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Timestamp:
Aug 15, 2007, 3:45:31 PM (16 years ago)
Author:
dominic
Message:

tab2mage exporter readme annd release note for the wiki page

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  • trunk/uk/ac/ebi/Tab2MageExporter/README.txt

    r366 r399  
    11Release Note: Tab2Mage Export Current Implementation
     2==============================================
     3General Information
    24----------------------------------------------------------------------------------------
    3 ----------------------------------------------------------------------------------------
    4 How do I define and configure the plugin
    5 -------------------------------------------------------
    6 Please note, to test the tab2mage plugin, you do not need to define and configure the plugin. It is automatically done for you. Once you have updated or installed Nutribase successfully proceed to the experiment page, select and click on an experiment and on the edit page, click on the export tab and follow subsequent instructions.
     5The Tab2Mage export  plugin exports an experiment meta - data and annotations in tab2mage specification from BASE. The tab2mage specification is provided by the microarray  informatics team at the EBI, Cambridge. The exported experiments along with the raw data and image files can later be exported by the corresponding tab2mage import plugin. (link).
    76
    8 On the export GUI, you can save the file to be exported on the base2 file system using the browse button for the Save As field. This is a mandatory field.
     7The entry point for this plugin in base is the detail view page of an experiment. Hence, the user needs to create an experiment and all the annotations and parameters first. select and click on an experiment and on the edit page, click on the export tab and follow subsequent instructions.
    98
    10 Important Notice:
    11 ----------------------
    12 Exported tab2mage file would be located on the base2 file system (in the location you have specified). This file can be downloaded to your desktop environment.  After download, please create an archive including the tab2mage export file and the associated raw data files, for onward submission to a repository like array express.
    139
    14 Controls:
    15 --------------
    16 Export fails with a message, if:
     10Installation
     11-----------------
    1712
    18 - No bioassay is assigned to an experiment
     13  - Place Tab2MageExporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server.
     14  - Place ebi-plugins-utils.jar in your base installation class path : $BASE2_HOME/web-inf/lib
     15  - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageExporter contained in $BASE_HOME/www/plugins/Tab2MageExporter.jar.
     16 
     17  1. In the BASE web client, go to Administrate -> Plugins -> Definitions.
     18  2. Click New.
     19  3. In the dialog that opens,
     20    for class enter " uk.ac.ebi.nugo.plugins.Tab2MageExporter".
     21     for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageExporter.jar
     22  4. Click Save.
     23  The new plugins appears under the name "Tab2Mage Exporter"  in the plugins list and is now ready for use.
     24 
     25   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 item.
    1926
    20 - If the logged in user do not own the experiment or has no read permission on the experiment.
     27 
     28  General Installation instruction is available at: http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
     29==========================================================================================
     30Use
     31-------
     32Important Notice/ Warning:
     33-----------------------------------
     34  To use the tab2mage export plugin, you do not need to configure the plugin as it requires no configuration.
    2135
    22 - If experimental factors have not been specified for an experiment.
     36  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 repository like     Array Express.
    2337
    24 - Also, 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.
     38  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. <link to documentation>
    2539
    26 -Finally, if an array slide has not been provided for Hybridization
     40  The Tab2Mage export fails with a message, if:
    2741
     42    - No bioassay is assigned to an experiment
     43
     44    - If the logged in user do not own the experiment or has no read permission on the experiment.
     45
     46    - If experimental factors have not been specified for an experiment.
     47
     48    - 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.
     49
     50    -Finally, if an array slide or array design has not been provided for Hybridization.
     51
     52  Besides, using the experiment overview functionality would help to prevent most of these failure points.
     53
     54
     551. In the BASE web client, go to View -> Experiment
     562. Go to the experiment detail view page.
     573. Verify your experiment with the BASE experiment overview functionality as mentioned above
     584. Click on the export tab and on the export GUI thats appears, the experiment has been configured as indicated by the black x.
     595. 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.
     606. 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.
     617.  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
     628. 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.
     63
     64==================================================================================================
     65Dependencies:
     66--------------------
     67
     68ebi-plugin.utils.jar - this should be in the base intstallation class path.
     69
     70
     71====================================================================================================
    2872Tab2Mage Sections
    29 --------
     73----------------------------
    3074Experiment Section
    3175-----------------------------
    32   - Provides information about an experiment.
     76- Provides information about an experiment.
    3377- The user must specify the release date for the experiment when initiating the tab2mage export.
    3478
    … …  
    3680------------------------
    3781- This section displays all the protocols used within an experiment. The associated parameters are also displayed if any
    38   - Protocol parameters are delimited with a semi colon.
     82- Protocol parameters are delimited with a semi colon.
    3983
    4084Hybridization Section
    … …  
    4286Hybridization - Protocol Section
    4387---------------------------------------------
    44   - If  protocol has not been utilized in the experiment then
    45     - no protocol id is displayed in the hybridization section.
     88- If  protocol has not been utilized in the experiment then
     89- no protocol id is displayed in the hybridization section.
    4690
    4791Hybridization - BiomaterialXteristics
    … …  
    5599- if experimental factors  have been declared for an experiment but has a null value (i.e. it’s value has not been specified).
    56100-  the default value for the experimental factor would be displayed, if it has been specified during the creation of  the linked annotation type.
    57    
     101==================================================================================
     102 
    58103What is not supported
    59104----------------------------------
    60105- Inherited annotations are not exported or supported for Protocol parameters in this current version.
    61106
    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 this would then be supported.
     107- 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.
    63108 
    64 - Pooling of biomaterials - Pooled sample, extract, and labeled extract are not exported with the current Tab2mage release, and this would be supported in another release.
     109- Pooling of biomaterials - Pooled sample, extract, and labeled extract are not exported with the current Tab2mage release, and would be supported in another release.
    65110
    66111- Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section
    … …  
    71116
    72117/**
    73 *This is a release note created for the tab2mage export *developed at the EBI for *Base2 and NutriBase.
     118*This is a release note created for the tab2mage export developed at the EBI for Base2 and NutriBase.
    74119/*
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