fix #3081

qiita_db/util.py

@@ -1976,6 +1976,62 @@ def generate_analysis_list(analysis_ids, public_only=False):
     return results
 
 
+def generate_analyses_list_per_study(study_id):
+    """Get study analyses and their preparations
+
+    Parameters
+    ----------
+    study_id : int
+        The study id
+
+    Returns
+    -------
+    list of dict
+        The available analyses and their general information
+    """
+    # for speed and SQL simplicity, we are going to split the search in two
+    # queries: 1. analysis_sql: to find analyses associated with this study
+    # and the artifacts used to generate the analyses; and 2. extra_sql: each
+    # analysis details, including the artifacts (children) that belong to
+    # the analysis.
+    analysis_sql = """
+        SELECT DISTINCT analysis_id, array_agg(DISTINCT artifact_id) AS aids
+        FROM qiita.analysis_sample analysis_sample
+        WHERE sample_id IN (SELECT sample_id
+                            FROM qiita.study_sample
+                            WHERE study_id = %s)
+        GROUP BY analysis_id
+        ORDER BY analysis_id
+    """
+    extra_sql = """
+        SELECT analysis_id, analysis.name, analysis.email, analysis.dflt,
+            array_agg(DISTINCT aa.artifact_id) FILTER (
+                      WHERE aa.artifact_id IS NOT NULL) as artifact_ids,
+            ARRAY(SELECT DISTINCT prep_template_id
+                  FROM qiita.preparation_artifact
+                  WHERE artifact_id IN %s) as prep_ids,
+            array_agg(DISTINCT visibility.visibility) FILTER (
+                    WHERE aa.artifact_id IS NOT NULL) as visibility
+        FROM qiita.analysis analysis
+        LEFT JOIN qiita.analysis_artifact aa USING (analysis_id)
+        LEFT JOIN qiita.artifact artifact USING (artifact_id)
+        LEFT JOIN qiita.visibility visibility USING (visibility_id)
+        WHERE analysis_id = %s
+        GROUP BY analysis_id, analysis.name, analysis.email, analysis.dflt
+    """
+    results = []
+    with qdb.sql_connection.TRN:
+        qdb.sql_connection.TRN.add(analysis_sql, [study_id])
+        aids = qdb.sql_connection.TRN.execute_fetchindex()
+        for aid, artifact_ids in aids:
+            qdb.sql_connection.TRN.add(
+                extra_sql, [tuple(artifact_ids), aid])
+            for row in qdb.sql_connection.TRN.execute_fetchindex():
+                results.append(dict(row))
+
+    return results
+
+
 def create_nested_path(path):
     """Wraps makedirs() to make it safe to use across multiple concurrent calls.
     Returns successfully if the path was created, or if it already exists.

qiita_pet/handlers/api_proxy/__init__.py

@@ -11,7 +11,7 @@
 # Qiita API once we build it. This will be removed and replaced with API calls
 # when the API is complete.
 from .sample_template import (
-    sample_template_filepaths_get_req,
+    sample_template_filepaths_get_req, analyses_associated_with_study,
     sample_template_get_req, sample_template_meta_cats_get_req,
     sample_template_samples_get_req, sample_template_category_get_req,
     get_sample_template_processing_status)
@@ -61,6 +61,6 @@
            'list_commands_handler_get_req',
            'list_options_handler_get_req', 'workflow_handler_post_req',
            'workflow_handler_patch_req', 'workflow_run_post_req',
-           'job_ajax_get_req',
+           'job_ajax_get_req', 'analyses_associated_with_study',
            'get_sample_template_processing_status', 'user_jobs_get_req',
            'job_ajax_patch_req', 'check_access', 'check_fp']

qiita_pet/handlers/api_proxy/sample_template.py

@@ -10,6 +10,7 @@
 
 from qiita_core.util import execute_as_transaction
 from qiita_core.qiita_settings import r_client
+from qiita_db.util import generate_analyses_list_per_study
 from qiita_db.metadata_template.sample_template import SampleTemplate
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.exceptions import QiitaDBColumnError
@@ -182,6 +183,36 @@ def sample_template_category_get_req(category, samp_id, user_id):
             'values': values}
 
