# HG changeset patch
# User ric
# Date 1474537466 14400
# Node ID 47bf0086e08287dbfd6dfabde6fd38a7df89ec6c
# Parent  32cfb524b957445707720b4d5e7de292372374e7
Deleted selected files

diff -r 32cfb524b957 -r 47bf0086e082 biosample.xml
--- a/biosample.xml	Fri Sep 16 09:16:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,247 +0,0 @@
-<tool id="vl_import_biosample" name="VLI.biosample">
-  <description>import BioSample definitions within omero/vl</description>
-  <command interpreter="python">
-    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
-    #else #unauthorized_access.py
-    #end if
-    #if $advanced_configuration.configuration_level == 'advanced'
-      --host=$advanced_configuration.vl_host
-      --user=$advanced_configuration.vl_user
-      --passwd=$advanced_configuration.vl_passwd
-    #end if
-    --operator=galaxy
-    --ifile=${input}
-    --ofile=${output}
-    --report_file=${report}
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-    #if $blocking_validation
-      --blocking-validator
-    #end if
-    biosample
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if
-    #if str($source_type) != 'use_provided'
-      --source-type ${source_type}
-    #end if
-    #if str($vessel_type_selector.vessel_type) != 'use_provided'
-      --vessel-type ${vessel_type_selector.vessel_type}
-    #end if
-    #if str($vessel_content) != 'use_provided'
-      --vessel-content=${vessel_content}
-    #end if
-    #if str($vessel_status) != 'use_provided'
-      --vessel-status=${vessel_status}
-    #end if
-    #if str($vessel_type_selector) == 'IlluminaBeadChipArray'
-        #if str($vessel_type_selector.assay_type) != 'use_provided'
-            --bead-chip-assay-type=${vessel_type_selector.assay_type}
-        #end if
-    #end if
-  </command>  
-
-  <inputs>
-    <param format="tabular" name="input" type="data"
-	   label="A tabular dataset with the following columns ..."/>
-
-    <param name="study" type="select" label="Context study" 
-	   help="Choose from the already defined studies. See below.">    
-      <options from_parameter="tool.app.known_studies" 
-	       transform_lines="[ &quot;%s%s%s:%s&quot; 
-                                  % ( l[0], self.separator, l[0], l[1][:40] ) 
-                                  for l in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Records provide study labels" 
-                value="use_provided" index="0"/>
-      </options>
-    </param>
-
-    <param name="source_type" type="select"
-	   label="type of the source object"
-	   help="Choose from the legal types. See below.">
-      <option value="use_provided" selected="true">
-      Use what provided by record</option>
-      <option value="Tube">Tube</option>
-      <option value="PlateWell">PlateWell</option>
-      <option value="Individual">Individual</option>
-      <option value="NO_SOURCE">No source provided</option>
-    </param>
-
-    <conditional name="vessel_type_selector">
-        <param name="vessel_type" type="select"
-	      label="type of the vessel object"
-	      help="Choose from the legal types. See below.">
-            <option value="use_provided" selected="true">
-                Use what provided by record
-            </option>
-            <option value="Tube">Tube</option>
-            <option value="PlateWell">PlateWell</option>
-            <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option>
-        </param>
-        <when value="IlluminaBeadChipArray">
-            <param name="assay_type" type="select" label="Illumina Bead Chip Array Assay type"
-                   help="Choose from the following assay types">
-                <options from_parameter="tool.app.known_illumina_beadchip_assay_type"
-                         transform_lines="[ &quot;%s%s%s&quot;
-                                          % (o[1], self.separator, o[1])
-                                          for o in obj ]">
-                    <column name="value" index="0"/>
-                    <column name="name" index="1"/>
-                    <filter type="sort_by" column="0"/>
-                    <filter type="add_value" name="Records provide assay type"
-                            value="use_provided" index="0"/>
-                </options>
-            </param>
-        </when>
-    </conditional>
-
-    <param name="vessel_content" type="select" label="Vessel content" 
-	   help="Choose from one of the available values. See below.">    
-      <options from_parameter="tool.app.kb.VesselContent.__enums__" 
-	       transform_lines="[ &quot;%s%s%s&quot; 
-                                  % (e.enum_label(),
-                                     self.separator,
-                                     e.enum_label()) 
-                                  for e in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Records provide vessel content" 
-                value="use_provided" index="0"/>
-      </options>
-    </param>
-    <param name="vessel_status" type="select" label="Vessel status" 
