source: trunk/doc/src/docbook/userdoc/file_system.xml @ 3487

Last change on this file since 3487 was 3487, checked in by Peter Johansson, 15 years ago

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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: file_system.xml 3487 2007-06-13 17:56:05Z peter $
7 
8  Copyright (C) Authors contributing to this file.
9 
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12 
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 2
16  of the License, or (at your option) any later version.
17 
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22 
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28
29<chapter id="file_system">
30  <?dbhtml dir="filesystem"?>
31  <title>File management</title>
32  <sect1 id="file_system.system">
33    <title>File system</title>
34    <para>
35      Files in BASE 2 are managed from the page at
36      <menuchoice>
37        <guimenu>View</guimenu>
38        <guimenuitem>Files</guimenuitem>
39      </menuchoice>. The basic layout on the page is the same as for all the other list pages
40      in BASE 2 but
41      there are some differences e.g. there is a navigation tree to the left, used to browse
42      the directory structure, and there are some buttons in the toolbar, that are special for
43      files and directories. The figure below is a representation of the files and
44      directories-page and is followed with a short description to some of the special
45      functions.
46    </para>
47    <figure id="file.system.figures.filepage">
48      <title>The file page</title>
49      <screenshot>
50        <mediaobject>
51          <imageobject>
52            <imagedata fileref="figures/filepage.png" format="PNG" 
53            scalefit="1" width="100%" />
54          </imageobject>
55        </mediaobject>
56      </screenshot>
57    </figure>
58    <variablelist>
59      <varlistentry>
60        <term>
61          <interface>1. Home directory for current user</interface>
62        </term>
63        <listitem>
64          <para>
65            This is the logged in user's home directory with sub directories. It is
66            visible if the current user has a home directory and is then always located at
67            the top of the navigation tree. More about this can be read in
68            <xref linkend="file_system.system.browse.tree.home" />.
69            Click on a directory to display it's contents to the right
70            or click on the plus sign to expand the directory and view the
71            sub directories (no plus sign = no sub directories).
72          </para>
73        </listitem>
74      </varlistentry>
75
76      <varlistentry>
77        <term>
78          <interface>2. Other users</interface>
79        </term>
80        <listitem>
81          <para>
82            The other users' home directories that the current user has permission
83            to read are listed here, including his/her own.
84          </para>
85        </listitem>
86      </varlistentry>
87
88      <varlistentry>
89        <term>
90          <interface>3. Refresh button</interface>
91        </term>
92        <listitem>
93          <para>
94            This button, which is located at the bottom of the navigation tree,
95            refreshes/updates the directory tree. It can for example be used to get a
96            recently created directory to appear in the tree.
97          </para>
98        </listitem>
99      </varlistentry>
100
101      <varlistentry>
102        <term>
103          <interface>4. Current directory</interface>
104        </term>
105        <listitem>
106          <para>Shows the full BASE 2 path to current directory.</para>
107        </listitem>
108      </varlistentry>
109
110      <varlistentry>
111        <term>
112          <interface>5. View a file's contents</interface>
113        </term>
114        <listitem>
115          <para>
116            A click on this icon will open the file's contents in a new window. If the
117            browser does not has support to view the file there will be a dialog window
118            to download the file instead.
119          </para>
120        </listitem>
121      </varlistentry>
122
123      <varlistentry>
124        <term>
125          <interface>6. Download file</interface>
126        </term>
127        <listitem>
128          <para>
129            Download the file to a local computer with this icon. The download will
130            start in a new dialog window.
131          </para>
132        </listitem>
133      </varlistentry>
134
135      <varlistentry>
136        <term>
137          <interface>7. Re-upload a file</interface>
138        </term>
139        <listitem>
140          <para>
141            This icon is only visible for those files that have been moved offline and
142            it can be used to re-upload the file to the BASE. Start to
143            upload the file to the same position by clicking on the icon.
144          </para>
145         
146          <note>
147            <title>Replace an existing file</title>
148            <para>
149              It is possible to re-upload file that are online, but this
150              has to be done from the single-item view.
151            </para>
152          </note>
153        </listitem>
154      </varlistentry>
155    </variablelist>
156
157    <sect2 id="file_system.system.browse">
158      <title>Browse the file system</title>
159      <para>
160        Browsing thr BASE 2 file system is done from the navigation bar by clicking on a
161        directory in the tree to view it's contents. Both sub directories and files in the
162        selected directory are showed. A directory with sub directories can be expand with a
163        click on the plus-sign.
