Mercurial > repos > bebatut > data_manager_qiime_database_downloader

changeset 14:36b38629191b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 6ec84085fd45b933ed8af2d46da4cd6c14be9bf2-dirty
author bebatut
date Fri, 05 May 2017 11:17:48 -0400
parents a34f082f9deb
children
files data_manager/data_manager_qiime_download.py data_manager/data_manager_qiime_download.xml
diffstat 2 files changed, 21 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_qiime_download.py	Fri May 05 09:33:42 2017 -0400
+++ b/data_manager/data_manager_qiime_download.py	Fri May 05 11:17:48 2017 -0400
@@ -161,7 +161,22 @@
     return filepath
 
 
-def extract_archive(filepath, ext):
+def find_archive_content_path(archive_content_path):
+    """
+    """
+    content = os.listdir(archive_content_path)
+    archive_content = []
+    for x in content:
+        if not x.startswith(".") and not x.startswith("_"):
+           archive_content.append(x) 
+    if len(archive_content) == 1:
+        archive_content_path = os.path.join(
+            archive_content_path,
+            archive_content[0])
+    return archive_content_path
+
+
+def extract_archive(filepath, ext, db):
     """
     """
     archive_content_path = "tmp"
@@ -169,19 +184,12 @@
         tar = tarfile.open(filepath)
         tar.extractall(path=archive_content_path)
         tar.close()
-        content = os.listdir(archive_content_path)
-        archive_content = []
-        for x in content:
-            if not x.startswith("."):
-               archive_content.append(x) 
-        if len(archive_content) == 1:
-            archive_content_path = os.path.join(
-                archive_content_path,
-                archive_content[0])
+        archive_content_path = find_archive_content_path(archive_content_path)
     elif ext == "zip":
         zip_ref = zipfile.ZipFile(filepath, 'r')
         zip_ref.extractall(archive_content_path)
         zip_ref.close()
+        archive_content_path = find_archive_content_path(archive_content_path)
     return archive_content_path
 
 
@@ -306,7 +314,7 @@
     filepath = download_archive(db, version, ext)
 
     print("Extract archive %s" % filepath)
-    archive_content_path = extract_archive(filepath, ext)
+    archive_content_path = extract_archive(filepath, ext, db)
 
     print("Moving file from %s" % archive_content_path)
     filename_prefix = "%s_%s" % (db, version)
--- a/data_manager/data_manager_qiime_download.xml	Fri May 05 09:33:42 2017 -0400
+++ b/data_manager/data_manager_qiime_download.xml	Fri May 05 11:17:48 2017 -0400
@@ -32,14 +32,13 @@
                 <param name="version" type="select" label="Version of SILVA OTUs">
                     <option value="128_release" selected="true">128</option>
                     <option value="123_release">123</option>
-                    <option value="119_release_aligned_rep_files">119 (aligned rep)</option>
+                    <!--<option value="119_release_aligned_rep_files">119 (aligned rep)</option>
                     <option value="119_release">119</option>
                     <option value="119_consensus_majority_taxonomy">119 (consensus majority taxonomy)</option>
                     <option value="111_release">111</option>
                     <option value="108_release">108</option>
                     <option value="108_release_curated">108 (curated)</option>
-                    <option value="108_release">108</option>
-                    <option value="104_release">104</option>
+                    <option value="104_release">104</option>-->
                 </param>
             </when>
             <when value="unite">