Changeset 5788


Ignore:
Timestamp:
Oct 6, 2011, 1:05:00 PM (11 years ago)
Author:
Nicklas Nordborg
Message:

References #1613: Extend the 'roles' test case with some sequence-related tests

Updated and synchronized the test instructions with the test code. Fixed a few issues with the test code.

The "Item overview" and analysis sections remains.

Location:
trunk
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/test/roles/index.html

    r5700 r5788  
    116116    <ul>
    117117    <li>Biomaterials: bioplate, biosources, samples, extracts, etc.</li>
    118     <li>Experiment: hybridizations, scans, images, raw bioassays</li>
     118    <li>Experiment: physical bioassays, derived bioassays, raw bioassays</li>
    119119    <li>Import raw data</li>
    120120    </ul>
    … …  
    144144    core developer. Read the instructions on the
    145145    <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
    146     page, <code>Test data</code> section on the Base 2 web site. The automated
     146    page, <code>Test data</code> section on the BASE web site. The automated
    147147    test programs require that file are placed (checked out) in the 'testdata'
    148148    directory located in the BASE root directory. NOTE! Some test data files are
    149     bzip-compressed. These need to be uncompressed before they are uploaded to BASE.
     149    bzip-compressed. Use the automatic unpacking that is built-in to BASE when
     150    uploading.
    150151  </p>
    151152 
    … …  
    286287        <li>Reporter map importer</li>
    287288        <li>Print map importer</li>
     289        <li>GTF reporter map importer</li>
    288290        <li>Array design importer</li>
    289291        <li>Array batch importer</li>
    … …  
    314316      <td>Reporter importer</td>
    315317      <td>
    316       <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
    317318      <table border="0" cellspacing="0" cellpadding="2">
     319      <tr>
     320        <td><b>File</b></td>
     321        <td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td>
     322      </tr>
    318323      <tr>
    319324        <td><i>Data header</i></td>
    … …  
    358363      <td>
    359364
    360       <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
    361365      <table border="0" cellspacing="0" cellpadding="2">
     366      <tr>
     367        <td><b>File</b></td>
     368        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
     369      </tr>
    362370      <tr>
    363371        <td><i>Data header</i></td>
    … …  
    392400      <td>Reporter importer</td>
    393401      <td>
    394       <b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code>
    395402      <table border="0" cellspacing="0" cellpadding="2">
     403      <tr>
     404        <td><b>File</b></td>
     405        <td><code>affymetrix/annotations/<br>MG_U74Av2_annot.csv.bz2</code></td>
     406      </tr>
    396407      <tr>
    397408        <td><i>Data header</i></td>
    … …  
    422433      </td>
    423434    </tr>   
     435    <tr class="evenrow">
     436      <td>Reporters from GTF file</td>
     437      <td>GTF Reporter importer</td>
     438      <td>
     439
     440      <table border="0" cellspacing="0" cellpadding="2">
     441      <tr>
     442        <td><b>File</b></td>
     443        <td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf.tar.bz2</code></td>
     444      </tr>
     445      <tr>
     446        <td><i>Data header</i></td>
     447        <td>&lt;seqname&gt;\t.*&lt;transcript_id&gt;.*</td>
     448      </tr>
     449      <tr>
     450        <td><i>Data splitter</i></td>
     451        <td>\t</td>
     452      </tr>
     453      <tr>
     454        <td><i>Min data columns</i></td>
     455        <td>4</td>
     456      </tr>
     457      <tr>
     458        <td><i>Remove quotes</i></td>
     459        <td>yes</td>
     460      </tr>
     461      <tr>
     462        <td><i>Complex mappings</i></td>
     463        <td>allow</td>
     464      </tr>
     465      <tr>
     466        <td><i>Name</i></td>
     467        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
     468      </tr>
     469      <tr>
     470        <td><i>External ID</i></td>
     471        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
     472      </tr>
     473      <tr>
     474        <td><i>Gene symbol</i></td>
     475        <td>\&lt;gene_id&gt;\</td>
     476      </tr>
     477      <tr>
     478        <td><i>Chromosome</i></td>
     479        <td>\&lt;seqname&gt;\</td>
     480      </tr>
     481      </table>
     482
     483      </td>
     484    </tr>
    424485    </table>
    425486    <p>
    … …  
    443504        the file contains data that is too large for the datbase.
