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changeset 26:bf6940ff60a8 draft

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planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty
author proteore
date Thu, 16 May 2019 07:29:01 -0400
parents 6e36dd9abcb5
children 9a400ce8e4e6
files data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_biogrid_dictionaries.loc.sample tool-data/proteore_bioplex_dictionaries.loc.sample tool-data/proteore_humap_dictionaries.loc.sample 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/proteore_protein_atlas_normal_tissue.loc.sample tool-data/proteore_protein_atlas_tumor_tissue.loc.sample tool_data_table_conf.xml.sample
diffstat 12 files changed, 37 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Fri May 10 04:50:22 2019 -0400
+++ b/data_manager/resource_building.py	Thu May 16 07:29:01 2019 -0400
@@ -53,10 +53,11 @@
     path = os.path.join(target_directory, output_file)
     unzip(url, path)    #download and save file
     tissue_name = tissue_name + " " + time.strftime("%d/%m/%Y")
-    tissue_id = tissue_name.replace(" ","_").replace("/","-")
+    release = tissue_name.replace(" ","_").replace("/","-")
+    id = str(10000000000 - int(time.strftime("%Y%m%d")))
 
 
-    data_table_entry = dict(id=tissue_id, name = tissue_name, tissue = tissue, value = path)
+    data_table_entry = dict(id=id, release=release, name = tissue_name, tissue = tissue, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, table)
 
 
@@ -501,12 +502,13 @@
     output_file = species+'_'+interactome+'_'+ time.strftime("%d-%m-%Y") + ".json"
     path = os.path.join(target_directory,output_file)
     name = species+" ("+species_dict[species]+") "+time.strftime("%d/%m/%Y")
-    id = species+"_"+interactome+"_"+ time.strftime("%d-%m-%Y")
+    release = species+"_"+interactome+"_"+ time.strftime("%d-%m-%Y")
+    id = str(10000000000 - int(time.strftime("%Y%m%d")))
 
     with open(path, 'w') as handle:
         json.dump(dico, handle, sort_keys=True)
 
-    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_"+interactome+"_dictionaries")
 
