Base for new study page

qiita_db/study.py

@@ -166,6 +166,18 @@ def status(self):
             return qdb.util.infer_status(
                 qdb.sql_connection.TRN.execute_fetchindex())
 
+    @staticmethod
+    def all_data_types():
+        """Returns list of all the data types available in the system
+        Returns
+        -------
+        list of str
+        """
+        with qdb.sql_connection.TRN:
+            sql = "SELECT DISTINCT data_type FROM qiita.data_type"
+            qdb.sql_connection.TRN.add(sql)
+            return qdb.sql_connection.TRN.execute_fetchflatten()
+
     @classmethod
     def get_by_status(cls, status):
         """Returns study id for all Studies with given status
@@ -500,9 +512,23 @@ def info(self):
             # remove non-info items from info
             for item in self._non_info:
                 info.pop(item)
-            # This is an optional column, but should not be considered part
-            # of the info
+            # removed because redundant to the id already stored in the object
             info.pop('study_id')
+
+            if info['principal_investigator_id']:
+                info['principal_investigator'] = qdb.study.StudyPerson(
+                    info["principal_investigator_id"])
+            else:
+                info['principal_investigator'] = None
+            del info['principal_investigator_id']
+
+            if info['lab_person_id']:
+                info['lab_person'] = qdb.study.StudyPerson(
+                    info["lab_person_id"])
+            else:
+                info['lab_person'] = None
+            del info['lab_person_id']
+
             return info
 
     @info.setter

qiita_pet/handlers/api_proxy.py

@@ -0,0 +1,117 @@
+# -----------------------------------------------------------------------------
+# 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
+
+# This is the only file in qiita_pet that should import from outside qiita_pet
+# The idea is that this proxies the call and response dicts we expect from the
+# QIITA API once we build it. This will be removed and replaced with API calls
+# when the API is complete.
+from qiita_core.qiita_settings import qiita_config
+from qiita_db.study import Study
+
+from qiita_pet.handlers.base_handlers import BaseHandler
+from qiita_pet.handlers.util import check_access
+
+html_error_message = "<b>An error occurred %s %s</b></br>%s"
+
+
+def _approve(level):
+    """Check if the study can be approved based on user level and configuration
+
+    Parameters
+    ----------
+    level : str
+        The level of the current user
+
+    Returns
+    -------
+    bool
+        Whether the study can be approved or not
+    """
+    return True if not qiita_config.require_approval else level == 'admin'
+
+
+class StudyAPIProxy(BaseHandler):
+    """Adds API proxy functions to the handler. Can be removed once the restful
+       API is in place."""
+    def study_prep_proxy(self, study_id):
+        """Proxies expected json from the API for existing prep templates
+
+        Parameters
+        ----------
+        study_id : int
+            Study id to get prep template info for
+
+        Returns:
+        dict of list of dict
+            prep template information seperated by data type, in the form
+            {data_type: [{prep 1 info dict}, ....], ...}
+        """
+        # Can only pass ids over API, so need to instantiate object
+        study = Study(study_id)
+        check_access(self.current_user, study, raise_error=True)
+        prep_info = {}
+        for dtype in study.data_types:
+            prep_info[dtype] = []
+            for prep in study.prep_templates(dtype):
+                start_artifact = prep.artifact
+                info = {
+                    'name': 'PREP %d NAME' % prep.id,
+                    'id': prep.id,
+                    'status': prep.status,
+                    'start_artifact': start_artifact.artifact_type,
+                    'start_artifact_id': start_artifact.id,
+                    'last_artifact': 'TODO new gui'
+                }
+                prep_info[dtype].append(info)
+        return prep_info
+
+    def study_data_types_proxy(self):
+        """Proxies expected json from the API for available data types
+
+        Returns
+        -------
+        list of str
+            Data types available on the system
+        """
+        data_types = Study.all_data_types()
+        return data_types if data_types else []
+
+    def study_info_proxy(self, study_id):
+        """Proxies expected json from the API for base study info
+
+        Parameters
+        ----------
+        study_id : int
+            Study id to get prep template info for
+
+        Returns:
+        dict of list of dict
+            prep template information seperated by data type, in the form
+            {data_type: [{prep 1 info dict}, ....], ...}
+        """
+        # Can only pass ids over API, so need to instantiate object
+        study = Study(study_id)
+        check_access(self.current_user, study, raise_error=True)
+        study_info = study.info
+        # Add needed info that is not part of the initial info pull
+        study_info['publications'] = study.publications
+        study_info['study_id'] = study.id
+        study_info['study_title'] = study.title
+
+        # Clean up StudyPerson objects to string for display
+        pi = study_info["principal_investigator"]
+        study_info["principal_investigator"] = '%s (%s)' % (pi.name,
+                                                            pi.affiliation)
+        lab_person = study_info["lab_person"]
+        study_info["lab_person"] = '%s (%s)' % (lab_person.name,
+                                                lab_person.affiliation)
+
+        samples = study.sample_template.keys()
+        study_info['num_samples'] = 0 if samples is None else len(set(samples))
+        return study_info

