Merge pull request #563 from NBISweden/develop

Fix bugs with file dl for new accounts and temporary links
NBISweden · May 20, 2019 · 24032e4 · 24032e4
2 parents 2446814 + 80a7d65
commit 24032e4
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Showing 10 changed files with 52 additions and 44 deletions.
diff --git a/backend/application.py b/backend/application.py
@@ -414,6 +414,7 @@ def post(self, dataset, event, target):
         user = self.current_user
 
         if event == 'consent':
+            user.save()
             dv = (db.DatasetVersion
                     .select()
                     .join(db.Dataset)

diff --git a/backend/handlers.py b/backend/handlers.py
@@ -226,15 +226,15 @@ class AuthorizedStaticNginxFileHandler(AuthorizedHandler, BaseStaticNginxFileHan
 
 
 class TemporaryStaticNginxFileHandler(BaseStaticNginxFileHandler):
-    def get(self, dataset, hash_value, file):
+    def get(self, dataset, ds_version, hash_value, file):
         logging.debug("Want to download hash {} ({})".format(hash_value, file))
         linkhash = (db.Linkhash
                         .select()
                         .join(db.DatasetVersion)
                         .join(db.DatasetFile)
-                        .where(db.Linkhash.hash       == hash_value,
-                               db.Linkhash.expires_on >  datetime.datetime.now(),
-                               db.DatasetFile.name    == file))
+                        .where(db.Linkhash.hash == hash_value,
+                               db.Linkhash.expires_on > datetime.datetime.now(),
+                               db.DatasetFile.name == file))
         if linkhash.count() > 0:
             logging.debug("Linkhash valid")
             # Get temporary user from hash_value
@@ -243,7 +243,7 @@ def get(self, dataset, hash_value, file):
                        .join(db.Linkhash)
                        .where(db.Linkhash.hash == hash_value)
                    ).get()
-            super().get(dataset, file, user)
+            super().get(dataset, file, ds_version, user)
         else:
             logging.debug("Linkhash invalid")
             self.send_error(status_code=403)

diff --git a/backend/modules/browser/browser_handlers.py b/backend/modules/browser/browser_handlers.py
@@ -142,6 +142,7 @@ def get(self, dataset:str, gene:str, ds_version:str=None):
         gene = lookups.get_gene(dataset, gene_id, ds_version)
         if not gene:
             self.send_error(status_code=404, reason='Gene not found')
+            return
         ret['gene'] = gene
 
         # Add exons from transcript

diff --git a/backend/modules/browser/lookups.py b/backend/modules/browser/lookups.py
@@ -507,6 +507,8 @@ def get_variants_in_gene(dataset:str, gene_id:str, ds_version:str=None):
     if not dataset_version:
         return None
     gene = get_gene(dataset, gene_id, ds_version)
+    if not gene:
+        return None
 
     variants = [variant for variant in db.Variant.select()
                                                  .join(db.VariantGenes)

diff --git a/backend/modules/browser/utils.py b/backend/modules/browser/utils.py
@@ -217,7 +217,9 @@ def get_coverage_pos(dataset:str, datatype:str, item:str, ds_version:str=None):
     else:
         if datatype == 'gene':
             gene = lookups.get_gene(dataset, item)
-            transcript = lookups.get_transcript(dataset, gene['canonical_transcript'], ds_version)
+            if gene:
+                transcript = lookups.get_transcript(dataset, gene['canonical_transcript'], ds_version)
+            else: transcript = None
         elif datatype == 'transcript':
             transcript = lookups.get_transcript(dataset, item, ds_version)
         if transcript:
@@ -361,33 +363,34 @@ def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None):
             return None
         refgene = transcript['gene_id']
 
