# HG changeset patch
# User kkonganti
# Date 1663265469 14400
# Node ID bdccef316f657ac42e888e35805031b98ebe0d3c
# Parent  530cafac56f9f0313851428e9aa5516d611e234c
"planemo upload"

diff -r 530cafac56f9 -r bdccef316f65 cfsan_lexmapr2.xml
--- a/cfsan_lexmapr2.xml	Thu Sep 15 13:55:38 2022 -0400
+++ b/cfsan_lexmapr2.xml	Thu Sep 15 14:11:09 2022 -0400
@@ -13,8 +13,8 @@
     </requirements>
     <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-    echo \$PYTHONPATH 1>&2;
     mkdir -p lexmapr2-input || exit 1;
+    ln -sf '/tool/tool-data/cfsan_lexmapr2/0/lexmapr' .;
     ln -sf '$input' './lexmapr2-input/$input.name';
     python $__tool_directory__/lexmapr2.py
     #if ($embl_ont != ""):
@@ -39,7 +39,6 @@
     ]]></command>
     <environment_variables>
         <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
-        <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
     </environment_variables>
     <inputs>
         <param name="input" type="data" format="csv" label="Input CSV"
diff -r 530cafac56f9 -r bdccef316f65 lexmapr_run.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lexmapr_run.log	Thu Sep 15 14:11:09 2022 -0400
@@ -0,0 +1,5 @@
+INFO:root:Run start: 2022-09-15 14:05:40.236514
+INFO:root:Run start: 2022-09-15 14:07:13.815176
+INFO:root:Run start: 2022-09-15 14:08:11.894380
+INFO:root:Database build/confirm: 2022-09-15 14:08:11.908013
+WARNING:root:Did not retrieve URL for https://www.ebi.ac.uk/ols/api/ontologies/foodon/ancestors?id=FOODON:00002703&page=1&size=20 during API search
diff -r 530cafac56f9 -r bdccef316f65 o.tsv
--- a/o.tsv	Thu Sep 15 13:55:38 2022 -0400
+++ b/o.tsv	Thu Sep 15 14:11:09 2022 -0400
@@ -1,8 +1,2 @@
-Sample_Id	Sample_Desc	Processed_Sample	Annotated_Sample	Matched_Components	Match_Status (Macro Level)	Match_Status (Micro Level)	Sample_Transformations	fo_product	fo_quality	fo_organism	ncbi_taxon
-small_simple1	Chicken Breast		Not annotated	chicken breast:FOODON_00002703	Full Term Match	[]	{}	poultry food product:FOODON_00001283|vertebrate animal food product:FOODON_00001092			
-small_simple2	Baked Potato		Not annotated	potato (whole, baked):FOODON_03302196	Full Term Match	['Used Processed Sample', 'Suffix Addition']	{}	plant food product:FOODON_00001015	food (baked):FOODON_00002456|food (cooked):FOODON_00001181		
-small_simple3	Canned Corn		Not annotated	corn (canned):FOODON_03302665	Full Term Match	[]	{}	plant food product:FOODON_00001015			
-small_simple4	Frozen Yogurt		Not annotated	frozen yogurt:FOODON_03307445	Full Term Match	[]	{}	dairy food product:FOODON_00001256|vertebrate animal food product:FOODON_00001092			
-small_simple5	Apple Pie		Not annotated	apple pie:FOODON_00002475	Full Term Match	[]	{}	bakery food product:FOODON_00001626|plant food product:FOODON_00001015|prepared food product:FOODON_00001180			
-small_simple5	Apple cider	apple cider	Not annotated	apple food product:FOODON_00001611	Component Match	['Inflection (Plural) Treatment: apple', 'Inflection (Plural) Treatment: cider', 'Suffix Addition']	{}	plant food product:FOODON_00001015			
-small_simple6	Chicken egg	chicken egg	Not annotated	chicken:FOODON_03411457|egg food product:FOODON_00001274	Component Match	['Inflection (Plural) Treatment: chicken', 'Inflection (Plural) Treatment: egg', 'Suffix Addition']	{}	poultry food product:FOODON_00001283|vertebrate animal food product:FOODON_00001092			Aves:NCBITaxon_8782
\ No newline at end of file
+Sample_Id	Sample_Desc	Processed_Sample	Annotated_Sample	Matched_Components	Match_Status (Macro Level)	Match_Status (Micro Level)	Sample_Transformations	ncbi_taxon
+small_simple1	Chicken Breast		Not annotated	chicken breast:FOODON_00002703	Full Term Match	[]	{}	
\ No newline at end of file