Changeset 407

Timestamp:

Aug 23, 2007, 2:56:34 PM (16 years ago)

Author:

dominic

Message:

added importer faq

Location:

trunk/uk/ac/ebi/Tab2MageImporter

Files:

• Importer FAQ.txt (modified) (1 diff)
• README.txt (modified) (5 diffs)

trunk/uk/ac/ebi/Tab2MageImporter/Importer FAQ.txt

@@ -1 @@
-
-Q1:  Why do I get net.sf.basedb.core.BaseException: IMPORT FAILS: Invalid File format:
+FAQ:
+======
+Q:  Why do I get net.sf.basedb.core.BaseException: IMPORT FAILS: Invalid File format:
 files supplied not appropriate for the experiment platform: [ raw data type/plaffrom] when I reun the plugin 
 
-A1:  If you have tried to unzip a zip file,  an unzipped file directory may have been created fornthe zip file. Whilst you run the plugin again, an existing directory cannot be re-created.  
+A:  If you have tried to unzip a zip file,  an unzipped file directory may have been created fornthe zip file. Whilst you run the plugin again, an existing directory cannot be re-created.  
 
-To solve this, do delete the previous unzipped directory from the file menu and the trash can. Then try to run the import again, using the same zipfile.  
+To solve this, delete the previously unzipped directory from the Base2 Views -> File menu and from the trash can (Views ->TrashCan). Then try to run the import again, using the same zipfile.  
+
+=========================
+
+Q: When importing GenePix files, I have an uneven number of imported rows. why is that so ?
+A.This is a known issue that will be fixed when we have upgraded our plugin to the latest BASE2.4.0 plugin API. The new API allows to account for invalid numeric value by dropping only that value instead of the entire record, as is the case now. This is why depending on the number of error met in the raw data file during import, the number of line/records created may vary. This is suboptimal but will be addressed shortly.
+
+=========================
+
+Q. I am doing some testing and have loading several times the same experiment. The plugin reports success during loading but the Message board report that files could not be loaded because they were already attached to a RawBioAssay, what does it means? Is it a  loading success or a failure ?
+A. Again, this is a known issue. Simply disregard these errors messages. The rawdatafiles have been parsed and data imported and attached to a raw bioassay created during the Import process.
+These errors messages will disappear with the plugin upgrade.
+
+=========================
+
+Q. I am trying to upload an Agilent Experiment but it fails saying. Are you supporting Agilent yes or no ?
+A. Please see readme.txt section on 'Limitations and Known Issues'.
+
+=========================

trunk/uk/ac/ebi/Tab2MageImporter/README.txt

@@ -33 +33 @@
    
 ===========================================================
+
  Use
 --------
@@ -38 +39 @@
   -- It is advisable not to execute the plugin as root but as a user with a specified quota.  The quota must be enough to store files and create base items.
   --  re- running the import plugin without having deleted the previously created directory from the zip file will make the   Importer fail.
-  --  Note that in its current implementation, only one RawDataImporter plugin configuration can be used during the import process. This means that raw data files must be consistent throughout. (this might be an issue when using different scanner versions).
-
+  --  Note that in its current implementation, only one RawDataImporter plugin configuration can be used during the import process. This means that raw data files must be  consistent throughout. (this might be an issue when using different scanner versions).
+  -- - Make sure that the user running Tab2Mage Importer plugin has enough permissions to do so. With the default Roles settings in BASE, User and PowerUser have not   enough permissions to run the plugin successfully.
   
-  1. Platform supported  are: Affymetrix, Agilent, Genepix etc.
+  1. Platform supported  are: Affymetrix, Agilent, Genepix 
   2. Create all the array design used in the experiment as the BASE administrator. Array Design must then be shared to everyone or a suitable group that all the target users belong.
   3. Create tab2mage spreadsheet and zip it together with the raw data files  that make up the experiment. Note: no cdf file. Upload this file to your account on BASE (go to View -> Files -> Upload File). Image files may be supplied by the user and contained in the zip file.
@@ -56 +57 @@
 