    444505        12,488 new reporters should be created.
     506      <li>
     507        Repeat the procedure with the <code>UCSC_Human_hg19_RefSeqGenes.gtf</code>
     508        file. The default error handling options can be used. This time
     509        38,977 new reporters should be created.
    445510      </ol>
    446511      <p>
    … …  
    521586      <td>-</td>
    522587      <td>-</td>
    523       <td>Scan</td>
     588      <td>Derived bioassay</td>
    524589    </tr>
    525590    </table>
    … …  
    670735      <td>
    671736     
    672       <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
    673737      <table border="0" cellspacing="0" cellpadding="2">
     738      <tr>
     739        <td><b>File</b></td>
     740        <td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td>
     741      </tr>
    674742      <tr>
    675743        <td><i>Data header</i></td>
    … …  
    710778      <td>
    711779     
    712       <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
    713780      <table border="0" cellspacing="0" cellpadding="2">
     781      <tr>
     782        <td><b>File</b></td>
     783        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
     784      </tr>
    714785      <tr>
    715786        <td><i>Data header</i></td>
    … …  
    750821   
    751822    <tr class="oddrow">
     823      <td>GTF features for project A</td>
     824      <td>GTF reporter map importer</td>
     825      <td>
     826     
     827      <table border="0" cellspacing="0" cellpadding="2">
     828      <tr>
     829        <td><b>File</b></td>
     830        <td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf</code></td>
     831      </tr>
     832      <tr>
     833        <td><i>Data header</i></td>
     834        <td>&lt;seqname&gt;\t.*&lt;transcript_id&gt;.*</td>
     835      </tr>
     836      <tr>
     837        <td><i>Data splitter</i></td>
     838        <td>\t</td>
     839      </tr>
     840      <tr>
     841        <td><i>Min data columns</i></td>
     842        <td>4</td>
     843      </tr>
     844      <tr>
     845        <td><i>Remove quotes</i></td>
     846        <td>yes</td>
     847      </tr>
     848      <tr>
     849        <td><i>Complex mappings</i></td>
     850        <td>allow</td>
     851      </tr>
     852      <tr>
     853        <td><i>Reporter ID</i></td>
     854        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
     855      </tr>
     856      <tr>
     857        <td><i>Feature ID</i></td>
     858        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
     859      </tr>
     860      </table>
     861
     862      </td>
     863    </tr>
     864   
     865    <tr class="evenrow">
    752866      <td>Raw data for project A</td>
    753867      <td>Raw data importer</td>
    754868      <td>
    755869     
    756       <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
    757870      <table border="0" cellspacing="0" cellpadding="2">
     871      <tr>
     872        <td><b>File</b></td>
     873        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
     874      </tr>
    758875      <tr>
    759876        <td><i>Raw data type</i></td>
    … …  
    8981015    </tr>
    8991016   
    900     <tr class="evenrow">
     1017    <tr class="oddrow">
    9011018      <td>Raw data for project A (dye-swap)</td>
    9021019      <td>Raw data importer</td>
    9031020      <td>
    9041021
    905       <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
    9061022      <table border="0" cellspacing="0" cellpadding="2">
     1023      <tr>
     1024        <td><b>File</b></td>
     1025        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td>
     1026      </tr>
    9071027      <tr>
    9081028        <td><i>Raw data type</i></td>
    … …  
    11251245    <tr>
    11261246      <th>Name</th>
    1127       <th>Platform</th>
     1247      <th>Platform/Variant</th>
