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-rw-r--r--wqflask/base/data_set/dataset.py90
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py4
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py27
-rw-r--r--wqflask/wqflask/database.py8
-rw-r--r--wqflask/wqflask/db_info.py128
-rw-r--r--wqflask/wqflask/metadata_edits.py9
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css17
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu.js169
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js253
-rw-r--r--wqflask/wqflask/templates/correlation_page.html4
-rw-r--r--wqflask/wqflask/templates/edit_probeset.html33
-rw-r--r--wqflask/wqflask/templates/search_result_page.html6
-rw-r--r--wqflask/wqflask/templates/show_metadata_details.html186
-rw-r--r--wqflask/wqflask/templates/show_trait.html14
-rw-r--r--wqflask/wqflask/views.py15
15 files changed, 404 insertions, 559 deletions
diff --git a/wqflask/base/data_set/dataset.py b/wqflask/base/data_set/dataset.py
index 69c842ad..dfe09921 100644
--- a/wqflask/base/data_set/dataset.py
+++ b/wqflask/base/data_set/dataset.py
@@ -2,13 +2,15 @@
import math
import collections
-
+import itertools
from redis import Redis
-
+from MySQLdb.cursors import DictCursor
from base import species
from utility import chunks
+from gn3.monads import MonadicDict, query_sql
+from pymonad.maybe import Maybe, Nothing
from .datasetgroup import DatasetGroup
from wqflask.database import database_connection
from utility.db_tools import escape, mescape, create_in_clause
@@ -30,7 +32,7 @@ class DataSet:
self.fullname = None
self.type = None
self.data_scale = None # ZS: For example log2
- self.accession_id = None
+ self.accession_id = Nothing
self.setup()
@@ -47,50 +49,58 @@ class DataSet:
self.group.get_samplelist(redis_conn)
self.species = species.TheSpecies(dataset=self)
- def as_dict(self):
- return {
+ def as_monadic_dict(self):
+ _result = MonadicDict({
'name': self.name,
'shortname': self.shortname,
'fullname': self.fullname,
'type': self.type,
'data_scale': self.data_scale,
- 'group': self.group.name,
- 'accession_id': self.accession_id
- }
-
- def get_accession_id(self):
- results = None
- with database_connection() as conn, conn.cursor() as cursor:
+ 'group': self.group.name
+ })
+ _result["accession_id"] = self.accession_id
+ return _result
+
+ def get_accession_id(self) -> Maybe[str]:
+ """Get the accession_id of this dataset depending on the
+ dataset type."""
+ __accession_id_dict = MonadicDict()
+ with database_connection() as conn:
if self.type == "Publish":
- cursor.execute(
- "SELECT InfoFiles.GN_AccesionId FROM "
- "InfoFiles, PublishFreeze, InbredSet "
- "WHERE InbredSet.Name = %s AND "
- "PublishFreeze.InbredSetId = InbredSet.Id "
- "AND InfoFiles.InfoPageName = PublishFreeze.Name "
- "AND PublishFreeze.public > 0 AND "
- "PublishFreeze.confidentiality < 1 "
- "ORDER BY PublishFreeze.CreateTime DESC",
- (self.group.name,)
- )
- results = cursor.fetchone()
+ __accession_id_dict, = itertools.islice(
+ query_sql(conn,
+ ("SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
+ "InfoFiles, PublishFreeze, InbredSet "
+ f"WHERE InbredSet.Name = '{conn.escape_string(self.group.name).decode()}' "
+ "AND PublishFreeze.InbredSetId = InbredSet.Id "
+ "AND InfoFiles.InfoPageName = PublishFreeze.Name "
+ "AND PublishFreeze.public > 0 AND "
+ "PublishFreeze.confidentiality < 1 "
+ "ORDER BY PublishFreeze.CreateTime DESC")
+ ), 1)
elif self.type == "Geno":
- cursor.execute(
- "SELECT InfoFiles.GN_AccesionId FROM "
- "InfoFiles, GenoFreeze, InbredSet "
- "WHERE InbredSet.Name = %s AND "
- "GenoFreeze.InbredSetId = InbredSet.Id "
- "AND InfoFiles.InfoPageName = GenoFreeze.ShortName "
- "AND GenoFreeze.public > 0 AND "
- "GenoFreeze.confidentiality < 1 "
- "ORDER BY GenoFreeze.CreateTime DESC",