164      </para>
165      <note>
166        <title>Browse a directory</title>
167        <para>
168          A directory can only be open from the navigation tree and never from the list. A
169          click on a directory's name in the list will open the directory's edit window.
170        </para>
171      </note>
172      <sect3 id="file_system.system.browse.tree">
173        <title>Navigation tree</title>
174        <para>
175          The navigation tree contains of folders/directories that the logged in user has
176          permission to read. At the top is the current user's home directory and under it
177          is a folder with all accessible home directories.
178        </para>
179        <para>
180          The tree can be updated with the refresh-button at the bottom of the panel (the
181          tree is not self-refreshing).
182        </para>
183        <sect4 id="file_system.system.browse.tree.home">
184          <title>Home directory - 'My home'</title>
185          <para>
186            To make it easier for the logged in user to find his/her directory without
187            having to scroll through the whole list of home directories, his or hers
188            home directory is located at the top of the navigation tree under the
189            <interface>My home</interface>
190            folder.
191          </para>
192          <note>
193            <title>No home directory</title>
194            <para>
195              Not all users have a home directory connected to their accounts. If
196              <interface>My home</interface>
197              is missing, it most certainly depends on that the current user account
198              have not got a home directory. Home directories are managed by the
199              administrator of the BASE server.
200            </para>
201          </note>
202        </sect4>
203      </sect3>
204    </sect2>
205    <sect2 id="file_system.system.quota">
206      <title>Disk space quota</title>
207      <para>
208        Normally, a user is assigned limited disk spacefor files.
209        More information about how much quota the current account has and how much of it
210        that is occupied can be found at the account's home page, described in
211        <xref linkend="webclient.intro.homepage" />.
212      </para>
213     
214      <para>
215        See <xref linkend="user_administration.quota" /> for more information about
216        the quota system.
217      </para>
218    </sect2>
219  </sect1>
220
221  <sect1 id="file_system.handling">
222    <title>Handling files</title>
223   
224    <sect2 id="file_system.handling.upload">
225      <title>Upload a new file</title>
226      <para>
227        Uploading a file is started by clicking on
228        <guibutton>Upload file&hellip;</guibutton>
229        in the toolbar. The uploaded file will be placed in current directory.
230      </para>
231     
232      <figure id="file_system.figures.upload">
233        <title>Upload new file</title>
234        <screenshot>
235          <mediaobject>
236            <imageobject><imagedata 
237              fileref="figures/upload_file.png" format="PNG"
238              /></imageobject>
239          </mediaobject>
240        </screenshot>
241      </figure>
242     
243      <helptext external_id="file.upload" title="Upload a file">
244        <para>
245          <variablelist>
246            <varlistentry>
247              <term>
248                <guilabel>Directory</guilabel>
249              </term>
250              <listitem>
251                <para>
252                  Shows the current directory, where the file will be uploaded.
253                  This property cannot be changed and is only for information.
254                </para>
255              </listitem>
256            </varlistentry>
257            <varlistentry>
258              <term>
259                <guilabel>File</guilabel>
260              </term>
261              <listitem>
262                <para>
263                  This field is required and needs to have a valid file path for
264                  the local computer before the upload is started. Use
265                  <guibutton>Browse&hellip;</guibutton>
266                  to choose which file to upload.
267                </para>
268              </listitem>
269            </varlistentry>
270            <varlistentry>
271              <term>
272                <guilabel>Write protected</guilabel>
273              </term>
274              <listitem>
275                <para>
276                  Mark this checkbox if you want the file to be write
277                  protected. A write protected file cannot be deleted,
278                  moved offline or replaced with another file. It is
279                  still possible to change other metadata, such as
280                  the name, description, file type, MIME type, etc.
281                </para>
282              </listitem>
283            </varlistentry>
284            <varlistentry>
285              <term>
286                <guilabel>Type</guilabel>
287              </term>
288              <listitem>
289                <para>
290                  This is the file-type that the uploaded file should get. The
291                  file-types to choose between from the drop-down list are
292                  described in
293                  <xref linkend="file_system.filetypes" />.
