# HG changeset patch # User ric # Date 1474547862 14400 # Node ID 8fdf5996c0fb71788e9e7d31a28c8636e7245ade # Parent 015f2dcc2510dbe362c43216896e275642c2dc1f Deleted selected files diff -r 015f2dcc2510 -r 8fdf5996c0fb boh/markers_set.xml --- a/boh/markers_set.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ - - import Marker definitions within omero/vl - - #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=${logfile} - markers_set - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($label) - --label ${label} - #end if - #if str($maker) != 'use_provided' - --maker ${maker} - #end if - #if str($model) != 'use_provided' - --model ${model} - #end if - #if str($release) - --release ${release} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - marker_vid marker_indx allele_flip - V902909090 0 False - V902909091 1 False - V902909092 2 True - ... - - - - - - - diff -r 015f2dcc2510 -r 8fdf5996c0fb boh/samples_container.xml --- a/boh/samples_container.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,287 +0,0 @@ - - import samples container definitions within omero/vl - - #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 $blocking_validation - --blocking-validator - #end if - samples_container - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($container_type_selector.container_type) != 'use_provided' - --container-type=${container_type_selector.container_type} - #if str($container_type_selector.container_type) == 'TiterPlate' - #if str($container_type_selector.plate_shape) != 'use_provided' - --plate-shape=${container_type_selector.plate_shape} - #end if - #elif str($container_type_selector.container_type) == 'FlowCell' - #if str($container_type_selector.flow_cell_slots) != 'use_provided' - --number-of-slots=${container_type_selector.flow_cell_slots} - #end if - #elif str($container_type_selector.container_type) == 'IlluminaArrayOfArrays' - #if str($container_type_selector.ill_shape) != 'use_provided' - --plate-shape=${container_type_selector.ill_shape} - #end if - #if str($container_type_selector.ill_slots) != 'use_provided' - --number_of_slots=${container_type_selector.ill_slots} - #end if - #if str($container_type_selector.array_type) != 'use_provided' - --illumina-array-type=${container_type_selector.array_type} - #end if - #if str($container_type_selector.array_class) != 'use_provided' - --illumina-array-class=${container_type_selector.array_class} - #end if - #if str($container_type_selector.assay_type) != 'use_provided' - --illumina-assay-type=${container_type_selector.assay_type} - #end if - #end if - #end if - #if str($container_status) != 'use_provided' - --container-status=${container_status} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -A container record will have the following fields:: - - label container_status creation_date - A_CONTAINER USABLE 13/02/2012 - B_CONTAINER INSTOCK 12/01/2001 - C_CONTAINER USABLE 25/04/2012 - .... - -the creation_date column is optional, if not specified current date -will be set as the object's creation date, also the container_status -column can be optional if this values is passed as input parameter. - - -When importing new containers, special fields can be included in the -CSV file depending on the type of the objects that you want to -import. - -For TITER PLATES objects the syntax can be the following:: - - label barcode container_status rows columns - A_TITERPLATE XXYYZZ111 INSTOCK 8 12 - B_TITERPLATE XXYYZZ112 INSTOCK 8 12 - C_TITERPLATE XXYYZZ113 READY 8 12 - .... - -rows and columns values can be optional if these values are passed as -input parameters, barcode column is optional. - -For ILLUMINA ARRAY OF ARRAYS objects the syntax can be the following:: - - label barcode container_status rows columns illumina_array_type illumina_array_class illumina_assay_type - A_ILLARRAY XXYYZZ111 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - B_ILLARRAY XXYYZZ112 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - C_ILLARRAY XXYYZZ113 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - -rows, columns, illumina_array_type, illumina_array_class and illumina_assay_type -can be optional if these values are passed as input parameters, barcode column -is optional. - -For FLOW CELL objects the syntax can be the following:: - - label barcode