Changeset 5091


Ignore:
Timestamp:
Aug 31, 2009, 11:21:04 AM (13 years ago)
Author:
Nicklas Nordborg
Message:

Merged pre-2.13-releases to the trunk.

Location:
trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/test/roles/index.html

    r4889 r5091  
    13801380      <td>Sampling A</td>
    13811381      <td>Biosource A</td>
    1382       <td>Bioplate A [0, 0]</td>
     1382      <td>Bioplate A [A1]</td>
    13831383      <td>
    13841384        <table border="0" cellspacing="0" cellpadding="2">
     
    13941394      <td>Sampling A</td>
    13951395      <td>Biosource A</td>
    1396       <td>Bioplate A [0, 1]</td>
     1396      <td>Bioplate A [A2]</td>
    13971397      <td>
    13981398        <table border="0" cellspacing="0" cellpadding="2">
     
    14081408      <td>Sampling A</td>
    14091409      <td>-</td>
    1410       <td>Bioplate A [0, 2]</td>
     1410      <td>Bioplate A [A3]</td>
    14111411      <td>-</td>
    14121412    </tr>
     
    14281428      <td>Extraction A</td>
    14291429      <td>Sample A.00h</td>
    1430       <td>Bioplate A [1, 0]</td>
     1430      <td>Bioplate A [B1]</td>
    14311431    </tr>
    14321432    <tr>
     
    14341434      <td>Extraction A</td>
    14351435      <td>Sample A.24h</td>
    1436       <td>Bioplate A [1, 1]</td>
     1436      <td>Bioplate A [B2]</td>
    14371437    </tr>
    14381438    <tr>
     
    14401440      <td>Extraction A</td>
    14411441      <td>Sample A.ref</td>
    1442       <td>Bioplate A [1, 2]</td>
     1442      <td>Bioplate A [B3]</td>
    14431443    </tr>
    14441444    </table>
     
    14611461      <td>Labeling A</td>
    14621462      <td>Extract A.00h</td>
    1463       <td>Bioplate A [2, 0]</td>
     1463      <td>Bioplate A [C1]</td>
    14641464    </tr>
    14651465    <tr>
     
    14681468      <td>Labeling A</td>
    14691469      <td>Extract A.24h</td>
    1470       <td>Bioplate A [2, 1]</td>
     1470      <td>Bioplate A [C2]</td>
    14711471    </tr>
    14721472    <tr>
     
    14751475      <td>Labeling A</td>
    14761476      <td>Extract A.ref</td>
    1477       <td>Bioplate A [2, 2]</td>
     1477      <td>Bioplate A [C3]</td>
    14781478    </tr>
    14791479    <tr class="shaded">
     
    14821482      <td>Labeling A</td>
    14831483      <td>Extract A.00h</td>
    1484       <td>Bioplate A [3, 0]</td>
     1484      <td>Bioplate A [D1]</td>
    14851485    </tr>
    14861486    <tr class="shaded">
     
    14891489      <td>Labeling A</td>
    14901490      <td>Extract A.24h</td>
    1491       <td>Bioplate A [3, 1]</td>
     1491      <td>Bioplate A [D2]</td>
    14921492    </tr>
    14931493    <tr class="shaded">
     
    14961496      <td>Labeling A</td>
    14971497      <td>Extract A.ref</td>
    1498       <td>Bioplate A [3, 2]</td>
     1498      <td>Bioplate A [D3]</td>
    14991499    </tr>
    15001500    </table>
     
    18861886      <td><code>Warning</code></td>
    18871887    </tr>
     1888    <tr>
     1889      <td>Other - Raw spots &lt;&gt; features</td>
     1890      <td><code>Ignore</code></td>
     1891    </tr>
    18881892    </table>
    18891893   
     
    19711975   
    19721976  <li>
    1973     Select the normalized bioassay set and check the overview plots and
     1977    Select the normalized bioassay set and check the MA plots and
    19741978    the correction factor plots. Here are four examples:
    19751979    <table class="listing" cellspacing="0" cellpadding="2" border="0">
    19761980    <tr>
    1977       <th>Overview plots</th>
     1981      <th>MA plots</th>
    19781982      <th>Correction factor plots</th>
    19791983    </tr>
  • trunk/src/core/net/sf/basedb/core/Keyring.java

    r5077 r5091  
    511511        Set<Integer> projectGroups = Group.getGroupsRecursive(session, HibernateUtil.loadList(Integer.class, query, null));
    512512       
    513         // Finally, filter away groups that has hiddenMembers=true
    514         query = HibernateUtil.getPredefinedQuery(session, "GET_GROUPS_WITH_NONHIDDENMEMBERS");
    515         /*
    516           SELECT grp.id
    517           FROM GroupData grp
    518           WHERE grp.hiddenMembers = false
    519           AND grp.id IN (:groups)
    520         */
    521         query.setParameterList("groups", projectGroups, org.hibernate.Hibernate.INTEGER);
    522         projectGroups.retainAll(HibernateUtil.loadList(Integer.class, query, null));
     513        if (projectGroups.size() > 0)
     514        {
     515          // Finally, filter away groups that has hiddenMembers=true
     516          query = HibernateUtil.getPredefinedQuery(session, "GET_GROUPS_WITH_NONHIDDENMEMBERS");
     517          /*
     518            SELECT grp.id
     519            FROM GroupData grp
     520            WHERE grp.hiddenMembers = false
     521            AND grp.id IN (:groups)
     522          */
     523          query.setParameterList("groups", projectGroups, org.hibernate.Hibernate.INTEGER);
     524          projectGroups.retainAll(HibernateUtil.loadList(Integer.class, query, null));
     525        }
    523526       
    524527        // Load users that are members of the project groups
  • trunk/src/test/net/sf/basedb/test/roles/AnalysisTest.java

