Mercurial > repos > proteore > proteore_data_manager

changeset 21:026177e4ff4b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty
author proteore
date Tue, 07 May 2019 10:17:48 -0400
parents 29cf75c83618
children 4296fb613d9d
files data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_id_mapping_Human.loc.sample tool-data/proteore_id_mapping_Mouse.loc.sample tool-data/proteore_id_mapping_Rat.loc.sample tool_data_table_conf.xml.sample
diffstat 7 files changed, 19 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Tue May 07 08:37:17 2019 -0400
+++ b/data_manager/resource_building.py	Tue May 07 10:17:48 2019 -0400
@@ -242,9 +242,10 @@
 
     name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"}
     name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
-    id = str(10000000000 - int(time.strftime("%d%m%Y")))
+    release = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
+    id = str(10000000000 - int(time.strftime("%d%m%Y")))    #new ids must be inferior to previous id -> sort by <filter> in xml only in descending order
 
-    data_table_entry = dict(id=id, name = name, species = species, value = path)
+    data_table_entry = dict(id=id, release=release , name = name, species = species, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species)
 
 def download_from_uniprot_ftp(file,target_directory) :
--- a/data_manager/resource_building.xml	Tue May 07 08:37:17 2019 -0400
+++ b/data_manager/resource_building.xml	Tue May 07 10:17:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.05.07" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.05.07.01" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Tue May 07 08:37:17 2019 -0400
+++ b/data_manager_conf.xml	Tue May 07 10:17:48 2019 -0400
@@ -47,6 +47,7 @@
         <data_table name="proteore_id_mapping_Human">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -54,7 +55,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -62,6 +63,7 @@
         <data_table name="proteore_id_mapping_Mouse">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -69,7 +71,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -77,6 +79,7 @@
         <data_table name="proteore_id_mapping_Rat">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -84,7 +87,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/tool-data/proteore_id_mapping_Human.loc.sample	Tue May 07 08:37:17 2019 -0400
+++ b/tool-data/proteore_id_mapping_Human.loc.sample	Tue May 07 10:17:48 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
-#<id>	<name>	<value>	<path>
-#human_id_mapping_01-01-2018	Human (homo sapiens)	human_id_mapping	tool-data/human_id_mapping.tsv
+#<id>	<release>   <name>	<value>	<path>
+#9979819899   human_id_mapping_01-01-2018	Human (homo sapiens)	human_id_mapping	tool-data/human_id_mapping.tsv
--- a/tool-data/proteore_id_mapping_Mouse.loc.sample	Tue May 07 08:37:17 2019 -0400
+++ b/tool-data/proteore_id_mapping_Mouse.loc.sample	Tue May 07 10:17:48 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
-#<id>	<name>	<value>	<path>
-#mouse_id_mapping_01-01-2018	Mouse (Mus musculus)	mouse_id_mapping	tool-data/mouse_id_mapping.tsv
+#<id>	<release>   <name>	<value>	<path>
+#9979819899 mouse_id_mapping_01-01-2018	Mouse (Mus musculus)	mouse_id_mapping	tool-data/mouse_id_mapping.tsv
--- a/tool-data/proteore_id_mapping_Rat.loc.sample	Tue May 07 08:37:17 2019 -0400
+++ b/tool-data/proteore_id_mapping_Rat.loc.sample	Tue May 07 10:17:48 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
-#<id>	<name>	<value>	<path>
-#rat_id_mapping_01-01-2018	Rat (Rattus norvegicus)	rat_id_mapping	tool-data/rat_id_mapping.tsv
+#<id>	<release>   <name>	<value>	<path>
+#9979819899 rat_id_mapping_01-01-2018	Rat (Rattus norvegicus)	rat_id_mapping	tool-data/rat_id_mapping.tsv
--- a/tool_data_table_conf.xml.sample	Tue May 07 08:37:17 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Tue May 07 10:17:48 2019 -0400
@@ -13,15 +13,15 @@
     <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
   </table>
   <table name="proteore_id_mapping_Human" comment_char="#">
-    <columns>id, name, species, value</columns>
+    <columns>id, release, name, species, value</columns>
     <file path="tool-data/proteore_id_mapping_Human.loc" />
   </table>
   <table name="proteore_id_mapping_Mouse" comment_char="#">
-    <columns>id, name, species, value</columns>
+    <columns>id, release, name, species, value</columns>
     <file path="tool-data/proteore_id_mapping_Mouse.loc" />
   </table>
   <table name="proteore_id_mapping_Rat" comment_char="#">
-    <columns>id, name, species, value</columns>
+    <columns>id, release, name, species, value</columns>
     <file path="tool-data/proteore_id_mapping_Rat.loc" />
   </table>
   <table name="proteore_biogrid_dictionaries" comment_char="#">