Mercurial > repos > estrain > data_manager_amrfinderplus

changeset 25:6ed79bff991f draft default tip

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Uploaded
author estrain
date Tue, 24 May 2022 00:19:05 +0000
parents 2cab00532d10
children
files data_manager_amrfinderplus/README data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml data_manager_amrfinderplus/data_manager_conf.xml data_manager_amrfinderplus/test-data/amrfinder_databases.loc data_manager_amrfinderplus/tool-data/amrfinder_databases.loc data_manager_amrfinderplus/tool_data_table_conf.xml.sample data_manager_amrfinderplus/tool_data_table_conf.xml.test data_manager_amrfinderplus/tool_data_table_conf_sample.xml.sample data_manager_amrfinderplus/tool_data_table_conf_sample.xml.test
diffstat 10 files changed, 35 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_amrfinderplus/README	Mon May 23 01:28:17 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-AMRFinderPlus Data Manager
--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py	Mon May 23 01:28:17 2022 +0000
+++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py	Tue May 24 00:19:05 2022 +0000
@@ -12,13 +12,16 @@
 from ftplib import FTP
 
 
-def download_from_ncbi():
+def download_from_ncbi(output_directory):
     NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
     FILENAME = 'version.txt' 
     NCBI_DOWNLOAD_PATH = '/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/'
     
     email = 'anonymous@example.com'
 
+    cwd = os.getcwd() 
+    os.chdir(output_directory)
+
     ftp = FTP( NCBI_FTP_SERVER )
     ftp.login( 'anonymous', email)
     ftp.cwd(NCBI_DOWNLOAD_PATH)
@@ -56,6 +59,8 @@
 
     ftp.quit()
     
+    os.chdir(cwd)    
+    
     return version 
 
 def print_json (version,argspath,argsname,argsout):
@@ -82,14 +87,20 @@
     parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')
 
     args = parser.parse_args()
-  
-    os.mkdir("amrdb")
-    os.chdir("amrdb") 
+
+    with open(args.out[0]) as fh:
+        params = json.load(fh)
+
+    output_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(output_directory)
+    data_manager_dict = {}
+
     #Fetch the files and build blast databases
-    version=download_from_ncbi()    
-    os.chdir("..")
+    version=download_from_ncbi(output_directory)    
+
+    tablename = "AMRFinderPlus Database " + version
 
     #shutil.copytree("amrdb",args.path[0])
-    print_json(version,os.path.abspath("amrdb"),args.name[0],args.out[0])
+    print_json(version,output_directory,tablename,args.out[0])
 
 if __name__ == "__main__": main()
--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml	Mon May 23 01:28:17 2022 +0000
+++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml	Tue May 24 00:19:05 2022 +0000
@@ -1,5 +1,4 @@
 <tool id="data_manager_amrfinderplus" name="AMRFinderPlus Data Manger" tool_type="manage_data" version="0.0.3" profile="20.01">
-    <description> Database builder</description>
     <requirements>
         <requirement type="package">blast</requirement>
         <requirement type="package">hmmer</requirement>
@@ -8,7 +7,7 @@
         python $__tool_directory__/data_manager_amrfinderplus.py --name $amrdbname --out ${output_file};
     ]]></command>
     <inputs>
-      <param name="amrdbname" type="text" label="Name of amrFinderPlus database"/>
+      <param name="amrdbname" type="text" value="latest" label="Release Version - Note: only latest release is supported"/>
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json"/>
@@ -21,6 +20,5 @@
     </help>
     <citations>
      Refer to https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ for latest database version number.
-
     </citations>
 </tool>
--- a/data_manager_amrfinderplus/data_manager_conf.xml	Mon May 23 01:28:17 2022 +0000
+++ b/data_manager_amrfinderplus/data_manager_conf.xml	Tue May 24 00:19:05 2022 +0000
@@ -8,9 +8,9 @@
           <column name="path" output_ref="output_file" >
             <move type="directory" relativize_symlinks="True">
               <src>${path}</src>
-              <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">amrfinderplus/</target>
+              <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">amrfinderplus/${value}</target>
             </move>
-            <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/amrfinderplus/#echo str($name)#</value_translation>
+            <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/amrfinderplus/${value}</value_translation>
             <value_translation type="function">abspath</value_translation>
           </column>
         </output>
--- a/data_manager_amrfinderplus/test-data/amrfinder_databases.loc	Mon May 23 01:28:17 2022 +0000
+++ b/data_manager_amrfinderplus/test-data/amrfinder_databases.loc	Tue May 24 00:19:05 2022 +0000
@@ -1,4 +1,4 @@
-# this is a tab separated file describing the location of amrfinder databases used for the
+# this is a tab separated file describing the location of amrfinder databases
 #
 # the columns are:
 # value name path
--- a/data_manager_amrfinderplus/tool-data/amrfinder_databases.loc	Mon May 23 01:28:17 2022 +0000
+++ b/data_manager_amrfinderplus/tool-data/amrfinder_databases.loc	Tue May 24 00:19:05 2022 +0000
@@ -1,4 +1,4 @@
-# this is a tab separated file describing the location of amrfinder databases used for the
+# this is a tab separated file describing the location of amrfinder databases
 #
 # the columns are:
 # value name path
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_amrfinderplus/tool_data_table_conf.xml.sample	Tue May 24 00:19:05 2022 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path</columns>
+        <file path="tool-data/amrfinderplus.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_amrfinderplus/tool_data_table_conf.xml.test	Tue May 24 00:19:05 2022 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False">
+        <columns>value,name, path</columns>
+        <file path="${__HERE__}/test-data/amrfinderplus.loc" />
+    </table>
+</tables>
--- a/data_manager_amrfinderplus/tool_data_table_conf_sample.xml.sample	Mon May 23 01:28:17 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/amrfinderplus.loc" />
-    </table>
-</tables>
--- a/data_manager_amrfinderplus/tool_data_table_conf_sample.xml.test	Mon May 23 01:28:17 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False">
-        <columns>value,name, path</columns>
-        <file path="${__HERE__}/test-data/amrfinderplus.loc" />
-    </table>
-</tables>