Merge pull request #3259 from antgonza/allow-plugin-prep-creation

Allow plugin prep creation

Author: charles-cowart

qiita_db/handlers/prep_template.py

@@ -115,7 +115,7 @@ def get(self, prep_id):
         self.write(response)
 
 
-class PrepTemplateAPItestHandler(OauthBaseHandler):
+class PrepTemplateAPIHandler(OauthBaseHandler):
     @authenticate_oauth
     def post(self):
         prep_info_dict = loads(self.get_argument('prep_info'))
@@ -126,3 +126,7 @@ def post(self):
         pt = qdb.metadata_template.prep_template.PrepTemplate.create(
             metadata, qdb.study.Study(study), data_type)
         self.write({'prep': pt.id})
+
+
+class PrepTemplateAPItestHandler(PrepTemplateAPIHandler):
+    pass

qiita_pet/support_files/doc/source/dev/rest.rst

@@ -64,6 +64,8 @@ the important parts of the values are described in the Parameters column.
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/prep_template/<prep_id>/``                                            |                                         | Retrieves the preparation information               | PrepTemplateDBHandler      |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
+|POST    | ``/qiita_db/prep_template/``                                                      |                                         | Adds a new preparation                              | PrepTemplateAPIHandler     |
++--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/plugins/<plugin_name>/<version>/commands/<command_name>/activate/``   |                                         | Activates the command                               | CommandActivateHandler     |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/plugins/<plugin_name>/<version>/commands/<command_name>/``            |                                         | Retrieve the command information                    | CommandHandler             |

qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst

@@ -81,8 +81,8 @@ wetlab processing and we provide the following host references for your convenie
 Note that the command produces up to 6 output artifacts based on the aligner and database selected:
 
 - Alignment Profile: contains the raw alignment file and the no rank classification BIOM table
-- Per genome Predictions: contains the per genome level taxonomic predictions BIOM table
-- Per gene Predictions: Only WoLr1 & WoLr2, contains the per gene level taxonomic predictions BIOM table
+- Per genome Predictions: contains the per genome level predictions BIOM table
+- Per gene Predictions: Only WoLr1 & WoLr2, contains the per gene level predictions BIOM table
 - KEGG Pathways: Only WoLr2, contains the functional profile
 - KEGG Ontology (KO): Only WoLr2, contains the functional profile
 - KEGG Enzyme (EZ): Only WoLr2, contains the functional profile

qiita_pet/webserver.py

@@ -69,7 +69,7 @@
 from qiita_db.handlers.user import UserInfoDBHandler, UsersListDBHandler
 from qiita_db.handlers.prep_template import (
     PrepTemplateDataHandler, PrepTemplateAPItestHandler,
-    PrepTemplateDBHandler)
+    PrepTemplateAPIHandler, PrepTemplateDBHandler)
 from qiita_db.handlers.oauth2 import TokenAuthHandler
 from qiita_db.handlers.reference import ReferenceHandler
 from qiita_db.handlers.core import ResetAPItestHandler
@@ -167,6 +167,7 @@ def __init__(self):
             (r"/prep_template/(.*)/graph/", PrepTemplateGraphHandler),
             (r"/prep_template/(.*)/jobs/", PrepTemplateJobHandler),
             (r"/ontology/", OntologyHandler),
+
             # ORDER FOR /study/description/ SUBPAGES HERE MATTERS.
             # Same reasoning as below. /study/description/(.*) should be last.
             (r"/study/description/sample_template/overview/",
@@ -224,6 +225,7 @@ def __init__(self):
             (r"/qiita_db/sample_information/(.*)/data/", SampleInfoDBHandler),
             (r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
             (r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
+            (r"/qiita_db/prep_template/", PrepTemplateAPIHandler),
             (r"/qiita_db/references/(.*)/", ReferenceHandler),
             (r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/activate/",
              CommandActivateHandler),