    11281248      <th>File(s)</th>
    11291249    </tr>
    … …  
    11311251      <td>Array design A</td>
    11321252      <td>Generic</td>
    1133       <td><i>Print map</i>: printmap.mouse.v4.37k.tam</td>
     1253      <td><i>Print map</i>: <code>mouse/printmap.mouse.v4.37k.tam</code></td>
    11341254    </tr>
    11351255    <tr>
    11361256      <td>Affymetrix A</td>
    11371257      <td>Affymetrix</td>
    1138       <td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td>
     1258      <td><i>CDF file</i>: <code>affymtrix/cdf/MG_U74Av2.cdf</code></td>
     1259    </tr>
     1260    <tr>
     1261      <td>RefSeqDesign A</td>
     1262      <td>Sequencing/Expression-like</td>
     1263      <td><i>GTF ref-seq file</i>: <code>sequencing/UCSC_Human_hg19_RefSeqGenes.gtf</code></td>
    11391264    </tr>
    11401265    </table>
    … …  
    11621287 
    11631288  <li>
    1164     Import features:
     1289    Import features to Array design A:
    11651290    <ol>
    11661291    <li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
    1167     <li>Choose <code>auto-detect</code> and upload the file
     1292    <li>Choose <code>auto-detect</code> and use the file
    11681293      <code>printmap.mouse.v4.37k.tam</code>.</li>
    11691294    <li>The <code>Print map importer</code> plug-in should be
    … …  
    11721297    </ol>
    11731298    <p>
     1299    Import features to RefSeqDesign A:
     1300    <ol>
     1301    <li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
     1302    <li>Choose <code>auto-detect</code> and use the file
     1303      <code>UCSC_Human_hg19_RefSeqGenes.gtf</code>.</li>
     1304    <li>The <code>GTF reporter map importer</code> plug-in should be
     1305      found. Select the <code>GTF features for project A</code> format.</li>
     1306    <li>Continue and wait for the import to finish. It should create 38,977 features and 1 block.</li>
     1307    </ol>
     1308    <p>
    11741309  </li>
    11751310
    … …  
    11961331    </tr>
    11971332    <tr>
     1333      <td>Platforms variants</td>
     1334      <td>
     1335        Sequencing / Expression-like
     1336      </td>
     1337    </tr>
     1338    <tr>
    11981339      <td>Array designs</td>
    11991340      <td>
    12001341        Array design A<br>
    1201         Affymetrix A
     1342        Affymetrix A<br>
     1343        RefSeqDesign A
    12021344      </td>
    12031345    </tr>
    … …  
    12541396      <td>Array batch A</td>
    12551397      <td>Array design A</td>
    1256       <td>Robot A</td>
     1398      <td>Print robot A</td>
    12571399      <td>Printing A</td>
    12581400    </tr>
    … …  
    15071649    <tr>
    15081650      <th>Name</th>
     1651      <th>Type</th>
    15091652      <th>Label</th>
    15101653      <th>Protocol</th>
    … …  
    15141657    <tr>
    15151658      <td>Labeled extract A.00h</td>
     1659      <td>Labeled extract</td>
    15161660      <td>cy3</td>
    15171661      <td>Labeling A</td>
    … …  
    15211665    <tr>
    15221666      <td>Labeled extract A.24h</td>
     1667      <td>Labeled extract</td>
    15231668      <td>cy3</td>
    15241669      <td>Labeling A</td>
    … …  
    15281673    <tr>
    15291674      <td>Labeled extract A.ref</td>
     1675      <td>Labeled extract</td>
    15301676      <td>cy5</td>
    15311677      <td>Labeling A</td>
    … …  
    15351681    <tr class="shaded">
    15361682      <td>Labeled extract A.00h (dye-swap)</td>
     1683      <td>Labeled extract</td>
    15371684      <td>cy5</td>
    15381685      <td>Labeling A</td>
    … …  
    15421689    <tr class="shaded">
    15431690      <td>Labeled extract A.24h (dye-swap)</td>
     1691      <td>Labeled extract</td>
    15441692      <td>cy5</td>
    15451693      <td>Labeling A</td>
    … …  
    15491697    <tr class="shaded">
    15501698      <td>Labeled extract A.ref (dye-swap)</td>
     1699      <td>Labeled extract</td>
    15511700      <td>cy3</td>