  ===========================================================
+
 Dependencies:
 --------------------
-  --Base 2.2.1 and above
-  --AnnotationTypeCvImporter Plugin – For loading annotation types. This must have a configuration that could import an annotation types (.txt) file.
-  --Reporter Importer - for loading reporter corresponding to the raw data file
-  --Reporter map importer – for adding features to array design
-  --Raw Data Importer Plugin – loads raw data. This must have a configuration that could import the raw data files.  Required for multi-channel experiments. The definition for the plug-in is available by default. The configuration should be done by administrator and shared to everyone or a suitable group that all the target users belong.
-  -- if  you want to use messaging, mail.jar and activation. jar for messaging is required- these jar files should be downloaded and copied to your base iinstallatiion claass path  /web-inf/lib folder.
+  
+  - Base 2.2 and above
 
-  Please ensure that you have used all the plugins above appropriately before running Tab2Mage importer. Further information on AnnotationTypeCvImporter is available  on Base2plugin website and for others, please read base2 documentation.
+  -Reporter Importer Plugin - Required for loading Reporters
+
+  Reporter Map Importer Plugin – Required for mapping features to Reporters when defining an Array Design
+  
+  Raw Data Importer Plugin – Required for loading raw data and import values associated to BASE rawBioassays. This is a critical requirement, for multi-channel experiments, before running the Tab2MageImporter. Users must ensure that raw data import plugin has   been properly configured and is able to import a raw datafile of the type of the submission.
+
+  The definition for the above plug-ins is available by default in Base 2. The plugins should be configured by a Base 2 administrator and shared to everyone or a suitable group of target users.
+
+  AnnotationTypeCvImporter Plugin – Required for loading annotation types. The plugin must have a proper configuration defined to import an annotation type file created by the Tab2MageImporter plugin when parsing the tab2mage file.
+
+  Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Click AnnotationTypeCvImporter for further information on Annotation Type and Cv Importer plugin and for other plugins, please read base2 documentation.
+
+  Also, do make sure that Array Design(s) corresponding to the one(s) referenced in the Array[accession] field of the tab2mage file have been properly created in BASE2. If not, the plugin will fail. For all non-Affymetrix Array Designs,this means that Reporters have been loaded and Feature to Reporter Map have been attached to Array Designs. Those tasks can be only be achieved if the above plugins have been properly set up and configured. 
 
 optional
 -------
-  -- AffyArrayDesignImproter Plugin – for batch uploading affymetrix array designs.  Useful to upload all array design in one go.
+  - AffyArrayDesignBatchImporter Plugin . – for batch uploading affymetrix array designs. Useful to upload all array designs used in an experiment in one go before running the Tab2Mage Importer.
+
+  If you want to use messaging, mail.jar and activation. jar is required- these jar files should be downloaded and copied to your base installation class path /web-inf/lib folder. 
 
 ================================================================
+
 AnnotationTypes and Cv Importer
 ----------------------------------------------
@@ -78 +91 @@
 
 ===============================================================
+
+Limitations and Known Issues
+----------------------------------
+i. Currently, Pooling event represented in tab2mage format are not supported. It would be supported from next plugin release .
+
+ii. Only one raw data importer plugin configuration can be used at any one time during an experiment import.
+This means that all raw  data files in a tab2mage.zip archive should have the same data header. For Raw datafile from Genepix (or .gpr files) and Agilent, there is a certain level of polymorphism that may occur should scanner models used in a experiment run different versions of the software. Users will have to harmonize the files to one layout in order to upload the Experiment in BASE2 using the current plugin.
+
+iii. Agilent support:
+
+Some Agilent Feature Extraction raw data files can be loaded but not all. BASE2.4.0 plugin API differs from BASE2.3.0 plugin API and even if users can successfully import Agilent Raw data files in BASE2.4, the tab2mage import plugin has yet to be updated to reflect the changes in the BASE plugin API. All the infrastructure is being modified to take advantage of the API modification and Agilent support will be available shortly. We will post an updated version of the plugin when ready and make an announcement through the base mailing lists 
+
+===============================================================
+
 Email alert:
 ---------------
@@ -85 +112 @@
 ---------------------
   Your antivirus server and anti spam software may prevent you from sending email messages. This is because they must have been configured to block all application requiring connection to your email sever on port 25 (smtp).
-  If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 20.
+  If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 25.
 
   The email alert should work on a linux / unix and may be mac machines.
-===============================================================
-What is not supported
-----------------------------------
-Pooled experiments are not supported in this release. It would be supported in future releases.