 
+def analyses_associated_with_study(study_id, user_id):
+    """Returns all available analyses in study_id
+
+    Parameters
+    ----------
+    study_id : int or str typecastable to int
+        Study id to get info for
+    user_id : str
+        User requesting the sample template info
+
+    Returns
+    -------
+    dict
+        Returns information in the form
+        {'status': str,
+         'message': str,
+         'values': list of [qiita_db.analysis.Analysis,
+                            prep_ids for this study]}
+    """
+    access_error = check_access(study_id, user_id)
+    if access_error:
+        return access_error
+
+    values = generate_analyses_list_per_study(study_id)
+
+    return {'status': 'success',
+            'message': '',
+            'values': values}
+
+
 def get_sample_template_processing_status(st_id):
     # Initialize variables here
     processing = False

qiita_pet/handlers/api_proxy/tests/test_sample_template.py

@@ -17,7 +17,7 @@
     sample_template_filepaths_get_req, sample_template_get_req,
     _check_sample_template_exists, sample_template_samples_get_req,
     sample_template_category_get_req, sample_template_meta_cats_get_req,
-    get_sample_template_processing_status,
+    get_sample_template_processing_status, analyses_associated_with_study,
     SAMPLE_TEMPLATE_KEY_FORMAT)
 
 
@@ -127,6 +127,30 @@ def test_sample_template_get_req_no_template(self):
                                'message': 'Sample template %d does not '
                                'exist' % self.new_study.id})
 
+    def test_analyses_associated_with_study(self):
+        obs = analyses_associated_with_study(self.new_study.id, 'test@foo.bar')
+        exp = {'status': 'success', 'message': '', 'values': []}
+        self.assertEqual(obs, exp)
+
+        obs = analyses_associated_with_study(1, 'test@foo.bar')
+        exp = {'status': 'success', 'message': '', 'values': [
+            {'analysis_id': 1, 'name': 'SomeAnalysis', 'email': 'test@foo.bar',
+             'dflt': False, 'artifact_ids': [8, 9], 'prep_ids': [1],
+             'visibility': ['sandbox']},
+            {'analysis_id': 2, 'name': 'SomeSecondAnalysis',
+             'email': 'admin@foo.bar', 'dflt': False, 'artifact_ids': None,
+             'prep_ids': [1], 'visibility': None},
+            {'analysis_id': 3, 'name': 'test@foo.bar-dflt-1',
+             'email': 'test@foo.bar', 'dflt': True, 'artifact_ids': None,
+             'prep_ids': [1], 'visibility': None}]}
+        self.assertEqual(obs, exp)
+
+        obs = analyses_associated_with_study(
+            self.new_study.id, 'shared@foo.bar')
+        exp = {'status': 'error',
+               'message': 'User does not have access to study'}
+        self.assertEqual(obs, exp)
+
     def test_get_sample_template_processing_status(self):
         key = SAMPLE_TEMPLATE_KEY_FORMAT % 1
 

qiita_pet/handlers/study_handlers/__init__.py

@@ -23,7 +23,7 @@
 from .artifact import (ArtifactGraphAJAX, NewArtifactHandler,
                        ArtifactAdminAJAX, ArtifactGetSamples, ArtifactGetInfo)
 from .sample_template import (
-    SampleTemplateHandler, SampleTemplateOverviewHandler,
+    SampleTemplateHandler, SampleTemplateOverviewHandler, AnalysesAjax,
     SampleTemplateColumnsHandler, SampleAJAX)
 
 __all__ = ['ListStudiesHandler', 'StudyApprovalList', 'ShareStudyAJAX',
@@ -36,6 +36,6 @@
            'ListCommandsHandler', 'ListOptionsHandler', 'SampleAJAX',
            'StudyDeleteAjax', 'NewPrepTemplateAjax',
            'DataTypesMenuAJAX', 'StudyFilesAJAX', 'PrepTemplateSummaryAJAX',
-           'WorkflowHandler', 'WorkflowRunHandler',
+           'WorkflowHandler', 'WorkflowRunHandler', 'AnalysesAjax',
            'JobAJAX', 'AutocompleteHandler', 'StudyGetTags', 'StudyTags',
            'Study', 'ArtifactGetSamples', 'ArtifactGetInfo']

qiita_pet/handlers/study_handlers/sample_template.py

@@ -13,6 +13,7 @@
 from tornado.web import authenticated, HTTPError
 
 from qiita_core.qiita_settings import r_client
+from qiita_pet.handlers.util import to_int
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_db.util import get_files_from_uploads_folders
 from qiita_db.study import Study
@@ -26,7 +27,7 @@
     data_types_get_req, sample_template_samples_get_req,
     prep_template_samples_get_req, study_prep_get_req,
     sample_template_meta_cats_get_req, sample_template_category_get_req,
-    get_sample_template_processing_status,
+    get_sample_template_processing_status, analyses_associated_with_study,
     check_fp)
 
 
@@ -533,3 +534,13 @@ def post(self):
                         'message': '',
                         'values': values['values']
                         })
+
+
+class AnalysesAjax(BaseHandler):
+    @authenticated
+    def get(self):
+        user_id = self.current_user.id
+        study_id = to_int(self.get_argument('study_id'))
+        result = analyses_associated_with_study(study_id, user_id)
+        self.render('study_ajax/study_analyses.html',
+                    analyses=result['values'])

qiita_pet/handlers/study_handlers/tests/test_sample_template.py

@@ -544,6 +544,15 @@ def test_get(self):
         self.assertIn(line, res.body.decode('ascii'))
 