    15521701      <td>Labeling A</td>
    … …  
    15561705    <tr>
    15571706      <td>Library A.00h</td>
     1707      <td>Library</td>
    15581708      <td>-</td>
    15591709      <td>Library preparation A</td>
    … …  
    15631713    <tr>
    15641714      <td>Library A.24h</td>
     1715      <td>Library</td>
    15651716      <td>-</td>
    15661717      <td>Library preparation A</td>
    … …  
    15701721    <tr>
    15711722      <td>Library A.ref</td>
     1723      <td>Library</td>
    15721724      <td>-</td>
    15731725      <td>Library preparation A</td>
    … …  
    16501802 
    16511803  <li>
    1652     Create derived bioassays (scans, assemblys, etc.):
     1804    Create derived bioassays (scans, arrangements, etc.):
    16531805    <table class="listing" cellspacing="0" cellpadding="2" border="0">
    16541806    <tr>
    … …  
    16631815      <td>Scan A.00h</td>
    16641816      <td>Hybridization A.00h</td>
    1665       <td>Labeled extract A.00h</td>
     1817      <td>-</td>
    16661818      <td>HW: Scanner A</td>
    16671819      <td>Scanning A</td>
    … …  
    16711823      <td>Scan A.24h</td>
    16721824      <td>Hybridization A.24h</td>
    1673       <td>Labeled extract A.24h</td>
     1825      <td>-</td>
    16741826      <td>HW: Scanner A</td>
    16751827      <td>Scanning A</td>
    … …  
    16791831      <td>Scan A.00h (dye-swap)</td>
    16801832      <td>Hybridization A.00h (dye-swap)</td>
    1681       <td>Labeled extract A.00h (dye-swap)</td>
     1833      <td>-</td>
    16821834      <td>HW: Scanner A</td>
    16831835      <td>Scanning A</td>
    … …  
    16871839      <td>Scan A.24h (dye-swap)</td>
    16881840      <td>Hybridization A.24h (dye-swap)</td>
    1689       <td>Labeled extract A.24h (dye-swap)</td>
     1841      <td>-</td>
    16901842      <td>HW: Scanner A</td>
    16911843      <td>Scanning A</td>
    … …  
    16951847      <td>Affymetrix scan A.1</td>
    16961848      <td>Affymetrix hyb A.1</td>
    1697       <td>Labeled extract A.00h</td>
     1849      <td>-</td>
    16981850      <td>HW: Scanner A</td>
    16991851      <td>Scanning A</td>
    … …  
    17031855      <td>Affymetrix scan A.2</td>
    17041856      <td>Affymetrix hyb A.2</td>
    1705       <td>Labeled extract A.24h</td>
     1857      <td>-</td>
    17061858      <td>HW: Scanner A</td>
    17071859      <td>Scanning A</td>
    … …  
    17111863      <td>Affymetrix scan A.3</td>
    17121864      <td>Affymetrix hyb A.3</td>
    1713       <td>Labeled extract A.ref</td>
     1865      <td>-</td>
    17141866      <td>HW: Scanner A</td>
    17151867      <td>Scanning A</td>
    … …  
    17251877    </tr>
    17261878    <tr class="shaded">
    1727       <td>Assembly A.00h</td>
     1879      <td>Arrangement A.00h</td>
    17281880      <td>Sequenced A</td>
    17291881      <td>Library A.00h</td>
    … …  
    17331885    </tr>
    17341886    <tr class="shaded">
    1735       <td>Assembly A.24h</td>
     1887      <td>Arrangement A.24h</td>
    17361888      <td>Sequenced A</td>
    17371889      <td>Library A.24h</td>
    … …  
    17401892      <td>-</td>
    17411893    </tr>
    1742     <tr class="shaded">
    1743       <td>Assembly A.ref</td>
    1744       <td>Sequenced A</td>
    1745       <td>Library A.ref</td>
    1746       <td>SW: TopHat</td>
    1747       <td>TopHat Settings A</td>
    1748       <td>-</td>
    1749     </tr>
    1750     </table>
    1751     <p>
    1752   </li>
    1753  
    1754   <li>
    1755     Add data files (TODO - we don't have any yet):
    1756     <table class="listing" cellspacing="0" cellpadding="2" border="0">
    1757     <tr>
    1758       <th>Scan</th>
    1759       <th>Data files</th>
    1760     </tr>
    1761     <tr>
    1762       <td>Scan A.00h</td>
    1763       <td>-</td>
    1764     </tr>
    1765     <tr>
    1766       <td>Scan A.24h</td>
    1767       <td>-</td>
    1768     </tr>
    1769     <tr class="shaded">
    1770       <td>Scan A.00h (dye-swap)</td>
    1771       <td>-</td>
    1772     </tr>
    1773     <tr class="shaded">
    1774       <td>Scan A.24h (dye-swap)</td>
    1775       <td>-</td>
    1776     </tr>
    1777     </table>
    1778     <p>
    1779   </li>
    1780 
     1894    </table>
     1895    <p>
     1896  </li>
     1897 
    17811898  <li>
    17821899    Create raw bioassays:
    … …  
    17961913      <td>Generic/GenePix</td>
    17971914      <td>Scan A.00h</td>
    1798       <td>Labeled extract A.00h</td>
     1915      <td>-</td>
    17991916      <td>Array design A</td>
    18001917      <td>Feature extraction A</td>
    18011918      <td>Software A</td>
    1802       <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td>
     1919      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.gpr</code></td>
    18031920    </tr>
    18041921    <tr>
    … …  
    18061923      <td>Generic/GenePix</td>
    18071924      <td>Scan A.24h</td>
    1808       <td>Labeled extract A.24h</td>
     1925      <td>-</td>
    18091926      <td>Array design A</td>
    18101927      <td>Feature extraction A</td>
    18111928      <td>Software A</td>
    1812       <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td>
     1929      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.gpr</code></td>
    18131930    </tr>   
    18141931    <tr class="shaded">
    … …  
    18161933      <td>Generic/GenePix</td>
    18171934      <td>Scan A.00h (dye-swap)</td>
    1818       <td>Labeled extract A.00h (dye-swap)</td>
     1935      <td>-</td>
    18191936      <td>Array design A</td>
    18201937      <td>Feature extraction A</td>
    18211938      <td>Software A</td>
    1822       <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
     1939      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td>
    18231940    </tr>
    18241941    <tr class="shaded">
    … …  
    18261943      <td>Generic/GenePix</td>
    18271944      <td>Scan A.24h (dye-swap)</td>
    1828       <td>Labeled extract A.24h (dye-swap)</td>
     1945      <td>-</td>
    18291946      <td>Array design A</td>
    18301947      <td>Feature extraction A</td>
    18311948      <td>Software A</td>
    1832       <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
     1949      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.dyeswap.gpr</code></td>
    18331950    </tr>
    18341951    <tr>
    … …  
    18361953      <td>Affymetrix</td>
    18371954      <td>Affymetrix scan A.1</td>
    1838       <td>Labeled extract A.00h</td>
     1955      <td>-</td>
    18391956      <td>Affymetrix A</td>
    18401957      <td>Feature extraction A</td>
    18411958      <td>Software A</td>
    1842       <td><i>CEL file</i>: jos1761.cel.bz2</td>
     1959      <td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1761.cel</code></td>
    18431960    </tr>   
    18441961    <tr>
    … …  
    18461963      <td>Affymetrix</td>
    18471964      <td>Affymetrix scan A.2</td>
    1848       <td>Labeled extract A.24h</td>
     1965      <td>-</td>
    18491966      <td>Affymetrix A</td>
    18501967      <td>Feature extraction A</td>
    18511968      <td>Software A</td>
    1852       <td><i>CEL file</i>: jos1762.cel.bz2</td>
     1969      <td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1762.cel</code></td>
    18531970    </tr>   
    18541971    <tr>
    … …  
    18561973      <td>Affymetrix</td>
    18571974      <td>Affymetrix scan A.3</td>
    1858       <td>Labeled extract A.ref</td>
     1975      <td>-</td>
    18591976      <td>Affymetrix A</td>
    18601977      <td>Feature extraction A</td>
    18611978      <td>Software A</td>
    1862       <td><i>CEL file</i>: jos1763.cel.bz2</td>
     1979      <td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1763.cel</code></td>
    18631980    </tr>   
    18641981    <tr class="shaded">
    18651982      <td>SeqRaw A.00h</td>
    1866       <td>Generic/GenePix</td>
