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-rw-r--r--wqflask/base/data_set/utils.py2
-rw-r--r--wqflask/base/trait.py6
-rw-r--r--wqflask/base/webqtlConfig.py1
-rw-r--r--wqflask/scripts/corr_compute.py3
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py14
-rw-r--r--wqflask/wqflask/templates/correlation_error_page.html8
-rw-r--r--wqflask/wqflask/templates/correlation_page.html28
-rw-r--r--wqflask/wqflask/templates/loading.html6
-rw-r--r--wqflask/wqflask/templates/loading_corrs.html6
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html4
-rw-r--r--wqflask/wqflask/views.py2
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(
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 12:09:20 +0000