fix #2622

qiita_db/software.py

@@ -682,13 +682,24 @@ class Software(qdb.base.QiitaObject):
     _table = "software"
 
     @classmethod
-    def iter_active(cls):
-        """Iterates over all active software"""
+    def iter(cls, active=True):
+        """Iterates over all active software
+
+        Parameters
+        ----------
+        active : bool, optional
+            If True will only return active software
+
+        Returns
+        -------
+        list of qiita_db.software.Software
+            The software objects
+        """
+        sql = """SELECT software_id
+                 FROM qiita.software {0}
+                 ORDER BY software_id""".format(
+                    'WHERE active = True' if active else '')
         with qdb.sql_connection.TRN:
-            sql = """SELECT software_id
-                     FROM qiita.software
-                     WHERE active = True
-                     ORDER BY software_id"""
             qdb.sql_connection.TRN.add(sql)
             for s_id in qdb.sql_connection.TRN.execute_fetchflatten():
                 yield cls(s_id)

qiita_db/test/test_software.py

@@ -397,31 +397,44 @@ def test_activate(self):
 
 
 @qiita_test_checker()
-class SoftwareTests(TestCase):
-    def setUp(self):
-        self._clean_up_files = []
+class SoftwareTestsIter(TestCase):
+    # different class to assure integrity of database
 
-    def tearDown(self):
-        for f in self._clean_up_files:
-            if exists(f):
-                remove(f)
+    def test_iter(self):
+        s1 = qdb.software.Software(1)
+        s2 = qdb.software.Software(2)
+        s3 = qdb.software.Software(3)
+        s4 = qdb.software.Software(4)
 
-    def test_iter_active(self):
         qdb.software.Software.deactivate_all()
-        obs = list(qdb.software.Software.iter_active())
+        obs = list(qdb.software.Software.iter())
         self.assertEqual(obs, [])
+        obs = list(qdb.software.Software.iter(False))
+        self.assertEqual(obs, [s1, s2, s3, s4])
 
-        s2 = qdb.software.Software(2)
         s2.activate()
-        obs = list(qdb.software.Software.iter_active())
+        obs = list(qdb.software.Software.iter())
         self.assertEqual(obs, [s2])
+        obs = list(qdb.software.Software.iter(False))
+        self.assertEqual(obs, [s1, s2, s3, s4])
 
-        s1 = qdb.software.Software(1)
-        s3 = qdb.software.Software(3)
         s1.activate()
         s3.activate()
-        obs = list(qdb.software.Software.iter_active())
+        obs = list(qdb.software.Software.iter())
         self.assertEqual(obs, [s1, s2, s3])
+        obs = list(qdb.software.Software.iter(False))
+        self.assertEqual(obs, [s1, s2, s3, s4])
+
+
+@qiita_test_checker()
+class SoftwareTests(TestCase):
+    def setUp(self):
+        self._clean_up_files = []
+
+    def tearDown(self):
+        for f in self._clean_up_files:
+            if exists(f):
+                remove(f)
 
     def test_from_name_and_version(self):
         obs = qdb.software.Software.from_name_and_version('QIIME', '1.9.1')

qiita_pet/handlers/software.py

@@ -0,0 +1,31 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from __future__ import division
+
+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(405, reason="User %s doesn't have sufficient "
+                            "privileges to view error page" %
+                            self.current_user)
+
+    @coroutine
+    @execute_as_transaction
+    def get(self):
+        self.check_access()
+        software = Software.iter(False)
+        self.render("software.html", software=software)

qiita_pet/templates/sitebase.html

@@ -384,6 +384,7 @@
                 <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>

qiita_pet/templates/software.html

@@ -0,0 +1,69 @@
+{% extends sitebase.html %}
+{% block head %}
+{% from future.utils import viewitems %}
+{% from qiita_core.qiita_settings import qiita_config %}
+
+<script type="text/javascript">
+$(document).ready(function() {
+    $('#error-table').dataTable({"order": [[1, "asc"]]});
+    $("#waiting").hide();
+} );
+</script>
+
+{% end %}
+
+{% block content %}
+  {% if software %}
+    <table class="table-bordered" width="100%">
+      <thead>
+        <tr>
+          <th>Software</th>
+          <th>Active</th>
+          <th>Commands</th>
+        </tr>
+      </thead>
+      <tbody>
+      {% for s in software %}
+        <tr>
+          <td>{{s.name}}, {{s.version}}</td>
+          <td>
+            {% if s.active %}
+              <span class="glyphicon glyphicon-thumbs-up" style="color:green"></span>
+            {% else %}
+              <span class="glyphicon glyphicon-thumbs-down" style="color:red"></span>
+            {% end %}
+          </td>
+          <td>
+            <table class="display table-bordered table-hover" width="100%">
+              <thead>
+                <tr>
+                  <th>Command</th>
+                  <th>Active</th>
+                </tr>
+              </thead>
+              <tbody>
+                {% for c in s.commands %}
+                  <tr>
+                    <td>{{c.name}}</td>
+                    <td>
+                      {% if c.active %}
+                        <span class="glyphicon glyphicon-thumbs-up" style="color:green"></span>
+                      {% else %}
+                        <span class="glyphicon glyphicon-thumbs-down" style="color:red"></span>
+                      {% end %}
+                    </td>
+                  </tr>
+                {% end %}
+              </tbody>
+            </table>
+          </td>
+        </tr>
+      {% end %}
+      </tbody>
+    </table>
+  {% else %}
+      <div id="jumbotron" class="jumbotron">
+          <h1><span class="glyphicon glyphicon-thumbs-down"></span> There is no plugin software in this system </h1>
+      </div>
+  {% end %}
+{% end %}

qiita_pet/test/test_software.py

@@ -0,0 +1,30 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from unittest import main
+from qiita_pet.test.tornado_test_base import TestHandlerBase
+
+from mock import Mock
+
+from qiita_db.user import User
+from qiita_pet.handlers.base_handlers import BaseHandler
+
+
+class TestSoftware(TestHandlerBase):
+    def test_get(self):
+        response = self.get('/admin/software/')
+        self.assertEqual(response.code, 405)
+
+        BaseHandler.get_current_user = Mock(return_value=User("admin@foo.bar"))
+        response = self.get('/admin/software/')
+        self.assertEqual(response.code, 200)
+        self.assertNotEqual(response.body, "")
+
+
+if __name__ == "__main__":
+    main()

qiita_pet/webserver.py

@@ -53,6 +53,7 @@
 from qiita_pet.handlers.prep_template import (
     PrepTemplateHandler, PrepTemplateGraphHandler, PrepTemplateJobHandler)
 from qiita_pet.handlers.ontology import OntologyHandler
+from qiita_pet.handlers.software import SoftwareHandler
 from qiita_db.handlers.processing_job import (
     JobHandler, HeartbeatHandler, ActiveStepHandler, CompleteHandler,
     ProcessingJobAPItestHandler)
@@ -122,6 +123,7 @@ 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),

scripts/qiita

@@ -311,7 +311,7 @@ def start(port, master):
 
     if master:
         def callback_function():
-            active_software = list(qdb.software.Software.iter_active())
+            active_software = list(qdb.software.Software.iter())
             sdefinition = [s for s in active_software
                            if s.type == 'artifact definition']
             stransformation = [s for s in active_software