    1867       <td>Assembly A.00h</td>
     1983      <td>Sequencing/Expression-like/Cufflinks</td>
     1984      <td>Arrangement A.00h</td>
    18681985      <td>Library A.00h</td>
    1869       <td>Array design A</td>
     1986      <td>RefSeqDesign A</td>
    18701987      <td>Cufflinks Settings A</td>
    18711988      <td>Cufflinks</td>
    1872       <td></td>
     1989      <td><i>FPKM tracking file</i>: <code>sequencing/dataset1_norm1/isoforms.fpkm_tracking</code></td>
    18731990    </tr>
    18741991    <tr class="shaded">
    18751992      <td>SeqRaw A.24h</td>
    1876       <td>Generic/GenePix</td>
    1877       <td>Assembly A.24h</td>
     1993      <td>Sequencing/Expression-like/Cufflinks</td>
     1994      <td>Arrangement A.24h</td>
    18781995      <td>Library A.24h</td>
    1879       <td>Array design A</td>
     1996      <td>RefSeqDesign A</td>
    18801997      <td>Cufflinks Settings A</td>
    18811998      <td>Cufflinks</td>
    1882       <td></td>
    1883     </tr>
    1884     <tr class="shaded">
    1885       <td>SeqRaw A.ref</td>
    1886       <td>Generic/GenePix</td>
    1887       <td>Assembly A.ref</td>
    1888       <td>Library A.ref</td>
    1889       <td>Array design A</td>
    1890       <td>Cufflinks Settings A</td>
    1891       <td>Cufflinks</td>
    1892       <td></td>
    1893     </tr>
    1894     </table>
    1895     TODO - create other raw data type for sequence raw bioassays
     1999      <td><i>FPKM tracking file</i>: <code>sequencing/dataset2_norm1/isoforms.fpkm_tracking</code></td>
     2000    </tr>
     2001    </table>
    18962002    <p>
    18972003  </li>
    … …  
    19252031    <tr>
    19262032      <td>Sequence A</td>
    1927       <td>GenePix</td>
    1928       <td>SeqRaw A.00h,<br>SeqRaw A.24h,<br>SeqRaw A.ref</td>
     2033      <td>Cufflinks</td>
     2034      <td>SeqRaw A.00h,<br>SeqRaw A.24h</td>
    19292035      <td>Drug resistance, Time</td>
    19302036    </tr>
    … …  
    19462052 
    19472053  <li>
    1948     Import GenePix raw data. There are two possible ways to do this:
     2054    Import raw data to the Genepix and Cufflinks raw bioassays.
     2055    There are two possible ways to do this:
    19492056    <ol>
    19502057    <li>Manually import to each raw bioassay.
    … …  
    19602067    <b>Batch import:</b> The batch import is started from the
    19612068    properties tab of the <i>experiment</i>. Click on "Import" and
    1962     use the auto-detect feature with one of the used files. Use the default
     2069    use the auto-detect feature with one of the files from the raw bioassays.
     2070    Use the default
    19632071    configuration values except for those listed in the table below.
    19642072    The batch import should import two raw data sets in one go (since it can
    … …  
    20272135      <td><i>Dye swap</i>: true</td>
    20282136    </tr>
    2029     </table>
    2030     <p>
    2031    
    2032   </li>
    2033  
    2034   <li>
    2035     Check the experiment overview page. It should display one warnings for the
    2036     Genepix experiment. The warning is related to a missing biosurce
     2137    <tr>
     2138      <td>SeqRaw A.00h</td>
     2139      <td>dataset1_norm1/isoforms.fpkm_tracking</td>
     2140      <td>38,293/0/0</td>
     2141      <td>-</td>
     2142    </tr>
     2143    <tr>
     2144      <td>SeqRaw A.24h</td>
     2145      <td>dataset2_norm1/isoforms.fpkm_tracking</td>
     2146      <td>38,293/0/0</td>
     2147      <td>-</td>
     2148    </tr>   
     2149    </table>
     2150    <p>
     2151   
     2152  </li>
     2153 
     2154  <li>
     2155    Check the experiment overview page and use the <b>Validate</b> function
     2156    for each of the three experiments.
     2157    <p>
     2158   
     2159    It should display one warning for the Genepix experiment. The warning is
     2160    related to a missing biosurce
    20372161    on the reference sample.
