adding GUI access to users for software (#3019)

Author: antgonza

qiita_db/software.py

@@ -705,6 +705,40 @@ def merging_scheme(self):
                     'outputs': outputs,
                     'ignore_parent_command': ipc}
 
+    @property
+    def resource_allocation(self):
+        """The resource allocation defined in the database for this command
+
+        Returns
+        -------
+        str
+        """
+
+        with qdb.sql_connection.TRN:
+            sql = """SELECT allocation FROM
+                     qiita.processing_job_resource_allocation
+                     WHERE name = %s and
+                        job_type = 'RESOURCE_PARAMS_COMMAND'"""
+            qdb.sql_connection.TRN.add(sql, [self.name])
+
+            result = qdb.sql_connection.TRN.execute_fetchflatten()
+
+            # if no matches for both type and name were found, query the
+            # 'default' value for the type
+
+            if not result:
+                sql = """SELECT allocation FROM
+                         qiita.processing_job_resource_allocation WHERE
+                         name = %s and job_type = 'RESOURCE_PARAMS_COMMAND'"""
+                qdb.sql_connection.TRN.add(sql, ['default'])
+
+                result = qdb.sql_connection.TRN.execute_fetchflatten()
+                if not result:
+                    raise ValueError("Could not match '%s' to a resource "
+                                     "allocation!" % self.name)
+
+        return result[0]
+
 
 class Software(qdb.base.QiitaObject):
     r"""A software package available in the system

qiita_db/test/test_software.py

@@ -463,6 +463,30 @@ def test_iter(self):
         obs = list(qdb.software.Software.iter(False))
         self.assertEqual(obs, [s1, s2, s3, s4])
 
+        # test command resouce allocations here to be able to delete
+        # allocations so we can tests errors.
+
+        # Command 2 is Split libraries and has defined resources
+        self.assertEqual(
+            qdb.software.Command(2).resource_allocation,
+            '-q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=25:00:00')
+
+        # Command 9 is Summarize Taxa and has no defined resources so it goes
+        # to defaults
+        self.assertEqual(
+            qdb.software.Command(9).resource_allocation,
+            '-q qiita -l nodes=1:ppn=5 -l pmem=8gb -l walltime=168:00:00')
+
+        # delete allocations to test errors
+        with qdb.sql_connection.TRN:
+            qdb.sql_connection.TRN.add(
+                "DELETE FROM qiita.processing_job_resource_allocation")
+            qdb.sql_connection.TRN.execute()
+
+        with self.assertRaisesRegex(ValueError, "Could not match 'Split "
+                                    "libraries' to a resource allocation!"):
+            qdb.software.Command(2).resource_allocation
+
 
 @qiita_test_checker()
 class SoftwareTests(TestCase):

qiita_pet/handlers/software.py

@@ -6,23 +6,21 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from tornado.gen import coroutine
-from tornado.web import HTTPError
 
 from qiita_core.util import execute_as_transaction
 from qiita_db.software import Software
 from .base_handlers import BaseHandler
 
 
 class SoftwareHandler(BaseHandler):
-    def check_access(self):
-        if self.current_user.level not in {'admin', 'dev'}:
-            raise HTTPError(403, reason="User %s doesn't have sufficient "
-                            "privileges to view error page" %
-                            self.current_user.email)
-
     @coroutine
     @execute_as_transaction
     def get(self):
-        self.check_access()
-        software = Software.iter(False)
+        # active True will only show active software
+        active = True
+        user = self.current_user
+        if user is not None and user.level in {'admin', 'dev'}:
+            active = False
+
+        software = Software.iter(active=active)
         self.render("software.html", software=software)

