source: plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageExporter/README.txt @ 1188

Last change on this file since 1188 was 1188, checked in by Jari Häkkinen, 12 years ago

Committing patch provided by Gildas Le Corguillé

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 6.5 KB
Line 
1$Id: README.txt 1188 2010-02-11 13:58:17Z jari $
2
3Release Note: Tab2Mage Export Current Implementation
4==============================================
5Installation
6-----------------
7
8  - Place Tab2MageExporter.jar and ebi-plugins-utils.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server.
9  - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageExporter contained in $BASE_HOME/www/plugins/Tab2MageExporter.jar.
10 
11  Note: If you get a class Loader error while installing the exporter, you have two options:
12 
13  i) Upgrade to BASE 2.14.1  or
14  ii)  Place the two jar files: Tab2MageExporter.jar and ebi-plugins-utils.jar in your base installation classpath - i.e. : $BASE2_HOME/web-inf/lib, restart the tomcat server and proceed to install the plugin. In step (3) below, do not specify the plugin's path. Note that BASE do not recommend this approach but it's just a work around for a bug in base versions earlier than 2.4.6.
15 
16  1. In the BASE web client, go to Administrate -> Plugins -> Definitions.
17  2. Click New.
18  3. In the dialog that opens,
19    for class enter " uk.ac.ebi.nugo.plugins.Tab2MageExporter".
20     for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageExporter.jar
21  4. Click Save.
22  The new plugins appears under the name "Tab2Mage Exporter"  in the plugins list and is now ready for use.
23 
24   For other users to use the plugin as detailed in the next section, please share it to the appropriate users by manually setting the permissions on the plugin (sharing it to group 'Everyone' should be sufficient in most cases).
25 
26  General Installation instruction is available at: http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
27==========================================================================================
28Use
29-------
30Important Notice/ Warning:
31-----------------------------------
32  To use the tab2mage export plugin, you do not need to configure the plugin as it requires no configuration.
33
34  The exported tab2mage file would be located on the base2 file system (in the location you have specified). This file can thereafter be downloaded to your desktop   environment.  After the download, please create an archive including the tab2mage export file and the associated raw data files, for onward submission to a the Array Express repository.
35
36  It is advisable to verify that your experiment has all the required annotations and that it is Miame Complaint before running the   exporter.  To do this go to the Experiment  detail view page and click on the overview tab.
37
38  The Tab2Mage export fails with a message, if:
39    - No bioassay is assigned to an experiment
40    - If the logged in user do not own the experiment or has no read permission on the experiment.
41    - If experimental factors have not been specified for an experiment.
42    - Also, note that if experimental factors (annotation type) for an experiment have been specified, and the annotation types are shared to Project. Do set the     Project active before exporting in Tab2mage otherwise export fails.
43    - Finally, if an array slide or array design has not been provided for Hybridization.
44
45  Besides, using the experiment overview functionality would help to prevent most of these failure points.
46
471. In the BASE web client, go to View -> Experiment
482. Go to the experiment detail view page.
493. Verify your experiment with the BASE experiment overview functionality as mentioned above
504. Click on the export tab and on the export GUI thats appears, the experiment has been configured as indicated by the black x.
515. The overwrite field has also been configured and set to false by default. Do change this to true if you want to overwrite an exisiting file.
526. Set the file path where the export file and it's name: (e.g. tab2mage.txt) should be saved on the base2 file system using the browse button for the Save As field. This is a mandatory field.
537.  Specify the date you would like the experiment to be made public or released by a public respository e.g. Array Express. and click Next
548. On the next screen click Finish and wait for the job to complete. You will be shown the progress of the Tab2mage export in the dialog, with the page refreshing itself regularly.
55
56==================================================================================
57 
58What is not supported
59----------------------------------
60- Inherited annotations are not exported or supported for Protocol parameters in this current version.
61
62- Material Characteristics - not available in the current base2 release and therefore cannot be exported. This requires MGED entries. Ontologies and control vocabularies would be distributed with base2 in the nearest future and can then be supported.
63 
64- Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section
65
66- Experiment publication’s pages, issues and volume are not supported.
67
68
69====================================================================================================
70Tab2Mage Sections
71----------------------------
72Experiment Section
73-----------------------------
74- Provides information about an experiment.
75- The user must specify the release date for the experiment when initiating the tab2mage export.
76
77Protocol Section
78------------------------
79- This section displays all the protocols used within an experiment. The associated parameters are also displayed if any
80- Protocol parameters are delimited with a semi colon.
81
82Hybridization Section
83-------------------------------
84Hybridization - Protocol Section
85---------------------------------------------
86- If  protocol has not been utilized in the experiment then
87- no protocol id is displayed in the hybridization section.
88
89Hybridization - BiomaterialXteristics
90-------------------------------------------------
91- These are all the xteristics and annotations of a biosource, excluding annotations of deleted annotation types or characteristics.
92- if a biosource exist i.e. has been used in an experiment , there might be biomaterial xteristics.
93- if no biosource is used, then there would be no biomaterial xteristics in the export.
94
95Hybridization - Experimental Factors
96--------------------------------------------------
97- if experimental factors  have been declared for an experiment but has a null value (i.e. it’s value has not been specified).
98-  the default value for the experimental factor would be displayed, if it has been specified during the creation of  the linked annotation type.
99
100
101
102/**
103*This is a release note created for the tab2mage export developed at the EBI for Base2 and NutriBase.
104/*
Note: See TracBrowser for help on using the repository browser.