    20382162    <p>
    … …  
    20452169    <p>
    20462170   
     2171    The sequencing experiment .... TODO
     2172   
     2173    <p>
    20472174    Change validation options to reduce the number of warnings:
    20482175    <table class="listing" cellspacing="0" cellpadding="2" border="0">

  • trunk/src/core/net/sf/basedb/core/Install.java

    r5773 r5788  
    893893      progressStep++;
    894894      if (progress != null) progress.display((int)(progressStep*progress_factor), "--Creating platforms...");
    895       createPlatform(Platform.GENERIC, "Generic microarray",
     895      createPlatform(Platform.GENERIC, "Generic",
    896896        "Generic platform which expects data to be imported into the database",
    897897        false, null, 0,

  • trunk/src/test/net/sf/basedb/test/roles/AdminTest.java

    r5778 r5788  
    4848import net.sf.basedb.plugins.batchimport.ArrayDesignImporter;
    4949import net.sf.basedb.plugins.batchimport.ArraySlideImporter;
     50import net.sf.basedb.plugins.gtf.GtfReporterMapImporter;
    5051import net.sf.basedb.test.AffymetrixData;
    5152import net.sf.basedb.test.FileUtil;
    … …  
    100101      plugins.add(PluginDefinition.getByClassName(dc, ReporterMapFlatFileImporter.class.getName()));
    101102      plugins.add(PluginDefinition.getByClassName(dc, PrintMapFlatFileImporter.class.getName()));
     103      plugins.add(PluginDefinition.getByClassName(dc, GtfReporterMapImporter.class.getName()));
    102104     
    103105      plugins.add(PluginDefinition.getByClassName(dc, ArrayDesignImporter.class.getName()));

  • trunk/src/test/net/sf/basedb/test/roles/UserTest.java

    r5778 r5788  
    274274        Software cufflinks = Util.findSoftware(dc, "Cufflinks");
    275275       
    276         rba1 = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.00h", sc1, le1, featureExtraction, softwareA, genericDesign);
    277         rba2 = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.24h", sc2, le2, featureExtraction, softwareA, genericDesign);
    278         rba1DyeSwap = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.00h (dye-swap)", sc1DyeSwap, le1DyeSwap, featureExtraction, softwareA, genericDesign);
    279         rba2DyeSwap = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.24h (dye-swap)", sc2DyeSwap, le2DyeSwap, featureExtraction, softwareA, genericDesign);
     276        rba1 = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.00h", sc1, null, featureExtraction, softwareA, genericDesign);
     277        rba2 = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.24h", sc2, null, featureExtraction, softwareA, genericDesign);
     278        rba1DyeSwap = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.00h (dye-swap)", sc1DyeSwap, null, featureExtraction, softwareA, genericDesign);
     279        rba2DyeSwap = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.24h (dye-swap)", sc2DyeSwap, null, featureExtraction, softwareA, genericDesign);
    280280       
    281281        // Affymetrix raw bioassays
    282         affyRaw1 = createRawBioAssay(dc, affymetrixPlatform, null, "Affymetrix raw A.1", affyScan1, le1, featureExtraction, softwareA, affymetrixDesign);
    283         affyRaw2 = createRawBioAssay(dc, affymetrixPlatform, null, "Affymetrix raw A.2", affyScan2, le2, featureExtraction, softwareA, affymetrixDesign);
    284         affyRaw3 = createRawBioAssay(dc, affymetrixPlatform, null, "Affymetrix raw A.3", affyScan3, leRef, featureExtraction, softwareA, affymetrixDesign);
     282        affyRaw1 = createRawBioAssay(dc, affymetrixPlatform, null, "Affymetrix raw A.1", affyScan1, null, featureExtraction, softwareA, affymetrixDesign);
     283        affyRaw2 = createRawBioAssay(dc, affymetrixPlatform, null, "Affymetrix raw A.2", affyScan2, null, featureExtraction, softwareA, affymetrixDesign);
     284        affyRaw3 = createRawBioAssay(dc, affymetrixPlatform, null, "Affymetrix raw A.3", affyScan3, null, featureExtraction, softwareA, affymetrixDesign);
    285285
    286286        // Assign Affymetrix CEL files
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