configs: Fix issues caught by mechanical-rob tests

11 files changed, 41 insertions, 39 deletions

diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
index 465538af..11391d69 100644
--- a/wqflask/base/data_set/utils.py
+++ b/wqflask/base/data_set/utils.py
@@ -27,7 +27,7 @@ def query_table_timestamp(dataset_type: str):
 
     # computation data and actions
     with database_connection() as conn, conn.cursor() as cursor:
-        fetch_db_name = parse_db_url(get_setting("SQL_URI"))
+        fetch_db_name = parse_db_url(get_setting(app, "SQL_URI"))
         cursor.execute(
             "SELECT UPDATE_TIME FROM "
             "information_schema.tables "
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 70afa2cc..3a52e889 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -172,13 +172,13 @@ class GeneralTrait:
         alias = 'Not available'
         if self.symbol:
             human_response = requests.get(
-                get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" +
                 self.symbol.upper())
             mouse_response = requests.get(
-                get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" +
                 self.symbol.capitalize())
             other_response = requests.get(
-                get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" +
                 self.symbol.lower())
 
             if human_response and mouse_response and other_response:
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 296bd314..600c6800 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -93,6 +93,7 @@ def init_app(app):
         TEMPDIR, child)
     WEBQTL_TMPDIR = mkdir_with_temp_dir("/gn2/")
     app.config["WEBQTL_TMPDIR"] = WEBQTL_TMPDIR
+    app.config["TMPDIR"] = WEBQTL_TMPDIR
     app.config["WEBQTL_CACHEDIR"] = mkdir_with_temp_dir(
         f"{WEBQTL_TMPDIR}cache/")
 
diff --git a/wqflask/scripts/corr_compute.py b/wqflask/scripts/corr_compute.py
index c98a66a4..c55559cd 100644
--- a/wqflask/scripts/corr_compute.py
+++ b/wqflask/scripts/corr_compute.py
@@ -8,7 +8,8 @@ import datetime
 
 from flask import g
 
-from wqflask import app
+from gn2_main import app
+
 from wqflask.user_session import UserSession
 from wqflask.correlation.show_corr_results import set_template_vars
 from wqflask.correlation.correlation_gn3_api import compute_correlation
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
index cd3af26f..1285b740 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -32,7 +32,7 @@ def query_probes_metadata(dataset, trait_list):
     if not bool(trait_list) or dataset.type != "ProbeSet":
         return []
 
-    with database_connection(get_setting("SQL_URI")) as conn:
+    with database_connection(get_setting(app, "SQL_URI")) as conn:
         with conn.cursor() as cursor:
 
             query = """
@@ -108,7 +108,7 @@ def chunk_dataset(dataset, steps, name):
                   ProbeSetXRef.ProbeSetId = ProbeSet.Id
     """.format(name)
 
-    with database_connection(get_setting("SQL_URI")) as conn:
+    with database_connection(get_setting(app, "SQL_URI")) as conn:
         with conn.cursor() as curr:
             curr.execute(query)
             traits_name_dict = dict(curr.fetchall())
@@ -132,7 +132,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list):
             sample_data=json.loads(samples_vals),
             dataset_samples=dataset.group.all_samples_ordered())
 
-        with database_connection(get_setting("SQL_URI")) as conn:
+        with database_connection(get_setting(app, "SQL_URI")) as conn:
             with conn.cursor() as curr:
                 curr.execute(
                     """
@@ -150,7 +150,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list):
     if len(trait_list) == 0:
         return {}
 
-    with database_connection(get_setting("SQL_URI")) as conn:
+    with database_connection(get_setting(app, "SQL_URI")) as conn:
         with conn.cursor() as curr:
             # fetching strain data in bulk
             query = (
@@ -186,7 +186,7 @@ def compute_top_n_lit(corr_results, target_dataset, this_trait) -> dict:
     geneid_dict = {trait_name: geneid for (trait_name, geneid)
                    in geneid_dict.items() if
                    corr_results.get(trait_name)}
-    with database_connection(get_setting("SQL_URI")) as conn:
+    with database_connection(get_setting(app, "SQL_URI")) as conn:
         return reduce(
             lambda acc, corr: {**acc, **corr},
             compute_all_lit_correlation(
@@ -260,7 +260,7 @@ def __compute_sample_corr__(
         return {}
 
     if target_dataset.type == "ProbeSet" and start_vars.get("use_cache") == "true":
-        with database_connection(get_setting("SQL_URI")) as conn:
+        with database_connection(get_setting(app, "SQL_URI")) as conn:
             file_path = fetch_text_file(target_dataset.name, conn)
             if file_path:
                 (sample_vals, target_data) = read_text_file(
@@ -341,7 +341,7 @@ def __compute_lit_corr__(
     (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
         this_trait, target_dataset)
 