- (self.group.name,)
- )
- results = cursor.fetchone()
-
- if results:
- return str(results[0])
- return "None"
+ __accession_id_dict, = itertools.islice(
+ query_sql(conn,
+ ("SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
+ "InfoFiles, GenoFreeze, InbredSet "
+ f"WHERE InbredSet.Name = '{conn.escape_string(self.group.name).decode()}' AND "
+ "GenoFreeze.InbredSetId = InbredSet.Id "
+ "AND InfoFiles.InfoPageName = GenoFreeze.ShortName "
+ "AND GenoFreeze.public > 0 AND "
+ "GenoFreeze.confidentiality < 1 "
+ "ORDER BY GenoFreeze.CreateTime DESC")
+ ), 1)
+ elif self.type == "ProbeSet":
+ __accession_id_dict, = itertools.islice(
+ query_sql(conn,
+ ("SELECT InfoFiles.GN_AccesionId AS accession_id "
+ f"FROM InfoFiles WHERE InfoFiles.InfoPageName = '{conn.escape_string(self.name).decode()}' "
+ f"AND InfoFiles.DB_Name = '{conn.escape_string(self.fullname).decode()}' "
+ f"OR InfoFiles.DB_Name = '{conn.escape_string(self.shortname).decode()}'")
+ ), 1)
+ else: # The Value passed is not present
+ raise LookupError
+ return __accession_id_dict["accession_id"]
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
index 3245d037..c57171c6 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -244,8 +244,8 @@ def __compute_sample_corr__(
sample_type=start_vars["corr_samples_group"],
sample_data= json.loads(start_vars["sample_vals"]),
all_samples=this_dataset.group.all_samples_ordered(),
- dataset_samples=this_dataset.group.samplelist)
-
+ dataset_samples=this_dataset.group.all_samples_ordered())
+
if not bool(sample_data):
return {}
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index d3e50972..5da8a6b9 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -19,15 +19,9 @@
# This module is used by GeneNetwork project (www.genenetwork.org)
import json
-import os
-from pathlib import Path
from base.trait import create_trait, jsonable
from base.data_set import create_dataset
-from base.webqtlConfig import TMPDIR
-
-from wqflask.correlation.pre_computes import fetch_all_cached_metadata
-from wqflask.correlation.pre_computes import cache_new_traits_metadata
from utility import hmac
from utility.type_checking import get_float, get_int, get_string
@@ -46,16 +40,17 @@ def set_template_vars(start_vars, correlation_data):
name=start_vars['trait_id'])
correlation_data['this_trait'] = jsonable(this_trait, this_dataset_ob)
- correlation_data['this_dataset'] = this_dataset_ob.as_dict()
+ correlation_data['this_dataset'] = this_dataset_ob.as_monadic_dict().data
target_dataset_ob = create_dataset(correlation_data['target_dataset'])
- correlation_data['target_dataset'] = target_dataset_ob.as_dict()
- correlation_data['table_json'] = correlation_json_for_table(
- start_vars,
- correlation_data,
- correlation_data['this_trait'],
- correlation_data['this_dataset'],
- target_dataset_ob)
+ correlation_data['target_dataset'] = target_dataset_ob.as_monadic_dict().data
+
+ table_json = correlation_json_for_table(correlation_data,
+ correlation_data['this_trait'],
+ correlation_data['this_dataset'],
+ target_dataset_ob)
+
+ correlation_data['table_json'] = table_json
if target_dataset_ob.type == "ProbeSet":
filter_cols = [7, 6]
@@ -80,12 +75,12 @@ def correlation_json_for_table(start_vars, correlation_data, this_trait, this_da
Keyword arguments:
correlation_data -- Correlation results
this_trait -- Trait being correlated against a dataset, as a dict
- this_dataset -- Dataset of this_trait, as a dict
+ this_dataset -- Dataset of this_trait, as a monadic dict
target_dataset_ob - Target dataset, as a Dataset ob
"""
this_trait = correlation_data['this_trait']
this_dataset = correlation_data['this_dataset']
- target_dataset = target_dataset_ob.as_dict()
+ target_dataset = target_dataset_ob.as_monadic_dict().data