 #######################################################################################################
--- a/data_manager/resource_building.xml	Fri May 10 04:50:22 2019 -0400
+++ b/data_manager/resource_building.xml	Thu May 16 07:29:01 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.05.10.2" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.05.16" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Fri May 10 04:50:22 2019 -0400
+++ b/data_manager_conf.xml	Thu May 16 07:29:01 2019 -0400
@@ -19,13 +19,14 @@
         <data_table name="proteore_protein_atlas_normal_tissue">
             <output>
                 <column name="id"/>
+                <column name="release"/>
                 <column name="name" />
                 <column name="tissue" />
                 <column name="value" output_ref="output" >
                     <move type="file">
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -33,13 +34,14 @@
         <data_table name="proteore_protein_atlas_tumor_tissue">
             <output>
                 <column name="id"/>
+                <column name="release"/>
                 <column name="name" />
                 <column name="tissue" />
                 <column name="value" output_ref="output" >
                     <move type="file">
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -95,6 +97,7 @@
         <data_table name="proteore_biogrid_dictionaries">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -102,7 +105,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -110,6 +113,7 @@
         <data_table name="proteore_bioplex_dictionaries">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -117,7 +121,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -125,6 +129,7 @@
         <data_table name="proteore_humap_dictionaries">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -132,7 +137,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/tool-data/proteore_biogrid_dictionaries.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_biogrid_dictionaries.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,4 +1,4 @@
-#id	name	species	value
-#biogrid_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/Human_biogrid.json
-#biogrid_mouse_08-01-2019	Mouse (Mus musculus) 08/01/2019	Mouse	PPI_dictionaries/Mouse_biogrid.json
-#biogrid_rat_08-01-2019	Rat (Rattus norvegicus) 08/01/2019 Rat	PPI_dictionaries/Rat_biogrid.json
+#id	release name	species	value
+#9979809892	biogrid_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/Human_biogrid.json
+#9979809892	biogrid_mouse_08-01-2019	Mouse (Mus musculus) 08/01/2019	Mouse	PPI_dictionaries/Mouse_biogrid.json
+#9979809892	biogrid_rat_08-01-2019	Rat (Rattus norvegicus) 08/01/2019 Rat	PPI_dictionaries/Rat_biogrid.json
--- a/tool-data/proteore_bioplex_dictionaries.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_bioplex_dictionaries.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,2 +1,2 @@
-#id	name	species	value
-#bioplex_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/human_bioplex.json
+#id	release name	species	value
+#9979809892	bioplex_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/human_bioplex.json
--- a/tool-data/proteore_humap_dictionaries.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_humap_dictionaries.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,2 +1,2 @@
-#id	name	species	value
-#humap_human_01-02-2019 Human (Homo sapiens) 01/02/19	Human	PPI_dictionaries/Human_humap_01-02-2019.json
+#id	release name	species	value
+#9979809799	humap_human_01-02-2019 Human (Homo sapiens) 01/02/19	Human	PPI_dictionaries/Human_humap_01-02-2019.json
--- a/tool-data/proteore_id_mapping_Human.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_id_mapping_Human.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
 #<id>	<release>   <name>	<species>	<value>
-9979818977	human_id_mapping_23-10-2018	Human (homo sapiens 23/10/2018)	Human	tool-data/human_id_mapping_23-10-2018.tsv
\ No newline at end of file
+#9979818977	human_id_mapping_23-10-2018	Human (homo sapiens 23/10/2018)	Human	tool-data/human_id_mapping_23-10-2018.tsv
\ No newline at end of file
--- a/tool-data/proteore_id_mapping_Mouse.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_id_mapping_Mouse.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
 #<id>	<release>   <name>	<species>	<value>
-9979818977	mouse_id_mapping_23-10-2018	Mouse (Mus musculus 23-10-2018)	Mouse	tool-data/mouse_id_mapping_23-10-2018.tsv
+#9979818977	mouse_id_mapping_23-10-2018	Mouse (Mus musculus 23-10-2018)	Mouse	tool-data/mouse_id_mapping_23-10-2018.tsv
--- a/tool-data/proteore_id_mapping_Rat.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_id_mapping_Rat.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
 #<id>	<release>   <name>	<species>	<value>
-9979818977	rat_id_mapping_23-10-2018	Rat (Rattus norvegicus 23-10-2018)	Rat	tool-data/rat_id_mapping_23-10-2018.tsv
+#9979818977	rat_id_mapping_23-10-2018	Rat (Rattus norvegicus 23-10-2018)	Rat	tool-data/rat_id_mapping_23-10-2018.tsv
--- a/tool-data/proteore_protein_atlas_normal_tissue.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_protein_atlas_normal_tissue.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,4 +1,4 @@
 #This file lists the locations name and values of reference files for Get expression data tool
 #This is a tab separated file (TAB, not 4 spaces !)
-#<id>	<name> <tissue>	<value>
-#HPA_normal_tissue_19-07-2018	HPA normal tissue 19/07/2018	HPA_normal_tissue	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19159/dataset_39307_files/HPA_normal_tissue_19-07-2018.tsv
+#<id>	<release>   <name> <tissue>	<value>
+#9979819281	HPA_normal_tissue_19-07-2018	HPA normal tissue 19/07/2018	HPA_normal_tissue	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19159/dataset_39307_files/HPA_normal_tissue_19-07-2018.tsv
--- a/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample	Thu May 16 07:29:01 2019 -0400
@@ -1,4 +1,4 @@
 #This file lists the locations name and values of reference files for Get expression data tool
 #This is a tab separated file (TAB, not 4 spaces !)
-#<id>	<name> <tissue>	<value>
-#HPA_pathology_19-07-2018	HPA pathology 19/07/2018	HPA_pathology	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19160/dataset_39308_files/HPA_pathology_19-07-2018.tsv
+#<id>	<release>	<name> <tissue>	<value>
+#9979819281	HPA_pathology_19-07-2018	HPA pathology 19/07/2018	HPA_pathology	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19160/dataset_39308_files/HPA_pathology_19-07-2018.tsv
--- a/tool_data_table_conf.xml.sample	Fri May 10 04:50:22 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 16 07:29:01 2019 -0400
@@ -5,11 +5,11 @@
     <file path="tool-data/proteore_peptide_atlas.loc"/>
   </table>
   <table name="proteore_protein_atlas_normal_tissue" comment_char="#">
-    <columns>id, name, tissue, value</columns>
+    <columns>id, release, name, tissue, value</columns>
     <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" />
   </table>
   <table name="proteore_protein_atlas_tumor_tissue" comment_char="#">
-    <columns>id, name, tissue, value</columns>
+    <columns>id, release, name, tissue, value</columns>
     <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
   </table>
   <table name="proteore_id_mapping_Human" comment_char="#">
@@ -25,15 +25,15 @@
     <file path="tool-data/proteore_id_mapping_Rat.loc" />
   </table>
   <table name="proteore_biogrid_dictionaries" comment_char="#">
-    <columns>id, name, species, value</columns>
+    <columns>id, release, name, species, value</columns>
     <file path="tool-data/proteore_biogrid_dictionaries.loc" />
   </table>
   <table name="proteore_bioplex_dictionaries" comment_char="#">
-    <columns>id, name, species, value</columns>
+    <columns>id, release, name, species, value</columns>
     <file path="tool-data/proteore_bioplex_dictionaries.loc" />
   </table>
   <table name="proteore_humap_dictionaries" comment_char="#">
-    <columns>id, name, species, value</columns>
+    <columns>id, release, name, species, value</columns>
     <file path="tool-data/proteore_humap_dictionaries.loc" />
   </table>
   <table name='proteore_nextprot_ref' comment_char="#">