    r4768 r5091  
    8787      options.setSeverity(Validator.MISSING_HARDWARE, Severity.IGNORE);
    8888      options.setSeverity(Validator.MISSING_PROTOCOL, Severity.IGNORE);
     89      options.setSeverity(Validator.NONMATCHING_SPOTCOUNT, Severity.IGNORE);
    8990      GenericOverview affyOverview = getExperimentOverview(dc, affyExperiment,
    9091        activeProject, options, 2);
  • trunk/www/include/scripts/main.js

    r5075 r5091  
    6363    if (wLeft == undefined) wLeft = 0;
    6464 
    65     var wHeight = window.innerHeight;
    66     if (wHeight == undefined) wHeight = document.body.clientHeight;
    67     if (wHeight == undefined) wHeight = screen.height;
    68  
    69     var wWidth = window.innerWidth;
    70     if (wWidth == undefined) wWidth = document.body.clientWidth;
    71     if (wWidth == undefined) wWidth = screen.width;
    72  
     65    var wHeight = this.getWindowHeight();
     66    var wWidth = this.getWindowWidth();
     67   
    7368    var top = Math.ceil(wTop+(wHeight-height) / 2);
    7469    var left = Math.ceil(wLeft+(wWidth-width) / 2);
     
    7772    if (options == null) options = "toolbar=no,location=no,directories=no,status=no,menubar=no,scrollbars=yes,resizable=yes";
    7873    options = "top="+top+",left="+left+",width="+width+",height="+height+"," + options;
    79     var newWin = window.open('', name, options);
    80     if (newWin.isOld)
     74
     75    var newWin = this.getPageValue('open.windows', name);
     76    if (newWin && !newWin.closed)
    8177    {
    8278      var msg = 'This window has already been opened. ';
     
    8985      url += '&warnIfOpen=0';
    9086    }
    91     newWin.isOld = true;
    92     window.newWindow = newWin;
     87    var newWin = window.open('', name, options);
     88    this.setPageValue('open.windows', name, newWin);
    9389    Main.safeSetLocation(url, newWin, true);
    94     setTimeout("window.newWindow.focus()", 100);
    95   }
    96 
     90    setTimeout("Main.focusWindow('" + name + "')", 100);
     91  }
     92
     93  /**
     94    Brings a named window to focus.
     95  */
     96  this.focusWindow = function(windowName)
     97  {
     98    var win = this.getPageValue('open.windows', windowName);
     99    if (win) win.focus();
     100  }
     101 
    97102  /*
    98103    Opens a popupwindow with a larger textarea field. The text is taken from
     
    723728 
    724729  /**
     730    Save a key-value pair for a page.
     731  */
     732  this.setPageValue = function(page, key, value)
     733  {
     734    if (!window.top.pageValues) window.top.pageValues = new Array();
     735    if (!window.top.pageValues[page]) window.top.pageValues[page] = new Array();
     736    window.top.pageValues[page][key] = value;
     737  }
     738
     739  /**
     740    Get the saved value for the given key on a page
     741  */
     742  this.getPageValue = function(page, key)
     743  {
     744    if (!window.top.pageValues) return null;
     745    if (!window.top.pageValues[page]) return null;
     746    return window.top.pageValues[page][key];
     747  }
     748
     749  /**
    725750    Get all elements with a given <tag> and class="..."
    726751  */
  • trunk/www/include/scripts/tabcontrol.js

    r4911 r5091  
    4444      if (!tabControl.activeTab)
    4545      {
    46         var theWindow = window.opener ? window.opener : window.top;
     46        var theWindow = window.opener ? window.opener : window;
    4747        var rememberedTabId = TabControl.getRememberedTabId(theWindow, tabControlId);
    4848        if (rememberedTabId) tabId = rememberedTabId
     
    8181  {
    8282    var tabControl = document.getElementById(tabControlId);
    83     var theWindow = window.opener ? window.opener : window.top;
     83    var theWindow = window.opener ? window.opener : window;
    8484 
    8585    var realTabId = tabControlId+'.'+tabId;
     
    124124  this.rememberActiveTab = function(window, tabControlId, tabId)
    125125  {
    126     if (!window.rememberedTabs) window.rememberedTabs = new Array();
    127     var rememberedTabs = window.rememberedTabs;
    128     var thisLocation = location.pathname;
    129     if (!rememberedTabs[thisLocation]) rememberedTabs[thisLocation] = new Array();
    130     rememberedTabs[thisLocation][tabControlId] = tabId;
     126    if (window.Main) window.Main.setPageValue(location.pathname, tabControlId, tabId);
    131127  }
    132128 
    133129  this.getRememberedTabId = function(window, tabControlId)
    134130  {
    135     if (!window.rememberedTabs) return null;
    136     var rememberedTabs = window.rememberedTabs;
    137     var thisLocation = location.pathname;
    138     if (!rememberedTabs[thisLocation]) return null;
    139     return rememberedTabs[thisLocation][tabControlId];
     131    if (!window.Main) return null;
     132    return window.Main.getPageValue(location.pathname, tabControlId);
    140133  }
    141134 
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