corr_results = correlation_data['correlation_results']
results_list = []
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 663e2ebf..d2929488 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -1,6 +1,7 @@
# Module to initialize sqlalchemy with flask
import os
import sys
+from SPARQLWrapper import JSON, SPARQLWrapper
from typing import Tuple, Protocol, Any, Iterator
from urllib.parse import urlparse
import importlib
@@ -60,3 +61,10 @@ def database_connection() -> Iterator[Connection]:
yield connection
finally:
connection.close()
+
+
+def sparql_connection():
+ """Create a sparql objection that is used to query RDF"""
+ return SPARQLWrapper(
+ get_setting("SPARQL_ENDPOINT")
+ )
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 376ce14c..3dff422f 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -1,11 +1,12 @@
-import http.client
import urllib.request
import urllib.error
import urllib.parse
import re
+from MySQLdb.cursors import DictCursor
from wqflask.database import database_connection
+
class InfoPage:
def __init__(self, start_vars):
self.info = None
@@ -18,39 +19,70 @@ class InfoPage:
self.get_datasets_list()
def get_info(self, create=False):
- query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, "
- "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, "
- "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, "
- "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, "
- "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, "
- "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, "
- "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, "
- "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics "
- "FROM InfoFiles "
- "LEFT JOIN Species USING (SpeciesId) "
- "LEFT JOIN Tissue USING (TissueId) "
- "LEFT JOIN InbredSet USING (InbredSetId) "
- "LEFT JOIN GeneChip USING (GeneChipId) "
- "LEFT JOIN AvgMethod USING (AvgMethodId) "
- "LEFT JOIN Datasets USING (DatasetId) "
- "LEFT JOIN Investigators USING (InvestigatorId) "
- "LEFT JOIN Organizations USING (OrganizationId) "
- "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+ query_base = (
+ "SELECT InfoPageName AS info_page_name, "
+ "GN_AccesionId AS accession_id, "
+ "Species.MenuName AS menu_name, "
+ "Species.TaxonomyId AS taxonomy_id, "
+ "Tissue.Name AS tissue_name, "
+ "InbredSet.Name AS group_name, "
+ "GeneChip.GeneChipName AS gene_chip_name, "
+ "GeneChip.GeoPlatform AS geo_platform, "
+ "AvgMethod.Name AS avg_method_name, "
+ "Datasets.DatasetName AS dataset_name, "
+ "Datasets.GeoSeries AS geo_series, "
+ "Datasets.PublicationTitle AS publication_title, "
+ "DatasetStatus.DatasetStatusName AS dataset_status_name, "
+ "Datasets.Summary AS dataset_summary, "
+ "Datasets.AboutCases AS about_cases, "
+ "Datasets.AboutTissue AS about_tissue, "
+ "Datasets.AboutDataProcessing AS about_data_processing, "
+ "Datasets.Acknowledgment AS acknowledgement, "
+ "Datasets.ExperimentDesign AS experiment_design, "
+ "Datasets.Contributors AS contributors, "
+ "Datasets.Citation AS citation, "
+ "Datasets.Notes AS notes, "
+ "Investigators.FirstName AS investigator_firstname, "
+ "Investigators.LastName AS investigator_lastname, "
+ "Investigators.Address AS investigator_address, "
+ "Investigators.City AS investigator_city, "
+ "Investigators.State AS investigator_state, "
+ "Investigators.ZipCode AS investigator_zipcode, "
+ "Investigators.Country AS investigator_country, "
+ "Investigators.Phone AS investigator_phone, "
+ "Investigators.Email AS investigator_email, "
+ "Investigators.Url AS investigator_url, "
+ "Organizations.OrganizationName AS organization_name, "
+ "InvestigatorId AS investigator_id, "
+ "DatasetId AS dataset_id, "
+ "DatasetStatusId AS dataset_status_id, "
+ "Datasets.AboutPlatform AS about_platform, "