 
+class TestAnalysesAjax(TestHandlerBase):
+    def test_get(self):
+        res = self.get("/study/analyses/", {'study_id': 1})
+        self.assertEqual(res.code, 200)
+        # making sure at least one analysis is in the page
+        line = '/analysis/description/1/'
+        self.assertIn(line, res.body.decode('ascii'))
+
+
 class TestSampleAJAX(TestHandlerBase):
 
     def test_post(self):

qiita_pet/templates/study_ajax/study_analyses.html

@@ -0,0 +1,44 @@
+{% from qiita_core.qiita_settings import qiita_config %}
+
+<script type="text/javascript" src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.validate.min.js"></script>
+<script type="text/javascript>">
+  $('#studies-analyses-table').dataTable();
+</script>
+<h3>Analyses that have used this study</h3>
+
+Note that if an analysis doesn't have a link, it means that is a "User default analysis"; which means that the analysis belongs to that user but the user has only selected artifacts and hasn't created the actual analysis. Please contact the user and ask them to delete that artifact from their analysis creation page.
+<br/><br/>
+<table id="studies-analyses-table" class="display table-bordered table-hover" style="width:100%">
+  <thead>
+    <tr>
+      <th>Analysis</th>
+      <th>Owner</th>
+      <th>Prep IDs Used</th>
+      <th>Is Public?</th>
+      <th>Artifacts in Analysis</th>
+    </tr>
+  </thead>
+  <tbody>
+    {% for a in analyses %}
+      <tr>
+        <td>
+          {% if a['dflt'] %}
+            {{a['name']}} (ID: {{a['analysis_id']}})
+          {% else %}
+            <a href="{% raw qiita_config.portal_dir %}/analysis/description/{{a['analysis_id']}}/" target="_blank">{{a['name']}} (ID: {{a['analysis_id']}})</a>
+          {% end %}
+        </td>
+        <td>{{a['email']}}</td>
+        <td>{{', '.join(map(str, a['prep_ids']))}}</td>
+        <td>{{a['visibility'] == ['public']}}</td>
+        <td>
+          {% if a['artifact_ids'] is None %}
+            0
+          {% else %}
+            {{len(a['artifact_ids'])}}
+          {% end %}
+        </td>
+      </tr>
+    {% end %}
+  </tbody>
+</table>

qiita_pet/templates/study_base.html

@@ -98,6 +98,7 @@
       {% if editable %}
         <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/study/upload/{{study_info['study_id']}}"><span class="glyphicon glyphicon-upload"></span> Upload Files</a>
         <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/new_prep_template/', { study_id: {{study_info['study_id']}} })" id="add-new-preparation-btn"><span class="glyphicon glyphicon-plus-sign"></span> Add New Preparation</button>
+        <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/analyses/', { study_id: {{study_info['study_id']}} })" id="analyses-btn"><span class="glyphicon glyphicon-info-sign"></span> Analyses using artifacts from this Study</button>
       {% end %}
       {% if study_info['show_biom_download_button'] %}
         <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/download_study_bioms/{{study_info['study_id']}}"><span class="glyphicon glyphicon-download-alt"></span> All QIIME maps and BIOMs</a>

qiita_pet/webserver.py

@@ -37,7 +37,7 @@
     ListCommandsHandler, ListOptionsHandler, PrepTemplateSummaryAJAX,
     PrepTemplateAJAX, NewArtifactHandler, SampleAJAX, StudyDeleteAjax,
     ArtifactAdminAJAX, NewPrepTemplateAjax, DataTypesMenuAJAX, StudyFilesAJAX,
-    ArtifactGetSamples, ArtifactGetInfo, WorkflowHandler,
+    ArtifactGetSamples, ArtifactGetInfo, WorkflowHandler, AnalysesAjax,
     WorkflowRunHandler, JobAJAX, AutocompleteHandler)
 from qiita_pet.handlers.artifact_handlers import (
     ArtifactSummaryAJAX, ArtifactAJAX, ArtifactSummaryHandler)
@@ -144,6 +144,7 @@ def __init__(self):
             (r"/study/sharing/", ShareStudyAJAX),
             (r"/study/sharing/autocomplete/", AutocompleteHandler),
             (r"/study/new_prep_template/", NewPrepTemplateAjax),
+            (r"/study/analyses/", AnalysesAjax),
             (r"/study/tags/(.*)", StudyTags),
             (r"/study/get_tags/", StudyGetTags),
             (r"/study/([0-9]+)$", Study),