container_status number_of_slots - A_FLOWCELL XXYYZZ221 INSTOCK 8 - B_FLOWCELL XXYYZZ222 INSTOCK 8 - C_FLOWCELL XXYYZZ223 INSTOCK 8 - .... - -number_of_slots column can be optional if this value is passed as -input paramter, barcode column is optional. - -For LANE objects the syntax can be the following:: - - flow_cell slot container_status - V112441441 1 INSTOCK - V112441441 2 INSTOCK - V112441441 3 INSTOCK - V351145519 1 INSTOCK - V351145519 2 INSTOCK - .... - -for Lane objects, no label column has to be provided, the importer -will automatically calculate the labels for each imported object. - - - - - - - diff -r 015f2dcc2510 -r 8fdf5996c0fb boh/sequencing_data_sample.xml --- a/boh/sequencing_data_sample.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,198 +0,0 @@ - - - Import sequencing related DataSample definitions within omero/vl - - - importer.py - --operator=galaxy - --ifile=${input} - --ofile=${output} - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - seq_data_sample - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source-type=${source_type} - #end if - #if str($seq_dsample_type) != 'use_provided' - --seq-dsample-type=${seq_dsample_type} - #end if - #if str($dsample_status) != 'use_provided' - --status=${dsample_status} - #end if - #if str($device) != 'use_provided' - --device=${device} - #end if - #if str($history) != 'None' - --history=${history} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read a tsv file with the following columns:: - - study label source source_type seq_dsample_type status device - FOOBAR seq_out_1 V012141 FlowCell SequencerOutput USABLE V123141 - FOOBAR seq_out_2 V012141 FlowCell SequencerOutput USABLE V123141 - FOOBAR seq_out_3 V1AD124 FlowCell SequencerOutput USABLE V123141 - ... - -where - * seq_dsample_type can assume one of the following values: SequencerOutput, RawSeqDataSample, SeqDataSample - * source_type can assume one of the following values: FlowCell, SequencerOutput, RawSeqDataSample - -study, source_type, seq_dsample_type, status and device columns can be -overwritten by using command line options. - -A special case of the previous file is when seq_dsample_type is -SeqDataSample, in this case a mandatory sample column is required, -this column has to contain IDs of Tube objects. -The file will look like this - - study label source source_type seq_dsample_type status device sample - FOOBAR seq_dsample_1 V041241 SequencerOutput SeqDataSample USABLE VBB2351 V124AA41 - FOOBAR seq_dsample_2 V051561 SequencerOutput SeqDataSample USABLE VBB2351 V4151AAE - FOOBAR seq_dsample_3 V151561 SequencerOutput SeqDataSample USABLE VBB2351 V15199CD - ... - -A file containing ax export of the Galaxy history that produced the -data that are going to be imported can be passed as input parameter, -history details must represented as a string serialized in JSON -format. - - - - - - - diff -r 015f2dcc2510 -r 8fdf5996c0fb boh/study.xml --- a/boh/study.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ - - import study definitions within omero/vl - - #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 - study - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will import a stream of new study definitions defined by the following -tab-separated columns. A typical file will look like the following:: - - label description - BSTUDY A basically empty description of BSTUDY - CSTUDY A basically empty description of CSTUDY - .... - - - - - - - diff -r 015f2dcc2510 -r 8fdf5996c0fb boh/unauthorized_access.py --- a/boh/unauthorized_access.py Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -# BEGIN_COPYRIGHT -# END_COPYRIGHT - -import sys - -sys.exit("You are not authorized to use this tool") diff -r 015f2dcc2510 -r 8fdf5996c0fb boh/vessels_collection.xml --- a/boh/vessels_collection.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ - - import VesselsCollection definitions within omero/vl - - #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 $blocking_validation - --blocking-validator - #end if - vessels_collection - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($vessel_type) != 'use_provided' - --vessel_type=${vessel_type} - #end if - #if str($label) - --label=${label} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -TODO: add doc here... - - - - - - - -