294                  Select
295                  <userinput>- none -</userinput>
296                  if the file should not be associated with any file type.
297                </para>
298              </listitem>
299            </varlistentry>
300            <varlistentry>
301              <term>
302                <guilabel>Description</guilabel>
303              </term>
304              <listitem>
305                <para>
306                  A description about the uploaded file can be put into this text
307                  area. Use the magnifying glass to edit the text in a pop-up
308                  window with a larger text area.
309                </para>
310              </listitem>
311            </varlistentry>
312            <varlistentry>
313              <term>
314                <guilabel>Max transfer rate</guilabel>
315              </term>
316              <listitem>
317                <para>
318                  This shows the maximum transfer rate that the upload will
319                  approximately reach. The transfer rate is set by the
320                  server admin and cannot be changed.
321                </para>
322              </listitem>
323            </varlistentry>
324            <varlistentry>
325              <term>
326                <guilabel>Compressed file</guilabel>
327              </term>
328              <listitem>
329                <para>
330                  These settings are only active if you select
331                  a compressed file format that BASE knows how to
332                  unpack. Currently, BASE ships with support for zip-files,
333                  but this can be extended by the use of plug-ins.
334                  <nohelp>See <xref linkend="plugin_developer.other.unpacker" 
335                    /> for more information.</nohelp>
336                   
337                  <itemizedlist>
338                    <listitem>
339                      <para>
340                        <guilabel>Unpack file</guilabel>:
341                        Mark this checkbox if the compressed file should
342                        be unpacked after it had been uploaded. The
343                        files will be unpacked with the same subdirectory
344                        structure as in the compressed file.
345                      </para>
346                    </listitem>
347                   
348                    <listitem>
349                      <para>
350                        <guilabel>Overwrite existing files</guilabel>:
351                        Mark this checkbox if the unpacking is allowed
352                        to overwrite existing files.
353                      </para>
354                    </listitem>
355                    <listitem>
356                      <para>
357                        <guilabel>Keep the compressed file</guilabel>:
358                        Mark this checkbox if you want to keep the
359                        compressed file after upload. Otherwise, only
360                        the unpacked files are kept.
361                      </para>
362                    </listitem>
363                  </itemizedlist>
364                </para>
365              </listitem>
366            </varlistentry>
367          </variablelist>
368        </para>
369        <para>
370          Finish the configuration by clicking on either
371          <guibutton>Upload</guibutton>, which will start uploading the selected file, or
372          &gbCancel; to abort the upload procedure.
373        </para>
374      </helptext>
375     
376      <sect3 id="file_system.handling.actions.reupload">
377        <title>Replace an existing file</title>
378        <para>
379          It is possible to replace an existing file. This is done by clicking
380          on the <guilabel>replace</guilabel> link on the single-item view
381          for the file you want to replace. If the file has been moved offline,
382          you can also use the icon
383          in the actions-column, see number 7 in
384          <xref linkend="file.system.figures.filepage" />.
385          The procedure to upload the file is the same as when uploading a new file,
386          except that compressed files cannot be unpacked. There is also an
387          extra option, <guilabel>Validate MD5</guilabel>, that tells BASE to
388          check that the file is the same as the one it is replacing. This option
389          is useful when you are re-uploading a file that has been moved offline
390          and want to be certain that it is the same file as the original.
391        </para>
392       
393        <para>
394          You cannot replace a file which has been marked as
395          <emphasis>write protected</emphasis>.
396        </para>
397      </sect3>
398     
399    </sect2>
400    <sect2 id="file_system.handling.edit">
401      <title>Edit a file</title>
402      <para>
403        The edit window to set a file's property in can either be open with
404        &gbEdit;
405        that is located in the toolbar at the file's view page or by holding down
406        <keycap>CTRL</keycap>, <keycap>ALT</keycap>
407        or <keycap>SHIFT</keycap>
408        when clicking on the file's name in the list. It requires that the current user has
409        write permission on the file to be able to edit and set the properties.
410      </para>
411
412      <helptext external_id="file.edit" title="Edit file properties">
413        <variablelist>
414          <varlistentry>
415            <term>
416              <guilabel>Path</guilabel>
417            </term>
418            <listitem>
419              <para>
420                This is the path where the file is located. This can only be changed
421                by moving the file.