qiita_pet/templates/sitebase.html

@@ -370,7 +370,6 @@
                 <a href="#" data-toggle="dropdown" class="dropdown-toggle">Admin<b class="caret"></b></a>
                 <ul class="dropdown-menu">
                   {% if qiita_config.portal == "QIITA" %}
-                  <li><a href="{% raw qiita_config.portal_dir %}/admin/software/">Available Software</a></li>
                   <li><a href="{% raw qiita_config.portal_dir %}/admin/error/">View Errors</a></li>
                   <li><a href="{% raw qiita_config.portal_dir %}/admin/approval/">View Studies awaiting approval</a></li>
                   <li><a href="{% raw qiita_config.portal_dir %}/admin/portals/studies/">Edit study portal connections</a></li>
@@ -483,6 +482,9 @@
                   <li>
                     <a href="{% raw qiita_config.portal_dir %}/stats/">Stats</a>
                   </li>
+                  <li>
+                    <a href="{% raw qiita_config.portal_dir %}/software/">Available Software</a>
+                  </li>
                   <li>
                     <a href="http://github.com/biocore/qiita">GitHub</a>
                   </li>

qiita_pet/templates/software.html

@@ -13,11 +13,16 @@
 
 {% block content %}
   {% if software %}
-    <h3>Available plugins</h3>
+    <h3>Available Software</h3>
+
+    <h5>
+      <a href="https://qiita.ucsd.edu/static/doc/html/processingdata/processing-recommendations.html">Here</a> you will find our current processing recommendations.
+    </h5>
+
     <table class="table-bordered" width="50%">
       <thead>
         <tr>
-          <th>Software</th>
+          <th>Plugin</th>
           <th>Commands</th>
         </tr>
       </thead>
@@ -38,6 +43,12 @@ <h3>Available plugins</h3>
           </td>
           <td>
             <table class="display table-bordered table-hover" width="100%">
+              <thead>
+                <tr>
+                  <th>Command Name</th>
+                  <th>Resource Allocation</th>
+                </tr>
+              </thead>
               <tbody>
                 {% for c in s.commands %}
                   <tr>
@@ -49,6 +60,7 @@ <h3>Available plugins</h3>
                       {% end %}
                       ID {{c.id}}: {{c.name}}
                     </td>
+                    <td>{{c.resource_allocation}}</td>
                   </tr>
                 {% end %}
               </tbody>

qiita_pet/test/test_software.py

@@ -17,13 +17,20 @@
 
 class TestSoftware(TestHandlerBase):
     def test_get(self):
-        response = self.get('/admin/software/')
-        self.assertEqual(response.code, 403)
+        response = self.get('/software/')
+        self.assertEqual(response.code, 200)
+        body = response.body.decode('ascii')
+        self.assertNotEqual(body, "")
+        # checking that this software is not displayed
+        self.assertNotIn('Target Gene', body)
 
         BaseHandler.get_current_user = Mock(return_value=User("[email protected]"))
-        response = self.get('/admin/software/')
+        response = self.get('/software/')
         self.assertEqual(response.code, 200)
-        self.assertNotEqual(response.body, "")
+        body = response.body.decode('ascii')
+        self.assertNotEqual(body, "")
+        # checking that this software is displayed
+        self.assertIn('Target Gene', body)
 
 
 if __name__ == "__main__":

qiita_pet/webserver.py

@@ -126,7 +126,6 @@ def __init__(self):
             (r"/admin/error/", LogEntryViewerHandler),
             (r"/admin/approval/", StudyApprovalList),
             (r"/admin/artifact/", ArtifactAdminAJAX),
-            (r"/admin/software/", SoftwareHandler),
             (r"/ebi_submission/(.*)", EBISubmitHandler),
             # Study handlers
             (r"/study/create/", StudyEditHandler),
@@ -177,6 +176,7 @@ def __init__(self):
             (r"/upload/", UploadFileHandler),
             (r"/check_study/", CreateStudyAJAX),
             (r"/stats/", StatsHandler),
+            (r"/software/", SoftwareHandler),
             (r"/download/(.*)", DownloadHandler),
             (r"/download_study_bioms/(.*)", DownloadStudyBIOMSHandler),
             (r"/download_raw_data/(.*)", DownloadRawData),