qiita_pet/handlers/study_handlers/__init__.py

@@ -14,8 +14,10 @@
 from .ebi_handlers import EBISubmitHandler
 from .metadata_summary_handlers import MetadataSummaryHandler
 from .vamps_handlers import VAMPSHandler
+from .base import StudyIndexHandler, StudyBaseInfoAJAX
 
 __all__ = ['ListStudiesHandler', 'StudyApprovalList', 'ShareStudyAJAX',
            'StudyEditHandler', 'CreateStudyAJAX', 'StudyDescriptionHandler',
            'PreprocessingSummaryHandler', 'EBISubmitHandler',
-           'MetadataSummaryHandler', 'VAMPSHandler', 'SearchStudiesAJAX']
+           'MetadataSummaryHandler', 'VAMPSHandler', 'SearchStudiesAJAX',
+           'StudyIndexHandler', 'StudyBaseInfoAJAX']

qiita_pet/handlers/study_handlers/base.py

@@ -0,0 +1,41 @@
+# -----------------------------------------------------------------------------
+# 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.web import authenticated
+
+from qiita_pet.handlers.util import to_int, doi_linkifier
+# ONLY IMPORT FROM qiita_pet HERE. All other imports must be made in
+# api_proxy.py so they will be removed when we get the API in place.
+from qiita_pet.handlers.api_proxy import StudyAPIProxy
+
+
+class StudyIndexHandler(StudyAPIProxy):
+    @authenticated
+    def get(self, study_id):
+        study = to_int(study_id)
+        # Proxies for what will become API requests
+        prep_info = self.study_prep_proxy(study)
+        data_types = self.study_data_types_proxy()
+        study_info = self.study_info_proxy(study)
+
+        self.render("study_base.html", prep_info=prep_info,
+                    data_types=data_types, study_info=study_info)
+
+
+class StudyBaseInfoAJAX(StudyAPIProxy):
+    @authenticated
+    def get(self):
+        study = to_int(self.get_argument('study_id'))
+        # Proxy for what will become API request
+        study_info = self.study_info_proxy(study)
+        study_doi = ' '.join(
+            [doi_linkifier(p) for p in study_info['publications']])
+
+        self.render('study_ajax/base_info.html',
+                    study_info=study_info, publications=study_doi)

qiita_pet/handlers/util.py

@@ -64,3 +64,28 @@ def download_link_or_path(is_local_request, filepath, fp_id, label):
 
 doi_linkifier = partial(
     linkify, "<a target=\"_blank\" href=\"http://dx.doi.org/{0}\">{0}</a>")
+
+
+def to_int(value):
+    """Transforms `value` to an integer
+
+    Parameters
+    ----------
+    value : str or int
+        The value to transform
+
+    Returns
+    -------
+    int
+        `value` as an integer
+
+    Raises
+    ------
+    HTTPError
+        If `value` cannot be transformed to an integer
+    """
+    try:
+        res = int(value)
+    except ValueError:
+        raise HTTPError(500, "%s cannot be converted to an integer" % value)
+    return res

qiita_pet/templates/study_ajax/base_info.html

@@ -0,0 +1,7 @@
+<p style="font-weight:bold;">Abstract</p>
+<p>{{study_info['study_abstract']}}</p>
+Study ID:  {{study_info['study_id']}}<br />
+Publications: {% raw publications %}<br />
+PI: {{study_info['principal_investigator']}}<br />
+Lab Contact: {{study_info['lab_person']}}<br />
+Samples: {{study_info['num_samples']}}