-    for variant in variants:
-        if datatype in ('gene', 'transcript'):
-            anno = None
-            if datatype == 'transcript':
-                anno = [ann for ann in variant['vep_annotations'] if ann['Feature'] == item]
-                if not anno:
-                    anno = [ann for ann in variant['vep_annotations'] if ann['Gene'] == refgene]
-            else:
-                anno = [ann for ann in variant['vep_annotations'] if ann['Gene'] == item]
-            if anno:
-                variant['vep_annotations'] = anno
-
-    add_consequence_to_variants(variants)
-
-    for variant in variants:
-        remove_extraneous_information(variant)
-
-    # Format output
-    def format_variant(variant):
-        variant['major_consequence'] = (variant['major_consequence'].replace('_variant','')
-                                        .replace('_prime_', '\'')
-                                        .replace('_', ' '))
-
-        # This is so an array values turns into a comma separated string instead
-        return {k: ", ".join(v) if isinstance(v,list) else v for k, v in variant.items()}
-
-    variants = list(map(format_variant, variants))
+    if variants:
+        for variant in variants:
+            if datatype in ('gene', 'transcript'):
+                anno = None
+                if datatype == 'transcript':
+                    anno = [ann for ann in variant['vep_annotations'] if ann['Feature'] == item]
+                    if not anno:
+                        anno = [ann for ann in variant['vep_annotations'] if ann['Gene'] == refgene]
+                else:
+                    anno = [ann for ann in variant['vep_annotations'] if ann['Gene'] == item]
+                if anno:
+                    variant['vep_annotations'] = anno
+
+        add_consequence_to_variants(variants)
+
+        for variant in variants:
+            remove_extraneous_information(variant)
+
+        # Format output
+        def format_variant(variant):
+            variant['major_consequence'] = (variant['major_consequence'].replace('_variant','')
+                                            .replace('_prime_', '\'')
+                                            .replace('_', ' '))
+
+            # This is so an array values turns into a comma separated string instead
+            return {k: ", ".join(v) if isinstance(v,list) else v for k, v in variant.items()}
+
+        variants = list(map(format_variant, variants))
 
     return {'variants': variants, 'headers': headers}
 

diff --git a/backend/route.py b/backend/route.py
@@ -41,7 +41,7 @@ def __init__(self, settings):
                                                                                          {"path": "static/"}),
             (r'/(favicon.ico)',                                                      tornado.web.StaticFileHandler,
                                                                                          {"path": "static/img/"}),
-            (r"/release/(?P<dataset>[^\/]+)/(?P<hash_value>[^\/]+)/(?P<file>[^\/]+)", handlers.TemporaryStaticNginxFileHandler,
+            (r"/release/(?P<dataset>[^\/]+)/versions/(?P<ds_version>[^/]+)/(?P<hash_value>[^\/]+)/(?P<file>[^\/]+)", handlers.TemporaryStaticNginxFileHandler,
                                                                                          {"path": "/release-files/"}),
             (r"/release/(?P<dataset>[^\/]+)/versions/(?P<ds_version>[^/]+)/(?P<file>[^\/]+)", handlers.AuthorizedStaticNginxFileHandler,
                                                                                          {"path": "/release-files/"}),

diff --git a/docs/source/backend.beacon.rst b/docs/source/backend.beacon.rst
diff --git a/docs/source/backend.rst b/docs/source/backend.rst
@@ -5,7 +5,6 @@ Backend
 
    backend.application
    backend.auth
-   backend.beacon
    backend.db
    backend.handlers
    backend.route

diff --git a/docs/source/docs.merge-accounts.md b/docs/source/docs.merge-accounts.md
@@ -0,0 +1,10 @@
+Merge accounts for Elixir AAI
+=============================
+
+It is possible to maintain the same dataset permissions with other logins (e.g. you are a dataset admin with your institutional account and want to be able to login with your ORCID account and still be an admin).
+
+To merge the accounts:
+
+1. Log in to the Perun Identity consolidator at https://perun.elixir-czech.cz/fed/gui with your account with admin access.
+2. Go to the authentication tab and click `identity consolidator >>`.
+3. Log in with your second account.
diff --git a/docs/source/docs.rst b/docs/source/docs.rst
@@ -6,3 +6,4 @@ Documentation
 
    docs.dev-setup.md
    docs.import-data.md
+   docs.merge-accounts.md