Changeset 447


Ignore:
Timestamp:
Oct 30, 2007, 3:50:08 PM (14 years ago)
Author:
dominic
Message:

added tab2mage export version 2

Location:
trunk/uk/ac/ebi/Tab2MageExporter
Files:
4 added
7 edited

Legend:

Unmodified
Added
Removed
  • trunk/uk/ac/ebi/Tab2MageExporter/ChangeLog.txt

    r365 r447  
    1 ,____First release
     1,____This file will contain information about changes in subsequent releases.
    22
    3 This file will contain information about changes iin subsequent releases.
     3Latest version 2.0
     4- Pooling of biomaterials - Pooled sample, extract, and labeled extract are now supported in this release.
     5- Redesigned code to improve reusability.
  • trunk/uk/ac/ebi/Tab2MageExporter/README.txt

    r410 r447  
    77The 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.
    88
    9 
    109Installation
    1110-----------------
     
    1514  - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageExporter contained in $BASE_HOME/www/plugins/Tab2MageExporter.jar.
    1615 
    17   Note: If you get a class Loader error while installing the exporter, do place the two jar files: Tab2MageExporter.jar and ebi-plugins-utils.jar in your base installation classpath - : $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.
     16  Note: If you get a class Loader error while installing the exporter, do place the two jar files: Tab2MageExporter.jar and ebi-plugins-utils.jar in your base installation classpath - : $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.
    1817
    1918  1. In the BASE web client, go to Administrate -> Plugins -> Definitions.
     
    3534  To use the tab2mage export plugin, you do not need to configure the plugin as it requires no configuration.
    3635
    37   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.
     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 the Array Express repository.
    3837
    39   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.
     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.
    4039
    4140  The Tab2Mage export fails with a message, if:
     
    4342    - If the logged in user do not own the experiment or has no read permission on the experiment.
    4443    - If experimental factors have not been specified for an experiment.
    45     - 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.
     44    - 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.
    4645    -Finally, if an array slide or array design has not been provided for Hybridization.
    4746
    4847  Besides, using the experiment overview functionality would help to prevent most of these failure points.
    49 
    5048
    51491. In the BASE web client, go to View -> Experiment
     
    6260--------------------
    6361
    64 ebi-plugin.utils.jar - this should be in the base intstallation class path.
     62ebi-plugin.utils.jar - this should be in the base installation class path.
     63
     64==================================================================================
     65 
     66What is not supported
     67----------------------------------
     68- Inherited annotations are not exported or supported for Protocol parameters in this current version.
     69
     70- 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.
     71 
     72- Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section
     73
     74- Experiment publication’s pages, issues and volume are not supported.
    6575
    6676
     
    96106-  the default value for the experimental factor would be displayed, if it has been specified during the creation of  the linked annotation type.
    97107
    98 ==================================================================================
    99  
    100 What is not supported
    101 ----------------------------------
    102 - Inherited annotations are not exported or supported for Protocol parameters in this current version.
    103 
    104 - 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.
    105  
    106 - Pooling of biomaterials - Pooled sample, extract, and labeled extract are not exported with the current Tab2mage release, and would be supported in another release.
    107 
    108 - Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section
    109 
    110 - Experiment publication’s pages, issues and volume are not supported.
    111 
    112108
    113109
  • trunk/uk/ac/ebi/Tab2MageExporter/ReleaseNote.txt

    r360 r447  
    4444- 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.
    4545 
    46 - 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.
    47 
    4846- Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section
    4947
  • trunk/uk/ac/ebi/Tab2MageExporter/build.xml

    r396 r447  
    3131      description="compile the common ebi -plugin util classes"
    3232      >
     33      <mkdir dir="${bin.plugins}"/>
    3334      <javac
    3435        encoding="ISO-8859-1"
  • trunk/uk/ac/ebi/Tab2MageExporter/credit.txt

    r399 r447  
    1 At this release, Nutribase developement team is :
     1At this release, Nutribase developement team are :
    22
    33 - Dominic Oyeniran (oyeniran@ebi.ac.uk)
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