422                <nohelp>Read more about how this is done in
423                <xref linkend="file_system.handling.move" /></nohelp>.
424              </para>
425            </listitem>
426          </varlistentry>
427          <varlistentry>
428            <term>
429              <guilabel>Name</guilabel>
430            </term>
431            <listitem>
432              <para>
433                The file's name, which cannot be left empty and must be unique in
434                current directory. The maximum length of the file name is 255
435                characters and it can contain blank spaces but not any of
436                <keycap>~</keycap>,
437                <keycap>\</keycap>,
438                <keycap>/</keycap>,
439                <keycap>:</keycap>,
440                <keycap>;</keycap>,
441                <keycap>*</keycap>,
442                <keycap>&#63;</keycap>,
443                <keycap>&lt;</keycap>,
444                <keycap>&gt;</keycap>
445                or
446                <keycap>|</keycap>.
447              </para>
448            </listitem>
449          </varlistentry>
450          <varlistentry>
451            <term>
452              <guilabel>Write protected</guilabel>
453            </term>
454            <listitem>
455              <para>
456                Mark this checkbox if you want the file to be write
457                protected. A write protected file cannot be deleted,
458                moved offline or replaced with another file. It is
459                still possible to change other metadata, such as
460                the name, description, file type, MIME type, etc.
461              </para>
462            </listitem>
463          </varlistentry>
464          <varlistentry>
465            <term>
466              <guilabel>Type</guilabel>
467            </term>
468            <listitem>
469              <para>
470                Sets which kind of type the file is. Select the file type to use
471                from the drop down list with available types. The option
472                <guilabel>-none-</guilabel>
473                should be used if the file should not be associated with any kind of
474                file type.
475              </para>
476            </listitem>
477          </varlistentry>
478          <varlistentry>
479            <term>
480              <guilabel>MIME type</guilabel>
481            </term>
482            <listitem>
483              <para>
484                The file's content/media type. This is normally set automatically
485                when uploading the file into BASE but it can be changed by an user,
486                that has write permissions, at any time.
487              </para>
488            </listitem>
489          </varlistentry>
490          <varlistentry>
491            <term>
492              <guilabel>Description</guilabel>
493            </term>
494            <listitem>
495              <para>
496                This text area can be used to store relevant information about file
497                and it's contents. Use the magnifying glass, located to the right
498                under the text area, to edit the text in a larger window.
499              </para>
500            </listitem>
501          </varlistentry>
502        </variablelist>
503        <para>
504          Finish the editing process by pressing either
505          &gbSave;
506          to save the properties to the database or
507          &gbCancel;
508          to abort and discard the changes.
509        </para>
510      </helptext>
511
512    </sect2>
513    <sect2 id="file_system.handling.move">
514      <title>Move files</title>
515     
516      <para>
517        These functions are used to manage the location of the files on the
518        server. They are all accessed from the <guibutton>Move</guibutton>
519        button on the list view of from the single-item view. On the list view,
520        you must first select one or more files / directories.
521      </para>
522     
523      <tip>
524        <title>Write protect your files!</title>
525        <para>
526        If you mark a file as <emphasis>write protected</emphasis> it will
527        not be possible to delete, move or replace the file. Use this options
528        for important data files that you do not want to loose by accident.
529        </para>
530      </tip>
531     
532      <sect3 id="file_system.handling.move.directory">
533        <title>To another directory</title>
534        <para>
535          Files and directories can be moved to other directories for re-organization. The
536          user need write permission on the target directory to be able to move the
537          files/directories to it.
538        </para>
539        <para>
540          First, select all files and directories in the current path that should be moved
541          and then click on
542          <menuchoice>
543            <guibutton>Move&hellip;</guibutton>
544            <guisubmenu>To another directory</guisubmenu>
545          </menuchoice>
546          in the toolbar to open a window with the directory tree where the target directory
547          can be picked.
548        </para>
549        <para>
550          Choose a directory which the selected items should be moved to. It
551          is possible to create new subdirectories with the
552          &gbNew; button.
553        </para>
554        <para>
555          Click on
556          &gbOk;
557          to carry out the move or
558          &gbCancel;
559          to abort.