+ "InfoFileTitle AS info_file_title, "
+ "Specifics AS specifics"
+ "FROM InfoFiles "
+ "LEFT JOIN Species USING (SpeciesId) "
+ "LEFT JOIN Tissue USING (TissueId) "
+ "LEFT JOIN InbredSet USING (InbredSetId) "
+ "LEFT JOIN GeneChip USING (GeneChipId) "
+ "LEFT JOIN AvgMethod USING (AvgMethodId) "
+ "LEFT JOIN Datasets USING (DatasetId) "
+ "LEFT JOIN Investigators USING (InvestigatorId) "
+ "LEFT JOIN Organizations USING (OrganizationId) "
+ "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE "
+ )
if not all([self.gn_accession_id, self.info_page_name]):
raise ValueError('No correct parameter found')
- results = None
- with database_connection() as conn, conn.cursor() as cursor:
+ results = {}
+ with database_connection() as conn, conn.cursor(DictCursor) as cursor:
if self.gn_accession_id:
cursor.execute(f"{query_base}GN_AccesionId = %s",
(self.gn_accession_id,))
- results = cursor.fetchone()
elif self.info_page_name:
cursor.execute(f"{query_base}InfoPageName = %s",
(self.info_page_name,))
- results = cursor.fetchone()
- if results:
- self.info = process_query_results(results)
+ if (results := cursor.fetchone()):
+ self.info = results
if ((not results or len(results) < 1)
and self.info_page_name and create):
return self.get_info()
@@ -80,49 +112,3 @@ class InfoPage:
self.filelist.append([filename, filedate, filesize])
except Exception as e:
pass
-
-
-def process_query_results(results):
- info_ob = {
- 'info_page_name': results[0],
- 'accession_id': results[1],
- 'menu_name': results[2],
- 'taxonomy_id': results[3],
- 'tissue_name': results[4],
- 'group_name': results[5],
- 'gene_chip_name': results[6],
- 'geo_platform': results[7],
- 'avg_method_name': results[8],
- 'dataset_name': results[9],
- 'geo_series': results[10],
- 'publication_title': results[11],
- 'dataset_status_name': results[12],
- 'dataset_summary': results[13],
- 'about_cases': results[14],
- 'about_tissue': results[15],
- 'about_data_processing': results[16],
- 'acknowledgement': results[17],
- 'experiment_design': results[18],
- 'contributors': results[19],
- 'citation': results[20],
- 'notes': results[21],
- 'investigator_firstname': results[22],
- 'investigator_lastname': results[23],
- 'investigator_address': results[24],
- 'investigator_city': results[25],
- 'investigator_state': results[26],
- 'investigator_zipcode': results[27],
- 'investigator_country': results[28],
- 'investigator_phone': results[29],
- 'investigator_email': results[30],
- 'investigator_url': results[31],
- 'organization_name': results[32],
- 'investigator_id': results[33],
- 'dataset_id': results[34],
- 'dataset_status_is': results[35],
- 'about_platform': results[36],
- 'info_file_title': results[37],
- 'specifics': results[38]
- }
-
- return info_ob
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index 0840d4dd..383316e4 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -447,6 +447,15 @@ def update_probeset(name: str):
json_data=json.dumps(diff_data),
),
)
+ edited_values = {k: v for (k, v) in diff_data['Probeset'].items() if k not in {"id_", "timestamp", "author"}}
+ changes = []
+ for k in edited_values.keys():
+ changes.append(f"<b><span data-message-id='{k}'></span></b>")
+ message = f"You successfully updated the following entries \
+ at {diff_data['timestamp']}: {', '.join(changes)}"
+ flash(f"You successfully edited: {message}", "success")
+ else:
+ flash("No edits were made!", "warning")
return redirect(
f"/datasets/traits/{name}"
f"?resource-id={request.args.get('resource-id')}"
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 3780a8f1..2ce07fec 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -6,6 +6,23 @@ table.dataTable tbody tr.selected {
background-color: #ffee99;
}
+table.metadata {
+ table-layout: fixed;
+}
+
