fix #2258

qiita_pet/handlers/analysis_handlers/sharing_handlers.py

@@ -49,8 +49,7 @@ def _unshare(self, analysis, user, callback):
     def get(self):
         analysis_id = int(self.get_argument('id'))
         analysis = Analysis(analysis_id)
-        if self.current_user != analysis.owner and \
-           self.current_user not in analysis.shared_with:
+        if not analysis.has_access(self.current_user):
             raise HTTPError(403, 'User %s does not have permissions to share '
                             'analysis %s' % (
                                 self.current_user.id, analysis.id))

qiita_pet/handlers/analysis_handlers/tests/test_sharing_handlers.py

@@ -8,9 +8,11 @@
 
 from unittest import main
 from json import loads
+from mock import Mock
 
 from qiita_db.analysis import Analysis
 from qiita_db.user import User
+from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 
 
@@ -49,6 +51,15 @@ def test_get(self):
             'Analysis <a href="/analysis/description/1">\'SomeAnalysis\'</a> '
             'has been shared with you.', u.messages()[0][1])
 
+        # admins can share
+        BaseHandler.get_current_user = Mock(return_value=User("admin@foo.bar"))
+        args = {'deselected': u.id, 'id': a.id}
+        response = self.get('/analysis/sharing/', args)
+        self.assertEqual(response.code, 200)
+        exp = {'users': [], 'links': ''}
+        self.assertEqual(loads(response.body), exp)
+        self.assertEqual(a.shared_with, [])
+
     def test_get_no_access(self):
         args = {'selected': 'demo@microbio.me', 'id': 2}
         response = self.get('/analysis/sharing/', args)

qiita_pet/handlers/download.py

@@ -7,7 +7,9 @@
 # -----------------------------------------------------------------------------
 
 from tornado.web import authenticated, HTTPError
+from tornado.gen import coroutine
 
+from future.utils import viewitems
 from os.path import basename, getsize, join
 from os import walk
 from datetime import datetime
@@ -17,11 +19,14 @@
 from qiita_db.study import Study
 from qiita_db.util import filepath_id_to_rel_path, get_db_files_base_dir
 from qiita_db.meta_util import validate_filepath_access_by_user
+from qiita_db.metadata_template.sample_template import SampleTemplate
+from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_core.util import execute_as_transaction, get_release_info
 
 
 class DownloadHandler(BaseHandler):
     @authenticated
+    @coroutine
     @execute_as_transaction
     def get(self, filepath_id):
         fid = int(filepath_id)
@@ -51,20 +56,36 @@ def get(self, filepath_id):
         self.finish()
 
 
-class DownloadStudyBIOMSHandler(BaseHandler):
+class BaseHandlerDownload(BaseHandler):
+    def _check_permissions(self, sid):
+        # Check general access to study
+        study_info = study_get_req(sid, self.current_user.id)
+        if study_info['status'] != 'success':
+            raise HTTPError(405, "%s: %s, %s" % (study_info['message'],
+                                                 self.current_user.email, sid))
+        return Study(sid)
+
+    def _generate_files(self, header_name, accessions, filename):
+        text = "sample_name\t%s\n%s" % (header_name, '\n'.join(
+            ["%s\t%s" % (k, v) for k, v in viewitems(accessions)]))
+
+        self.set_header('Content-Description', 'text/csv')
+        self.set_header('Expires', '0')
+        self.set_header('Cache-Control', 'no-cache')
+        self.set_header('Content-Disposition', 'attachment; '
+                        'filename=%s' % filename)
+        self.write(text)
+        self.finish()
+
+
+class DownloadStudyBIOMSHandler(BaseHandlerDownload):
     @authenticated
+    @coroutine
     @execute_as_transaction
     def get(self, study_id):
         study_id = int(study_id)
-        # Check access to study
-        study_info = study_get_req(study_id, self.current_user.id)
-
-        if study_info['status'] != 'success':
-            raise HTTPError(405, "%s: %s, %s" % (study_info['message'],
-                                                 self.current_user.email,
-                                                 str(study_id)))
+        study = self._check_permissions(study_id)
 
-        study = Study(study_id)
         basedir = get_db_files_base_dir()
         basedir_len = len(basedir) + 1
         # loop over artifacts and retrieve those that we have access to
@@ -125,6 +146,7 @@ def get(self, study_id):
 
 
 class DownloadRelease(BaseHandler):
+    @coroutine
     def get(self, extras):
         _, relpath, _ = get_release_info()
 
@@ -147,19 +169,13 @@ def get(self, extras):
         self.finish()
 