qiita_pet/templates/study_base.html

@@ -0,0 +1,72 @@
+{% extends sitebase.html %}
+{% block head %}
+<script type="text/javascript">
+  function fill_base(sid) {
+  $.get( "/study/description/baseinfo/", { study_id: sid} )
+    .done(function( data ) {
+      $("#study-main").html(data);
+      $("#study-prep-graph").hide();
+      $("#study-file-breadcrumbs").hide();
+    });
+  }
+
+  $(document).ready(function() {
+    fill_base({{study_info['study_id']}});
+  });
+</script>
+{% end %}
+{% block content %}
+<div class="row">
+  <div class="col-md-3">
+  <h3>Study Information</h3>
+    <a href="#">Sample Template</a><br />
+    <a href="#">Sample Summary</a><br />
+    <a href="/study/upload/{{study_info['study_id']}}">Upload Files</a><br />
+    <a href="#">Edit Study Information</a><br />
+    <a href="#">Delete Study</a>
+
+    <h3>Data Types</h3>
+    <div class="panel-group" id="accordion" role="tablist" aria-multiselectable="true">
+      <div class="panel panel-default">
+      {% for dt in prep_info %}
+      {% set cleaned_dt = dt.replace(' ', '_') %}
+        <div class="panel-heading" role="tab" id="heading{{cleaned_dt}}">
+          <h4 class="panel-title">
+            <a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapse{{cleaned_dt}}" aria-expanded="true" aria-controls="collapse{{cleaned_dt}}">{{dt}}</a>
+          </h4>
+        </div>
+        {% end %}
+        {% for prep in prep_info[dt] %}
+        <div id="collapse{{cleaned_dt}}" class="panel-collapse collapse" role="tabpanel" aria-labelledby="heading{{cleaned_dt}}">
+          <div class="panel-body">
+            <a href="#" style="display:block;color:black;">
+            {{prep['name']}} - ID {{prep['id']}} - {{prep['status']}}<br/>
+            {{prep['start_artifact']}} - ID {{prep['start_artifact_id']}}<br/>
+            {{prep['last_artifact']}}
+            </a>
+          </div>
+        </div>
+        {% end %}
+      </div>
+    </div>
+  </div>
+  <div class="col-md-9">
+    <div class="row">
+      <div class="col-md-12" id="study-base-info">
+        <h2>{{study_info['study_title']}} - ID {{study_info['study_id']}}</h2>
+        <h3>{{study_info['study_alias']}}</h3>
+      </div>
+    </div>
+    {% if user_level == 'admin' %}
+    <div class="row">
+      <div class="col-md-12" id="study-admin">
+        ADMIN STUFF HERE
+      </div>
+    </div>
+    {% end %}
+    <div class="row"><div class="col-md-12" id="study-prep-graph"></div></div>
+    <div class="row"><div class="col-md-12" id="study-file-breadcrumbs"></div></div>
+    <div class="row"><div class="col-md-12" id="study-main"></div></div>
+  </div>
+</div>
+{% end %}

qiita_pet/webserver.py

@@ -22,6 +22,7 @@
     ShowAnalysesHandler, ResultsHandler, SelectedSamplesHandler,
     AnalysisSummaryAJAX)
 from qiita_pet.handlers.study_handlers import (
+    StudyIndexHandler, StudyBaseInfoAJAX,
     StudyEditHandler, ListStudiesHandler, SearchStudiesAJAX,
     StudyDescriptionHandler, MetadataSummaryHandler, EBISubmitHandler,
     CreateStudyAJAX, ShareStudyAJAX, StudyApprovalList,
@@ -103,7 +104,10 @@ def __init__(self):
             (r"/study/preprocess", PreprocessHandler),
             (r"/study/process", ProcessHandler),
             (r"/study/sharing/", ShareStudyAJAX),
-            (r"/study/description/(.*)", StudyDescriptionHandler),
+            # ORDER FOR /study/description/ SUBPAGES HERE MATTERS.
+            # Same reasoning as below. /study/description/(.*) should be last.
+            (r"/study/description/baseinfo/", StudyBaseInfoAJAX),
+            (r"/study/description/(.*)", StudyIndexHandler),
             (r"/study/upload/(.*)", StudyUploadFileHandler),
             (r"/upload/", UploadFileHandler),
             (r"/check_study/", CreateStudyAJAX),