+table.metadata td:nth-child(1) {
+ width: 10%;
+}
+
+table summary b {
+ cursor: pointer;
+ text-decoration: underline;
+}
+
+table details[open] {
+ width: 80%;
+}
+
#bar_chart_container {
overflow-x:scroll;
}
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
deleted file mode 100644
index 9ad38102..00000000
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ /dev/null
@@ -1,169 +0,0 @@
-$(function() {
- var gndata; // loaded once for all to use
- process_json = function(data) {
- populate_species();
- return apply_default();
- };
- $.getJSON(gn_server_url+"int/menu/main.json",
- function(data) {
- gndata = data;
- console.log("***** GOT DATA from GN_SERVER ****");
- console.log(gndata);
- populate_species();
- }).error(function() {
- console.log("ERROR: GN_SERVER not responding");
- alert("ERROR: GN_SERVER internal REST API is not responding");
- });
-
- var populate_species = function() {
- var species_list = Object.keys(gndata.menu).map(function(species) {
- var mitem = gndata.menu[species].menu
- // console.log("Species menu:",species,mitem)
- return [species,mitem];
- });
- redo_dropdown($('#species'), species_list);
- return populate_group();
- };
- window.populate_species = populate_species;
-
- var populate_group = function() {
- var species = $('#species').val();
- var groups = gndata.groups[species].map(function(item) {
- console.log("group:",item);
- return item.slice(1,3);
- })
- redo_dropdown($('#group'), groups);
- return populate_type();
- };
- window.populate_group = populate_group;
-
- var populate_type = function() {
- var species = $('#species').val();
- var group = $('#group').val();
- var type_list = gndata.menu[species].types[group].map(function(item) {
- return [item,item];
- });
-
- redo_dropdown($('#type'), type_list);
- return populate_dataset();
- };
- window.populate_type = populate_type;
-
- var populate_dataset = function() {
- var species = $('#species').val();
- var group = $('#group').val();
- var type = $('#type').val();
- var dataset_list = gndata.datasets[species][group][type].map(function(item) {
- return item.slice(1,3);
- })
-
- return redo_dropdown($('#dataset'), dataset_list);
- };
- window.populate_dataset = populate_dataset;
-
- var redo_dropdown = function(dropdown, items) {
- var item, _i, _len, _results;
- console.log("in redo:", dropdown, items);
- dropdown.empty();
- _results = [];
- for (_i = 0, _len = items.length; _i < _len; _i++) {
- item = items[_i];
- if (item.length > 2){
- _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2])));
- } else {
- _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
- }
- }
- return _results;
- };
- $('#species').change((function(_this) {
- return function() {
- return populate_group();
- };
- })(this));
- $('#group').change((function(_this) {
- return function() {
- return populate_type();
- };
- })(this));
- $('#type').change((function(_this) {
- return function() {
- return populate_dataset();
- };
- })(this));
- open_window = function(url, name) {
- var options;
- options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
- return open(url, name, options).focus();
- };
- var group_info = function() {
- var group, species, url;
- species = $('#species').val();
- group = $('#group').val();
- url = "/" + species + "Cross.html#" + group;
- return open_window(url, "Group Info");
- };
- $('#group_info').click(group_info);
- var dataset_info = function() {
- var dataset, url;
- accession_id = $('#dataset option:selected').data("id");
- url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + accession_id;
- return open_window(url, "Dataset Info");
- };
- $('#dataset_info').click(dataset_info);
- var make_default = function() {
- var holder, item, jholder, _i, _len, _ref;
- alert("The current settings are now your default.")