-	   help="Choose from one of the available values. See below.">    
-      <options from_parameter="tool.app.kb.VesselStatus.__enums__" 
-	       transform_lines="[ &quot;%s%s%s&quot; 
-                                  % (e.enum_label(),
-                                     self.separator,
-                                     e.enum_label()) 
-                                  for e in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Records provide vessel status" 
-                value="use_provided" index="0"/>
-      </options>
-    </param>
-
-    <conditional name="extra_fields">
-      <param name="enabled" type="select" 
-	     label="Enable extra optional fields">
-	<option value="no" selected="true">no</option>	
-	<option value="yes">yes</option>
-      </param>
-      <when value="no"/>
-      <when value="yes">
-	<param name="current_volume" type="float"
-	       value="20" 
-	       help="fluid (FIXME UNITS) currently held in the vessel">
-	  <validator type="in_range" message="Volume must be positive" 
-		     min="0" max="inf"/>
-	</param>
-	<param name="used_volume" type="float"
-	       value="20" 
-	       help="amount of source fluid (FIXME UNITS) used">
-	  <validator type="in_range" message="Volume must be positive" 
-		     min="0" max="inf"/>
-	</param>
-      </when>
-    </conditional>
-
-    <!-- ************************************************** -->
-    <param name="blocking_validation" type="boolean" checked="false"
-	   label="Blocking validation"
-	   help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
-
-    <conditional name="wait_for_trigger">
-      <param name="enable_trigger" type="boolean" checked="false"
-	     label="Wait for another tool to end before running this tool"/>
-      <when value="true">
-	<param format="txt" name="trigger_file" type="data"
-	       label="Select the LOG file that will be used as trigger"/>
-      </when>
-    </conditional>
-
-    <conditional name="advanced_configuration">
-      <param name="configuration_level" type="select" 
-	     label="Configuration level">
-	<option value="default" selected="true">Default configuration</option>	
-	<option value="advanced">Advanced configuration</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-	<param name="vl_host" size="40" type="text" value="localhost" 
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="root" 
-	       label="Omero/VL user"/>
-	<param name="vl_passwd" size="20" type="text" value="What? Me_worry?" 
-	       label="Omero/VL passwd"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="output" label="${tool.name}.mapping"/>
-    <data format="tabular" name="report" label="${tool.name}.report"/>
-    <data format="txt" name="logfile" label="${tool.name}.logfile"/>
-  </outputs>
-
-  <help>
-A biosample record will have, at least, the following fields::
-
-  label     source
-  I001-bs-2 V932814892
-  I002-bs-2 V932814892
-  I003-bs-2 None
-
-Where label is the label of the biosample container. If a 'None' value
-has been passed in the source column, the biosample will be imported
-as a new unlinked object into the biobanks. Another example, this time
-involving DNA samples::
-
-  label    source     used_volume current_volume activation_date
-  I001-dna V932814899 0.3         0.2            17/03/2007
-  I002-dna V932814900 0.22        0.2            21/01/2004
-
-A special case is when records refer to biosamples contained in plate
-wells. In this case, an additional column must be present with the VID
-of the corresponding TiterPlate object. For instance::
-
-  plate  label source
-  V39030 A01   V932814892
-  V39031 A02   V932814893
-  V39032 A03   V932814894
-
-where the label column is now the label of the well position.
-
-If row and column (optional) are provided, the program will use them;
-if they are not provided, it will infer them from label (e.g., J01 ->
-row=10, column=1). Missing labels will be generated as::
-
-  '%s%03d' % (chr(row+ord('A')-1), column)
-
-A badly formed label will result in the rejection of the record; the
-same will happen if label, row and column are inconsistent. The well
-will be filled by current_volume material produced by removing
-used_volume material taken from the bio material contained in the
-vessel identified by source. row and column are base 1.
-
-If the sample is a IlluminaBeadChipArray the plate column used in the
-PlateWell case will become a illumina_array column and a new column, named
-bead_chip_assay_type, is required::
-
-  illumina_array  label   source   bead_chip_assay_type
-  V1351235        R01C01  V412441  HUMANEXOME_12V1_B
-  V1351235        R01C02  V351151  HUMANEXOME_12V1_B
-  V1351235        R02C01  V345115  HUMANEXOME_12V1_B
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 32cfb524b957 -r 47bf0086e082 importer.py
--- a/importer.py	Fri Sep 16 09:16:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# BEGIN_COPYRIGHT
-# END_COPYRIGHT
-
-import sys
-from bl.vl.app.importer.main import main
-
-main(sys.argv[1:])