/SoftwareTransfer.java

    r2614 r2622  
    5757  {
    5858    softwareTypeId = SystemItems.getId(SoftwareType.FEATURE_EXTRACTION);
    59     startProgress(getInt("countSoftware"));
     59    int count = getInt("countSoftware");
     60    initIdMap(count);
     61    startProgress(count);
    6062    run(prepareStatementFromFile("selectSoftware"), 0, getBatchSize());
    6163    done();
    … …  
    7779    return software;
    7880  }
     81 
     82  /**
     83  Returns a Software by the given base 1 software id.
     84 
     85  @param dbc <code>DbControl</code> used to get the Software.
     86  @param base1SoftwareId
     87  @return <code>Software</code> or null if the given software id does not exist.
     88   */
     89  public Software getSoftwareById(DbControl dbc, int base1SoftwareId)
     90  {
     91    try
     92    {
     93      Integer base2Id = getBase2Id(base1SoftwareId);
     94      return base2Id == null ? null : Software.getById(dbc, base2Id);
     95    }
     96    catch (BaseException e)
     97    {
     98      log("getSoftwareById", e);
     99    }
     100    return null;
     101  }
     102 
    79103}

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/Transfer.java

    r2614 r2622  
    289289        if (item != null)
    290290        {
     291          if (!item.isInDatabase()) dc.saveItem(item);
    291292          WrappedItem<BasicItem> wi = new WrappedItem<BasicItem>(
    292293              item, rs.getInt(1), rowCount);
    … …  
    299300        progress.increase();
    300301      }
    301       dc.close();
     302      dc.commit();
    302303      // Reset our ResultSet
    303       rs.beforeFirst();
    304       processItemList(rs);
     304      //rs.beforeFirst();
    305305      rs.close();
     306      processItemList();
    306307      if (rowCount > 0 && rowCount == size)
    307308      {
    … …  
    346347        if (item != null)
    347348        {
     349          if (!item.isInDatabase()) dc.saveItem(item);
    348350          WrappedItem<BasicItem> wi = new WrappedItem<BasicItem>(
    349351              item, rs.getInt(1), rowCount);
    … …  
    356358        progress.increase();
    357359      }
    358       dc.close();
     360      dc.commit();
     361      rs.close();
    359362      // Reset our ResultSet
    360       rs.beforeFirst();
    361       processItemList(rs);
    362       rs.close();
     363      //rs.beforeFirst();
     364      processItemList();
    363365    }
    364366    catch (SQLException e)
    … …  
    413415  }
    414416
    415   private void processItemList(ResultSet rs)
    416   {
    417     DbControl dc = newDbControl();
    418     saveItemList(dc);
    419     commit(dc);
     417  private void processItemList()
     418  {
     419    //DbControl dc = newDbControl();
     420    //saveItemList(dc);
     421    //commit(dc);
    420422    if (mapIds)
    421423    {
    422424      mapItemList();
    423425    }
    424     processSavedItemList(itemList, rs);
     426    //processSavedItemList(itemList, rs);
    425427    itemList.clear();
    426428    cleanUpMemory();
    427429  }
    428430
     431  /*
    429432  protected void processSavedItemList(
    430433      List<WrappedItem<BasicItem>> itemList, ResultSet rs)
    431434  {}
     435  */
    432436
    433437  private void mapItemList()
    … …  
    438442      int base2Id = wi.getId();
    439443      idMap.put(base1Id, base2Id);
    440     }
    441   }
    442 
    443   private void saveItemList(DbControl dc)
    444   {
    445     for (WrappedItem<BasicItem> wi : itemList)
    446     {
    447       if (wi != null)
    448       {
    449         BasicItem<?> item = wi.getItem();
    450         if (!item.isInDatabase())
    451         {
    452           dc.saveItem(item);
    453         }
    454       }
    455       else
    456       {
    457         log("saveItemList", "wi is null");
    458       }
    459444    }
    460445  }