560        </para>
561      </sect3>
562     
563      <sect3 id="file_system.handling.move.offline">
564        <title>Offline</title>
565        <para>
566          Moving a file offline means that the actual file contents is deleted from the
567          server's disk space but information about the file will still exist as an item
568          in the database. This makes it possible to save disk space but still be
569          able to associated the file with other items in BASE.
570        </para>
571        <para>
572          First, select all files in current path that should be moved offline
573          and then click on
574          <menuchoice>
575            <guibutton>Move&hellip;</guibutton>
576            <guisubmenu>Offline</guisubmenu>
577          </menuchoice>
578          in the toolbar.
579        </para> 
580        <warning>
581          <para>
582          Be careful! The selected files will be removed from the server.
583          The only way to recover the contents again is to re-upload the files.
584          </para>
585        </warning>
586      </sect3>
587
588      <sect3 id="file_system.handling.move.secondary">
589        <title>To the secondary storage</title>
590
591        <para>
592          This option is only available if the server administrator
593          has enabled it.
594        </para>
595
596        <para>
597          The secondary storage is a kind of storage were it is appropriate
598          to store files that have been used and no longer requires immediate
599          access. Moving a file to and from the secondary storage is the job
600          of a plug-in, which is usually executed once or twice a day.
601        </para>
602       
603        <para>
604          First, select all files in the current path that should be moved
605          and then click on
606          <menuchoice>
607            <guibutton>Move&hellip;</guibutton>
608            <guisubmenu>To secondary location</guisubmenu>
609          </menuchoice>
610          in the toolbar. The only thing that will happen is that BASE sets a flag
611          on each file. The next time the secondary storage plug-in
612          is executed, the files will be moved to the secondary storage. The
613          actual file contents is deleted from the server's disk.
614        </para>
615       
616        <para>
617          While the file is in the secondary storage BASE behaves in the same way as
618          if the file is offline. Th file cannot be used to import data from, or
619          other things. To use the file again, the file must be moved back to
620          the primary storage.
621        </para>
622       
623        <para>
624          To bring files back from the secondary storage, select the files
625          and then click on
626          <menuchoice>
627            <guibutton>Move&hellip;</guibutton>
628            <guisubmenu>To primary location</guisubmenu>
629          </menuchoice> in the toolbar. The files will be moved back the next
630          time the secondary storage plug-in is executed.
631        </para>
632       
633        <note>
634          <title>Do not forget to set quota for the secondary storage</title>
635          <para>
636            The default installation does not assign quota for the
637            secondary storage. Unless the administrator assigns quota
638            the move will silently fail.
639          </para>
640        </note>
641      </sect3>
642
643    </sect2>
644
645    <sect2 id="file_system.handling.actions">
646      <title>Viewing and downloading files</title>
647      <para>
648        In <guilabel>Actions</guilabel> column in the list view there
649        are icons you can click on to perform different kinds of actions on a
650        file, like downloading the file and viewing the file. The same icons appear
651        on the single-item view and in most other places where files are used.
652        You cannot view or download files that have been moved offline or to the
653        secondary storage.
654      </para>
655      <sect3 id="file_system.handling.actions.download">
656        <title>Download a file</title>
657        <para>
658          This will let the user to download the contents of a file to a path on a local
659          computer. The window that opens contains the selected file's name, size e.t.c.
660          and it will also open a download dialog window where the user can choose what to
661          do with the file locally.
662          <tip>
663            <title>Download does not start</title>
664            <para>
665              Click on the file's path name in the pop-up window if the download
666              dialog window does not appears.
667            </para>
668          </tip>
669        </para>
670        <para>
671          Close the pop-up window and return to file page with
672          &gbClose;.
673        </para>
674      </sect3>
675      <sect3 id="file_system.handling.actions.view">
676        <title>View the contents of file</title>
677        <para>
678          A file's contents can be displayed directly in the web browser if the
679          browser supports displaying that kind of files. Typically all HTML, text
680          files and images are supported. Click on the icon to view the contents
681          in a new window. If the type is not supported by the browser there will be
682          a dialog-window to download the file instead.
683        </para>
684      </sect3>
685    </sect2>
686    <sect2 id="file_system.handling.directories">
687      <title>Directories</title>
688      <para>
689        Directories in BASE are folders where files can be organized into. Click on
690        <guibutton>New directory&hellip;</guibutton>
691        in the toolbar to create a directory in current path and edit the properties as
692        described below.