 
-class DownloadRawData(BaseHandler):
+class DownloadRawData(BaseHandlerDownload):
     @authenticated
+    @coroutine
     @execute_as_transaction
     def get(self, study_id):
         study_id = int(study_id)
-        # Check general access to study
-        study_info = study_get_req(study_id, self.current_user.id)
-        if study_info['status'] != 'success':
-            raise HTTPError(405, "%s: %s, %s" % (study_info['message'],
-                                                 self.current_user.email,
-                                                 str(study_id)))
-
-        study = Study(study_id)
+        study = self._check_permissions(study_id)
         user = self.current_user
         # Check "owner" access to the study
         if not study.has_access(user, True):
@@ -222,3 +238,32 @@ def get(self, study_id):
         self.set_header('Content-Disposition',
                         'attachment; filename=%s' % zip_fn)
         self.finish()
+
+
+class DownloadEBISampleAccessions(BaseHandlerDownload):
+    @authenticated
+    @coroutine
+    @execute_as_transaction
+    def get(self, study_id):
+        sid = int(study_id)
+        self._check_permissions(sid)
+
+        self._generate_files(
+            'sample_accession', SampleTemplate(sid).ebi_sample_accessions,
+            'ebi_sample_accessions_study_%s.tsv' % sid)
+
+
+class DownloadEBIPrepAccessions(BaseHandlerDownload):
+    @authenticated
+    @coroutine
+    @execute_as_transaction
+    def get(self, prep_template_id):
+        pid = int(prep_template_id)
+        pt = PrepTemplate(pid)
+        sid = pt.study_id
+
+        self._check_permissions(sid)
+
+        self._generate_files(
+            'experiment_accession', pt.ebi_experiment_accessions,
+            'ebi_experiment_accessions_study_%s_prep_%s.tsv' % (sid, pid))

qiita_pet/templates/study_ajax/base_info.html

@@ -134,6 +134,10 @@
   </tr>
 </table>
 
+{% if study_info['ebi_submission_status'] == 'submitted' %}
+  <a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download_ebi_accessions/samples/{{study_info['study_id']}}"><span class="glyphicon glyphicon-download-alt"></span> EBI sample accessions</a>
+{% end %}
+
 {% if share_access %}
 <a class="btn btn-default" data-toggle="modal" data-target="#share-study-modal-view" onclick="modify_sharing({{study_info['study_id']}});"><span class="glyphicon glyphicon-share"></span> Share</a>
 {% end %}

qiita_pet/templates/study_ajax/prep_summary.html

@@ -473,13 +473,14 @@ <h4>
   <div class="col-md-12">
     There are <b>{{num_samples}}</b> samples and <b>{{num_columns}}</b> columns in this preparation.</br>
     {% if is_submitted_to_ebi %}
-      <b>EBI status: </b> Submitted
+      <a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download_ebi_accessions/experiments/{{prep_id}}"><span class="glyphicon glyphicon-download-alt"></span> EBI experiment accessions</a>
     {% end %}
   </div>
 </div>
 
 {% if editable %}
   <!-- Update prep template -->
+  <hr/>
   <div class="row">
     <div class="col-md-12">
       <b>Update information:</b>
@@ -523,6 +524,7 @@ <h4>
       <button class="btn btn-info btn-sm" onclick="add_new_investigation_type_term_and_update();">Add</button>
     </div>
   </div>
+  <hr/>
 {% end %}
 
 <!-- Files graph or add artifact -->

qiita_pet/test/test_download.py

@@ -203,5 +203,75 @@ def test_download_raw_data(self):
         self.assertEqual(response.code, 405)
 