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/UserTransfer.java

    r2614 r2622  
    2424package net.sf.basedb.clients.migrate;
    2525
    26 import net.sf.basedb.core.DateUtil;
    2726import net.sf.basedb.core.DbControl;
    2827import net.sf.basedb.core.Directory;
    … …  
    3029import net.sf.basedb.core.ItemQuery;
    3130import net.sf.basedb.core.ItemResultList;
    32 import net.sf.basedb.core.Location;
    3331import net.sf.basedb.core.Quota;
    34 import net.sf.basedb.core.QuotaType;
    3532import net.sf.basedb.core.Role;
    3633import net.sf.basedb.core.SystemItems;
    … …  
    3936import java.sql.ResultSet;
    4037import java.sql.SQLException;
    41 import java.util.ArrayList;
    4238import java.util.HashMap;
    4339import java.util.Map;
    44 import java.util.TreeMap;
     40import java.util.Set;
    4541
    4642/**
    … …  
    5349defaultGid, defaultGroupAccess, defaultWorldAccess<br/> <b>UserGroupParent</b>:
    5450isReviewer</dd>
    55 <dt><b>Notes</b></dt>
    56 <dd>
    57 <ul>
    58 <li>The database must support the BIT_OR method</li>
    59 </ul>
    60 </dd>
     51
    6152</dl>
    6253
    … …  
    6960   */
    7061  private RoleTransfer roleT = null;
     62 
     63  private QuotaTransfer quotaT = null;
     64 
    7165  /**
    7266  File quotas are stored and later used to calculate a users new filequota.
     67  Maps Base 1 ID -> total quota min bytes
    7368   */
    7469  private Map<Integer, Long> base1FileQuota = null;
    … …  
    8681
    8782  /**
    88   Maps base 1 ids to Base 2 user objects
    89    */
    90   // private User[] idUserMap = null;
    91   /**
    9283  @param roleT {@link RoleTransfer}
    9384   */
    94   UserTransfer(RoleTransfer roleT)
    95   {
    96     if (roleT.isDone())
     85  UserTransfer(RoleTransfer roleT, QuotaTransfer quotaT)
     86  {
     87    if (roleT.isDone() && quotaT.isDone())
    9788    {
    9889      this.roleT = roleT;
     90      this.quotaT = quotaT;
    9991      existingUsers = new HashMap<String, User>();
    10092    }
    … …  
    158150          {
    159151            home = Directory.createHomeDirectory(b2c, user, true);
    160             user.setHomeDirectory(home);
    161152            progress.increase();
    162153          }
    … …  
    225216        user.setName(name);
    226217        // fileQuota is saved for later use in finalizeQuota()
    227         base1FileQuota.put(userId, rs.getLong(11));
     218        long byteQuota = rs.getLong(11);
     219        if (rs.wasNull()) byteQuota = Quota.UNLIMITED;
     220        base1FileQuota.put(userId, byteQuota);
    228221        /*
    229222         * Initially quota is set to unlimited. When all transfers are
    230223         * finished quota is updated to a suitible level.
    231224         */
    232         Quota quota = Quota.getById(
    233             dc, SystemItems.getId(Quota.UNRESTRICTED));
    234         user.setQuota(quota);
     225        Quota unlimitedQuota = Quota.getById(dc, SystemItems.getId(Quota.UNRESTRICTED));
     226        user.setQuota(unlimitedQuota);
    235227        try
    236228        {
    237           user.setExpirationDate(DateUtil.parseString(rs.getString(12)));
     229          user.setExpirationDate(rs.getDate(12));
    238230        }
    239231        catch (SQLException e)
    … …  
    248240      user.setPhone(rs.getString(9));
    249241      user.setRemoved(rs.getBoolean(10));
    250       QuotaType quotaType = QuotaType.getById(
    251           dc, SystemItems.getId(QuotaType.TOTAL));
    252       long byteQuota = rs.getLong(11);
    253       if (rs.wasNull())
    254       {
    255         byteQuota = -1;
    256       }
    257       ItemQuery<Quota> query = Quota.getQuery();
    258       ItemResultList<Quota> quotas = query.list(dc);
    259       TreeMap<Long, Quota> sortedQuotas = new TreeMap<Long, Quota>();
    260       for (Quota quota : quotas)
    261       {
    262         long quotaValue = quota.getQuotaValue(
    263             quotaType, Location.PRIMARY);
    264         sortedQuotas.put(new Long(quotaValue), quota);
    265       }
    266       Object[] sortedKeys = sortedQuotas.keySet().toArray();
    267       for (Object quotaValue : sortedKeys)
    268       {
    269         if (byteQuota <= ((Long) quotaValue).longValue())
    270         {
    271           user.setQuota(sortedQuotas.get((Long) quotaValue));
    272           break;
    273         }
    274       }
     242      dc.saveItem(user);
     243
    275244      // Combine(OR) user accessMask with group accessMask
    276245      Integer mask = rs.getInt(13);
    277246      Integer groupMask = groupUserAccessMap.get(userId);
    278247      if (groupMask != null) mask |= groupMask;
    279       ArrayList<Integer> roleIds = roleT.getRoleIds(mask);
    280       dc.saveItem(user);
    281       dc.commit();
    282       mapId(userId, user.getId());
    283       dc = newDbControl();
     248      Set<Integer> roleIds = roleT.getRoleIds(mask);
    284249      for (Integer roleId : roleIds)
    285250      {
    … …  
    291256      }
    292257      dc.commit();
     258      mapId(userId, user.getId());
    293259    }
    294260    catch (Exception e)
    … …  
    302268  }
    303269
     270  public void finalizeQuota()
     271  {
     272    startProgress(base1FileQuota.size());
     273    DbControl dc = newDbControl();
     274    try
     275    {
     276      for (Map.Entry<Integer, Long> entry : base1FileQuota.entrySet())
     277      {
     278        Integer base1Id = entry.getKey();
     279        Long base1Quota = entry.getValue();
     280       
     281        User user = getUserById(dc, base1Id);
     282        Quota quota = quotaT.getQuotaForTotal(dc, base1Quota);
     283        user.setQuota(quota);
     284        progress.increase();
     285      }
     286      dc.commit();
     287    }
     288    finally
     289    {
     290      if (dc != null) dc.close();
     291      progress.stop();
     292    }
     293  }
     294 
    304295  public User getUserById(DbControl dc, int base1Id)
    305296  {