693      </para>
694      <sect3 id="file_system.handling.directories.edit">
695        <title>Edit a directory</title>
696        <para>
697          The window to edit a directory's properties is opened either by clicking on the
698          directory's name in the list or when creating a new directory.
699        </para>
700        <helptext external_id="directory.edit" title="Edit directory">
701          <para>
702            <variablelist>
703              <title>Properties</title>
704              <varlistentry>
705                <term>
706                  <guilabel>Path</guilabel>
707                </term>
708                <listitem>
709                  <para>
710                    This property is read-only in the edit window but can be
711                    change instead by moving the directory, described in
712                    <xref linkend="file_system.handling.move" />.
713                  </para>
714                </listitem>
715              </varlistentry>
716              <varlistentry>
717                <term>
718                  <guilabel>Name</guilabel>
719                </term>
720                <listitem>
721                  <para>
722                    The directory's name to identify it with in the list. This
723                    field must have a value and it has to be an unique name for
724                    the current directory.
725                  </para>
726                </listitem>
727              </varlistentry>
728              <varlistentry>
729                <term>
730                  <guilabel>Description</guilabel>
731                </term>
732                <listitem>
733                  <para>
734                    Any relevant information about the directory can be written
735                    in this text area. The magnifying glass down to the right
736                    can be used to edit the description text in a larger text
737                    area, just click on the icon to open it in a separate pop-up
738                    window.
739                  </para>
740                </listitem>
741              </varlistentry>
742            </variablelist>
743          </para>
744          <para>
745            The editing process is completed with either
746            &gbSave;, to save the properties into the database, or with
747            &gbCancel;
748            to discard the changes. Both of the buttons will close the edit window and
749            if the directory is updated the list will be reloaded with the directory's
750            new properties.
751          </para>
752         
753          <note>
754            The new directory does not appear in the navigation tree
755            to the left automatically. You must click on the
756            <guibutton>Refresh</guibutton> button.
757          </note>
758         
759        </helptext>
760      </sect3>
761    </sect2>
762
763  </sect1>
764
765  <sect1 id="file_system.filetypes">
766    <title>File types</title>
767    <para>
768      A file can be associated with one of the file types that exists in BASE 2. File types
769      make it possible to filter the files depending of what kind of file it is. Here
770      is a list of file types that are defined in BASE.
771      <menuchoice>
772        <guimenu>Administrate</guimenu>
773        <guisubmenu>Types</guisubmenu>
774        <guimenuitem>File types</guimenuitem>
775      </menuchoice>
776    </para>
777    <variablelist>
778      <title>File types</title>
779      <varlistentry>
780        <term>Image</term>
781        <listitem>
782          <para>Indicates that the file is an image file.</para>
783        </listitem>
784      </varlistentry>
785      <varlistentry>
786        <term>Plate</term>
787        <listitem>
788          <para>The associated file is a file with information about plate/plates.</para>
789        </listitem>
790      </varlistentry>
791      <varlistentry>
792        <term>Plate mapping</term>
793        <listitem>
794          <para>Files with information about plate mapping.</para>
795        </listitem>
796      </varlistentry>
797      <varlistentry>
798        <term>Print map</term>
799        <listitem>
800          <para>Print map files</para>
801        </listitem>
802      </varlistentry>
803      <varlistentry>
804        <term>Protocol</term>
805        <listitem>
806          <para>Files with protocol information</para>
807        </listitem>
808      </varlistentry>
809      <varlistentry>
810        <term>Raw data</term>
811        <listitem>
812          <para>Raw data files</para>
813        </listitem>
814      </varlistentry>
815      <varlistentry>
816        <term>Reporter</term>
817        <listitem>
818          <para>Files with information about reporters</para>
819        </listitem>
820      </varlistentry>
821      <varlistentry>
822        <term>Reporter map</term>
823        <listitem>
824          <para>
825            Files of this type contain information about how the reporters are mapped.
826          </para>
827        </listitem>
828      </varlistentry>
829      <varlistentry>
830        <term>Spot images</term>
831        <listitem>
832          <para>A zip-file containing generated spot images in JPEG format.</para>
833        </listitem>
834      </varlistentry>
835    </variablelist>
836  </sect1>
837</chapter>
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