Update qcv tools (#179)

* Update version + add logs

* versio + logs

* fix typo error

* Update bgc_calib.xml

Author: Marie59

tools/ocean_data_view_manager/bgc_calib.xml

@@ -2,7 +2,7 @@
     <description>for sensors according to Argo recommendations</description>
     <macros>
         <token name="@VERSION@">1.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <requirements>
         <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_tool:@VERSION@</container>

tools/ocean_data_view_manager/tool_odv.xml

@@ -1,11 +1,11 @@
 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
     <description>tool for qualificiation and validation</description>
     <macros>
-        <token name="@VERSION@">1.2</token>
+        <token name="@VERSION@">1.3</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
-        <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container>
+        <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:oc@VERSION@</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export HOME=\$PWD &&
@@ -37,6 +37,7 @@
 
         /app/launchers/start-app.sh &&
         cp '/runtime/data-out/odv_collection.txt' '$output' &&
+        cp -r '/runtime/log/' './outputs/' &&
 
         cp -r '/runtime/data-out/' './outputs/'
     ]]></command>
@@ -123,7 +124,7 @@
                     <has_n_lines n="26363"/>
                 </assert_contents>
             </output>
-            <output_collection name="files" type="list" count="3"/>
+            <output_collection name="files" type="list" count="6"/>
         </test>
         <test expect_num_outputs="2">
             <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_raw.nc"/>
@@ -139,7 +140,7 @@
                     <has_n_lines n="17952"/>
                 </assert_contents>
             </output>
-            <output_collection name="files" type="list" count="3"/>
+            <output_collection name="files" type="list" count="6"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -157,17 +158,11 @@ This tool present two type of actions :
 
     - file_name_raw : nc file to be qualified
     - file_name_ref : nc file used for validation / comparison. noted NULL if no files
-    - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw
-    - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting
-    - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
-
-with default values different from NULL :
-
-    - odv_collection$name : odv_collection.txt
-    - odv_collection$qc_convention : ARGO
-    - tool_action :
-    - tool_option$subsetting :
-    - tool_option$plt :
+    - operator : (optional) name of the person working on dataset qualification / validation
+    - odv_collection$name : name of the odv collection created by the tool (by default = odv_collection.txt)
+    - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw (by default = ARGO)
+    - tool_option$subsetting : 1 apply a subsetting to ref data searching the smallest box (by default) / 0 no subsetting / -1 apply an inverse subsetting
+    - tool_option$plt : figure option to see the subsetted box (0 - by default - or 1) - default name *subset_box.png*
 
 If the list of raw file name is empty, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-ref
 

tools/ocean_data_view_manager/tool_odv_history.xml

@@ -1,11 +1,11 @@
 <tool id="tool_odv_history" name="ODV history manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
     <description>reports user action performed with ODV</description>
     <macros>
-        <token name="@VERSION@">1.1</token>
+        <token name="@VERSION@">1.2</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
-        <container type="docker">easyqcvbgc/easy-qcv_odv-history-manager_tool:@VERSION@</container>
+        <container type="docker">easyqcvbgc/easy-qcv_odv-history-manager_tool:oh@VERSION@</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export HOME=\$PWD &&
@@ -38,7 +38,7 @@
         #end if 
 
         /app/launchers/start-app.sh &&
-        ###cp '/runtime/data-out/*data_0_qced.nc' '$output' &&
+        cp -r '/runtime/log/' './outputs/' &&
 
         cp -r '/runtime/data-out/' './outputs/'
     ]]></command>
@@ -78,7 +78,7 @@
         </configfile>
     </configfiles>
     <inputs>
-        <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input netcdf data" help="This netcdf should come from the QCV harmonizer tool"/>
+        <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input netcdf data" help="This netcdf should come from the QCV harmonizer tool or the BioGeoChemical calibration tool "/>
         <param name="input_hist" type="data" format="txt" multiple="true" label="Input history text file" help="This text file should be the history extracted from the Ocean Data View (ODV) tool"/>
         <param name="input_odv" type="data" format="txt" multiple="true" optional="true" label="Input odv file" help="This ODV file should be the odv_collection.txt from the ODV collection manager tool."/>
         <conditional name="config">
@@ -120,9 +120,12 @@
         <collection type="list" name="csv_files" label="ODV history manager csv collection">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv" directory="./outputs" recurse="true" format="csv"/>
         </collection>
+        <collection type="list" name="log_files" label="ODV history manager log files">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.log" directory="./outputs" recurse="true" format="txt"/>
+        </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/QCV_harmonizer_NetCDF_data_0.nc"/>
             <param name="input_hist" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/history_from_odv_collection.txt"/>
             <param name="input_odv" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/odv_collection.txt"/>
@@ -131,8 +134,9 @@
             </conditional>
             <output_collection name="nc_files" type="list" count="1"/>
             <output_collection name="csv_files" type="list" count="1"/>
+            <output_collection name="log_files" type="list" count="3"/>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/QCV_harmonizer_NetCDF_data_0.nc"/>
             <param name="input_hist" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/history_from_odv_collection.txt"/>
             <param name="input_odv" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/odv_collection.txt"/>
@@ -143,6 +147,7 @@
             </conditional>
             <output_collection name="nc_files" type="list" count="1"/>
             <output_collection name="csv_files" type="list" count="1"/>
+            <output_collection name="log_files" type="list" count="3"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -152,12 +157,11 @@ ODV history manager
 
 **What it does**
 
-This tool present two type of actions :
-    - history : the tool report in the input file the ODV history including the change of QC flag 
+This tool reports in the input file (a netcdf from the QCV harmonizer tool or the BioGeoChemical calibration tool) the ODV history including the change of QC flag.
 
 **Input description**
 
-    file_name_raw : nc file to be qualified
+    file_name_raw : nc file to be qualified, this netcdf should come from the QCV harmonizer tool or  from the BioGeoChemical calibration tool 
     file_name_history : history txt file extracted from ODV (manualy or automatically)
     odv_collection$name : name of the odv collection view with webODV and updated
     odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw