Mercurial > repos > iuc > ncbi_eutils_efetch

changeset 4:c26d1863f3f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit e0575333e6f08ef02fc66c2764b43ebd15c6b04b
author iuc
date Fri, 10 Jun 2016 15:03:49 -0400
parents aa88712a7536
children e269b3b5185b
files efetch.xml eutils.py test tmp
diffstat 4 files changed, 35 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/efetch.xml	Fri Jun 10 14:49:12 2016 -0400
+++ b/efetch.xml	Fri Jun 10 15:03:49 2016 -0400
@@ -11,7 +11,7 @@
 
 @LIST_OR_HIST@
 
-#set retmode, rettype = str($db.output_format).split('-')
+#set rettype, retmode = str($db.output_format).split('-')
 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
 #if retmode != "null":
 --retmode $retmode
@@ -35,7 +35,7 @@
   <tests>
     <test>
       <param name="db_select" value="taxonomy"/>
-      <param name="output_format" value="docsum-xml"/>
+      <param name="output_format" value="full-xml"/>
       <param name="qss" value="id_list"/>
       <param name="id_list" value="10239"/>
       <output name="default" file="viruses.tax.xml">
--- a/eutils.py	Fri Jun 10 14:49:12 2016 -0400
+++ b/eutils.py	Fri Jun 10 15:03:49 2016 -0400
@@ -27,7 +27,6 @@
         if history_file is not None:
             with open(history_file, 'r') as handle:
                 data = json.loads(handle.read())
-                print data
                 self.query_key = data['QueryKey']
                 self.webenv = data['WebEnv']
                 self.using_history = True
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test	Fri Jun 10 15:03:49 2016 -0400
@@ -0,0 +1,4 @@
+{
+    "QueryKey": "1", 
+    "WebEnv": "NCID_1_29968407_130.14.22.215_9001_1465585167_557791559_0MetA0_S_MegaStore_F_1"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp	Fri Jun 10 15:03:49 2016 -0400
@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+<!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd">
+<TaxaSet><Taxon>
+    <TaxId>10239</TaxId>
+    <ScientificName>Viruses</ScientificName>
+    <OtherNames>
+        <BlastName>viruses</BlastName>
+        <Synonym>Vira</Synonym>
+        <Synonym>Viridae</Synonym>
+    </OtherNames>
+    <ParentTaxId>1</ParentTaxId>
+    <Rank>superkingdom</Rank>
+    <Division>Viruses</Division>
+    <GeneticCode>
+        <GCId>1</GCId>
+        <GCName>Standard</GCName>
+    </GeneticCode>
+    <MitoGeneticCode>
+        <MGCId>0</MGCId>
+        <MGCName>Unspecified</MGCName>
+    </MitoGeneticCode>
+    <Lineage/>
+    <CreateDate>1995/02/27 09:24:00</CreateDate>
+    <UpdateDate>2010/11/23 11:40:11</UpdateDate>
+    <PubDate>1993/04/20 01:00:00</PubDate>
+</Taxon>
+
+</TaxaSet>
+