  • branches/2.0/src/clients/migrate/net/sf/basedb/clients/migrate/WizzzardTransfer.java

    r2614 r2622  
    6666  public void start()
    6767  {
    68     startProgress(getInt("countWizzzards"));
     68    int count = getInt("countWizzzards");
     69    initIdMap(count);
     70    startProgress(count);
    6971    runUnBatched(prepareStatementFromFile("selectWizzzards"), 0, getBatchSize());
    7072    done();
    … …  
    8385      setCommonItemData(dc, pluginConfiguration, rs);
    8486      PluginConfigurationRequest request = pluginConfiguration.configure();
    85       String fieldSeparator = rs.getString(17);
    86       fieldSeparator = fieldSeparator.replaceAll("\\t", "\\\\t"); // Replace tab character with \t
     87     
     88      String dataHeaderRegexp = fixRegexp(rs.getString(12));
     89      String dataFooterRegexp = fixRegexp(rs.getString(16));
     90      String fieldSeparator = fixRegexp(rs.getString(17));
     91      int minDataColumns = rs.getInt(10);
     92      int maxDataColumns = rs.getInt(11);
     93     
    8794      HashMap<String, String> mappings = getParameterMappings(rs.getString(15));
    8895      // Plugin dependent parameters
    … …  
    100107          // General parameters
    101108          request = response.getNextRequest();
    102           request.setParameterValue(
    103               "dataSplitterRegexp", fieldSeparator);
    104           request.setParameterValue(
    105               "dataHeaderRegexp", rs.getString(12));
    106           request.setParameterValue(
    107               "dataFooterRegexp", rs.getString(16));
    108           request.setParameterValue("minDataColumns", rs.getInt(10));
    109           request.setParameterValue("maxDataColumns", rs.getInt(11));
     109          request.setParameterValue("dataSplitterRegexp", fieldSeparator);
     110          request.setParameterValue("dataHeaderRegexp", dataHeaderRegexp);
     111          request.setParameterValue("dataFooterRegexp", dataFooterRegexp);
     112          request.setParameterValue("minDataColumns", minDataColumns);
     113          request.setParameterValue("maxDataColumns", maxDataColumns);
    110114          // RawBioAssayData
    111115          request.setParameterValue(
    … …  
    197201      {
    198202        request.setParameterValue("dataSplitterRegexp", fieldSeparator);
    199         request.setParameterValue("dataHeaderRegexp", rs.getString(12));
    200         request.setParameterValue("dataFooterRegexp", rs.getString(16));
    201         request.setParameterValue("minDataColumns", rs.getInt(10));
    202         request.setParameterValue("maxDataColumns", rs.getInt(11));
     203        request.setParameterValue("dataHeaderRegexp", dataHeaderRegexp);
     204        request.setParameterValue("dataFooterRegexp", dataFooterRegexp);
     205        request.setParameterValue("minDataColumns", minDataColumns);
     206        request.setParameterValue("maxDataColumns", maxDataColumns);
    203207        request.setParameterValue(
    204208            "nameColumnMapping", mappings.get("_p_name"));
    … …  
    215219      {
    216220        request.setParameterValue("dataSplitterRegexp", fieldSeparator);
    217         request.setParameterValue("dataHeaderRegexp", rs.getString(12));
     221        request.setParameterValue("dataHeaderRegexp", dataHeaderRegexp);
     222        request.setParameterValue("dataFooterRegexp", dataFooterRegexp);
     223        request.setParameterValue("minDataColumns", minDataColumns);
     224        request.setParameterValue("maxDataColumns", maxDataColumns);
    218225        request.setParameterValue(
    219226            "reporterIdColumnMapping", mappings.get("reporterId"));
    … …  
    255262            "extendedColumnMapping.locusLink",
    256263            mappings.get("locusLink"));
    257         request.setParameterValue("minDataColumns", rs.getInt(10));
    258         request.setParameterValue("maxDataColumns", rs.getInt(11));
    259264      }
    260265      else if (formatType != null && formatType.equals("reportermap"))
    261266      {
    262267        request.setParameterValue("dataSplitterRegexp", fieldSeparator);
    263         request.setParameterValue("dataHeaderRegexp", rs.getString(12));
     268        request.setParameterValue("dataHeaderRegexp", dataHeaderRegexp);
     269        request.setParameterValue("dataFooterRegexp", dataFooterRegexp);
     270        request.setParameterValue("minDataColumns", minDataColumns);
     271        request.setParameterValue("maxDataColumns", maxDataColumns);
    264272        request.setParameterValue(
    265273            "reporterIdColumnMapping", mappings.get("reporterId"));
    … …  
    305313  private HashMap<String, String> getParameterMappings(String mapping)
    306314  {
    307     log("getParameterMappings", mapping);
    308315    String regexp = "([^:]+):([^,]*),?";
    309316    // Split on comma, group by colon: key1:value1,key2:value2
    … …  
    318325      }
    319326    }
    320     log("getParameterMappings", mappings.toString());
    321327    return mappings;
    322328  }
    … …  
    362368    return pluginDefinition;
    363369  }
     370 
     371  private String fixRegexp(String base1Regexp)
     372  {
     373    String fixedRegexp = null;
     374    if (base1Regexp != null)
     375    {
     376      fixedRegexp = base1Regexp.replaceAll("\\t", "\\\\t"); // Replace tab character with \t
     377    }
     378    return fixedRegexp;
     379  }
     380 
    364381}

  • branches/2.0/src/clients/migrate/sql/mysql-migration-queries.sql

    r2614 r2622  
    9393
    9494/* selectGroups */
    95 SELECT `id`, `name`, `descr`, `removed`, `accessMask` 
     95SELECT `id`, `name`, `descr`, `removed`, `accessMask`, `byteQuota`
    9696FROM `UserGroup`
    9797WHERE `isAccount` = 0
    … …  
    542542SELECT  `h`.`id`, `h`.`owner`, `h`.`gid`, `h`.`groupAccess`, `h`.`worldAccess`, `h`.`name`, `h`.`descr`, `h`.`removed`,
    543543  `h`.`hybridizationDate`,
     544  `h`.`protocol`,
    544545  `s`.`id` as arraySlideId,
    545546  `s`.`hybridization`
    … …  
    647648LIMIT   ?,?;
    648649
    649 
     650/* selectLabeledExtractsByHybridization */
     651SELECT  `labeled`, `quantity`
     652FROM  `HybridizedLabeled`
     653WHERE hybridization = ?
     654ORDER BY `channel`;
    650655
    651656
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