-    with database_connection(get_setting("SQL_URI")) as conn:
+    with database_connection(get_setting(app, "SQL_URI")) as conn:
         return reduce(
             lambda acc, lit: {**acc, **lit},
             compute_all_lit_correlation(
diff --git a/wqflask/wqflask/templates/correlation_error_page.html b/wqflask/wqflask/templates/correlation_error_page.html
index 7d11daf0..34f4c601 100644
--- a/wqflask/wqflask/templates/correlation_error_page.html
+++ b/wqflask/wqflask/templates/correlation_error_page.html
@@ -2,10 +2,10 @@
 {%block title%}Correlation Results{%endblock%}
 
 {%block css%}
-<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
-<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
-<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
-<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/>
+<link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.css', filename='DataTables/css/jquery.dataTables.css') }}" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.css', filename='fontawesome/css/all.min.css') }}"/>
 <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
 <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {%endblock%}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 84fa4648..70b996db 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,10 +1,10 @@
 {% extends "base.html" %}
 {% block title %}Correlation Results{% endblock %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
-    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
-    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
-    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/>
+    <link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
+    <link rel="stylesheet" type="text/css" href="{{ url_for('toplevel.main_views.css', filename='fontawesome/css/all.min.css') }}"/>
     <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
@@ -131,16 +131,16 @@
 {% endblock %}
 
 {% block js %}
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='fontawesome/js/all.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='js_alt/md5.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='js_alt/underscore.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='jszip/jszip.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='js_alt/underscore.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='fontawesome/js/all.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('toplevel.main_views.js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script type="text/javascript" src="/static/new/javascript/table_functions.js"></script>
     <script type="text/javascript" src="/static/new/javascript/create_datatable.js"></script>
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index a6d9ae5e..35a58586 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,5 +1,5 @@
 <title>Loading {{ start_vars.tool_used }} Results</title>
-<link REL="stylesheet" TYPE="text/css" href="{{ url_for('css', filename='bootstrap/css/bootstrap.css') }}" />
+<link REL="stylesheet" TYPE="text/css" href="{{ url_for('toplevel.main_views.css', filename='bootstrap/css/bootstrap.css') }}" />
 <link REL="stylesheet" TYPE="text/css" href="/static/new/css/bootstrap-custom.css" />
 <form method="post" action="" name="loading_form" id="loading_form" class="form-horizontal">
   {% for key, value in start_vars.items() %}
@@ -100,8 +100,8 @@
     </div>
   </div>
 </form>
-<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
-<script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
+<script src="{{ url_for('toplevel.main_views.js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+<script src="{{ url_for('toplevel.main_views.js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
 <script  type="text/javascript">
 $('#show_full_diff').click(function() {
   if ($('#diff_table_container').is(':visible')){
diff --git a/wqflask/wqflask/templates/loading_corrs.html b/wqflask/wqflask/templates/loading_corrs.html
index 8abd5464..4772b8ce 100644
--- a/wqflask/wqflask/templates/loading_corrs.html
+++ b/wqflask/wqflask/templates/loading_corrs.html
@@ -8,7 +8,7 @@
     <meta http-equiv="refresh" content="5">
 
     <link rel="stylesheet" type="text/css"
-	  href="{{url_for('css', filename='bootstrap/css/bootstrap.css')}}" />
+	  href="{{url_for('toplevel.main_views.css', filename='bootstrap/css/bootstrap.css')}}" />
     <link rel="stylesheet" type="text/css"
 	  href="/static/new/css/bootstrap-custom.css" />
   </head>
@@ -21,8 +21,8 @@
       </div>
     </div>
 
-    <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
-    <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
+    <script src="{{ url_for('toplevel.main_views.js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+    <script src="{{ url_for('toplevel.main_views.js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
   </body>
 
 </html>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c745fce8..e8cedb95 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -63,7 +63,7 @@
                 {{ dataset.fullname }}
             </a>
 	    <br/>
-	    <a href="{{ url_for('get_dataset', name=dataset.name) }}" target="_blank">
+	    <a href="{{ url_for('toplevel.main_views.get_dataset', name=dataset.name) }}" target="_blank">
                 GN2 Link: {{ dataset.fullname }}
             </a>
         </td>
@@ -229,7 +229,7 @@
         {% endif %}
         {% if this_trait.symbol != None %}
 	<button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">(GN1) GeneWiki</button>
-        <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('{{ url_for('display_generif_page', symbol=this_trait.symbol) }}', '_blank')">(GN2) GeneWiki</button>
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('{{ url_for('toplevel.main_views.display_generif_page', symbol=this_trait.symbol) }}', '_blank')">(GN2) GeneWiki</button>
         {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
         <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
         {% endif %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 689e3436..95019219 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -876,7 +876,7 @@ def corr_compute_page():
                     })
                 jobs.run(job_id, get_setting(app, "REDIS_URL"))
 
-            return redirect(url_for("corr_compute_page", job_id=str(job_id)))
+            return redirect(url_for("toplevel.main_views.corr_compute_page", job_id=str(job_id)))
 
         job = jobs.job(
             rconn, UUID(request.args.get("job_id"))).maybe(