 
+class TestDownloadEBISampleAccessions(TestHandlerBase):
+
+    def setUp(self):
+        super(TestDownloadEBISampleAccessions, self).setUp()
+
+    def tearDown(self):
+        super(TestDownloadEBISampleAccessions, self).tearDown()
+
+    def test_download(self):
+        # check success
+        response = self.get('/download_ebi_accessions/samples/1')
+        exp = ("sample_name\tsample_accession\n1.SKB2.640194\tERS000008\n"
+               "1.SKM4.640180\tERS000004\n1.SKB3.640195\tERS000024\n"
+               "1.SKB6.640176\tERS000025\n1.SKD6.640190\tERS000007\n"
+               "1.SKM6.640187\tERS000022\n1.SKD9.640182\tERS000019\n"
+               "1.SKM8.640201\tERS000014\n1.SKM2.640199\tERS000015\n"
+               "1.SKD2.640178\tERS000009\n1.SKB7.640196\tERS000002\n"
+               "1.SKD4.640185\tERS000023\n1.SKB8.640193\tERS000000\n"
+               "1.SKM3.640197\tERS000018\n1.SKD5.640186\tERS000017\n"
+               "1.SKB1.640202\tERS000011\n1.SKM1.640183\tERS000025\n"
+               "1.SKD1.640179\tERS000012\n1.SKD3.640198\tERS000013\n"
+               "1.SKB5.640181\tERS000006\n1.SKB4.640189\tERS000020\n"
+               "1.SKB9.640200\tERS000016\n1.SKM9.640192\tERS000003\n"
+               "1.SKD8.640184\tERS000001\n1.SKM5.640177\tERS000005\n"
+               "1.SKM7.640188\tERS000010\n1.SKD7.640191\tERS000021")
+        self.assertEqual(response.code, 200)
+        self.assertRegexpMatches(response.body, exp)
+
+        # changing user so we can test the failures
+        BaseHandler.get_current_user = Mock(
+            return_value=User("demo@microbio.me"))
+        response = self.get('/download_ebi_accessions/samples/1')
+        self.assertEqual(response.code, 405)
+
+
+class TestDownloadEBIPrepAccessions(TestHandlerBase):
+
+    def setUp(self):
+        super(TestDownloadEBIPrepAccessions, self).setUp()
+
+    def tearDown(self):
+        super(TestDownloadEBIPrepAccessions, self).tearDown()
+
+    def test_download(self):
+        # check success
+        response = self.get('/download_ebi_accessions/experiments/1')
+        exp = ("sample_name\texperiment_accession\n1.SKB2.640194\tERX0000008\n"
+               "1.SKM4.640180\tERX0000004\n1.SKB3.640195\tERX0000024\n"
+               "1.SKB6.640176\tERX0000025\n1.SKD6.640190\tERX0000007\n"
+               "1.SKM6.640187\tERX0000022\n1.SKD9.640182\tERX0000019\n"
+               "1.SKM8.640201\tERX0000014\n1.SKM2.640199\tERX0000015\n"
+               "1.SKD2.640178\tERX0000009\n1.SKB7.640196\tERX0000002\n"
+               "1.SKD4.640185\tERX0000023\n1.SKB8.640193\tERX0000000\n"
+               "1.SKM3.640197\tERX0000018\n1.SKD5.640186\tERX0000017\n"
+               "1.SKB1.640202\tERX0000011\n1.SKM1.640183\tERX0000026\n"
+               "1.SKD1.640179\tERX0000012\n1.SKD3.640198\tERX0000013\n"
+               "1.SKB5.640181\tERX0000006\n1.SKB4.640189\tERX0000020\n"
+               "1.SKB9.640200\tERX0000016\n1.SKM9.640192\tERX0000003\n"
+               "1.SKD8.640184\tERX0000001\n1.SKM5.640177\tERX0000005\n"
+               "1.SKM7.640188\tERX0000010\n1.SKD7.640191\tERX0000021")
+        self.assertEqual(response.code, 200)
+        self.assertRegexpMatches(response.body, exp)
+
+        # changing user so we can test the failures
+        BaseHandler.get_current_user = Mock(
+            return_value=User("demo@microbio.me"))
+        response = self.get('/download_ebi_accessions/experiments/1')
+        self.assertEqual(response.code, 405)
+
+
 if __name__ == '__main__':
     main()

qiita_pet/webserver.py

@@ -47,7 +47,7 @@
 from qiita_pet.handlers.stats import StatsHandler
 from qiita_pet.handlers.download import (
     DownloadHandler, DownloadStudyBIOMSHandler, DownloadRelease,
-    DownloadRawData)
+    DownloadRawData, DownloadEBISampleAccessions, DownloadEBIPrepAccessions)
 from qiita_pet.handlers.prep_template import PrepTemplateHandler
 from qiita_pet.handlers.ontology import OntologyHandler
 from qiita_db.handlers.processing_job import (
@@ -162,8 +162,12 @@ def __init__(self):
             (r"/stats/", StatsHandler),
             (r"/download/(.*)", DownloadHandler),
             (r"/download_study_bioms/(.*)", DownloadStudyBIOMSHandler),
-            (r"/release/download/(.*)", DownloadRelease),
             (r"/download_raw_data/(.*)", DownloadRawData),
+            (r"/download_ebi_accessions/samples/(.*)",
+                DownloadEBISampleAccessions),
+            (r"/download_ebi_accessions/experiments/(.*)",
+                DownloadEBIPrepAccessions),
+            (r"/release/download/(.*)", DownloadRelease),
             (r"/vamps/(.*)", VAMPSHandler),
             (r"/redbiom/(.*)", RedbiomPublicSearch),
             # Plugin handlers - the order matters here so do not change