- holder = {};
- _ref = ['species', 'group', 'type', 'dataset'];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- item = _ref[_i];
- holder[item] = $("#" + item).val();
- }
- jholder = JSON.stringify(holder);
- return $.cookie('search_defaults', jholder, {
- expires: 365
- });
- };
- var apply_default = function() {
- var defaults, item, populate_function, _i, _len, _ref, _results;
- defaults = $.cookie('search_defaults');
- if (defaults) {
- defaults = $.parseJSON(defaults);
- } else {
- defaults = {
- species: "mouse",
- group: "BXD",
- type: "Hippocampus mRNA",
- dataset: "HC_M2_0606_P"
- };
- }
- _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- item = _ref[_i];
- $("#" + item[0]).val(defaults[item[0]]);
- if (item[1]) {
- populate_function = "populate_" + item[1];
- console.log("Calling:", populate_function);
- _results.push(window[populate_function]());
- } else {
- _results.push(void 0);
- }
- }
- return _results;
- };
- var check_search_term = function() {
- var or_search_term, and_search_term;
- or_search_term = $('#or_search').val();
- and_search_term = $('#and_search').val();
- console.log("or_search_term:", or_search_term);
- console.log("and_search_term:", and_search_term);
- if (or_search_term === "" && and_search_term === "") {
- alert("Please enter one or more search terms or search equations.");
- return false;
- }
- };
- $("#make_default").click(make_default);
- return $("#btsearch").click(check_search_term);
-});
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js
deleted file mode 100644
index 1d4a94d9..00000000
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js
+++ /dev/null
@@ -1,253 +0,0 @@
-var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown;
-process_json = function(data) {
- window.jdata = data;
- populate_species();
- if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option)
- return apply_default();
- }
-};
-
-$.ajax('/api/v_pre1/gen_dropdown', {
- dataType: 'json',
- success: process_json
-});
-
-populate_species = function() {
- var species_list;
- species_list = this.jdata.species;
- redo_dropdown($('#species'), species_list);
- return populate_group();
-};
-window.populate_species = populate_species;
-populate_group = function() {
- var group_list, species;
- console.log("in populate group");
- species = $('#species').val();
- group_list = this.jdata.groups[species];
- for (_i = 0, _len = group_list.length; _i < (_len - 1); _i++) {
- if (group_list[_i][0] == "BXD300"){
- group_list.splice(_i, 1)
- }
- }
- redo_dropdown($('#group'), group_list);
- if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option)
- return populate_type();
- }
-};
-window.populate_group = populate_group;
-populate_type = function() {
- var group, species, type_list;
- console.log("in populate type");
- species = $('#species').val();
- group = $('#group').val();
- type_list = this.jdata.types[species][group];
- redo_dropdown($('#type'), type_list);
- return populate_dataset();
-};
-window.populate_type = populate_type;
-populate_dataset = function() {
- var dataset_list, group, species, type;
- console.log("in populate dataset");
- species = $('#species').val();
- group = $('#group').val();
- type = $('#type').val();
- console.log("sgt:", species, group, type);
- dataset_list = this.jdata.datasets[species][group][type];
- console.log("pop_dataset:", dataset_list);
- return redo_dropdown($('#dataset'), dataset_list);
-};
-window.populate_dataset = populate_dataset;
-redo_dropdown = function(dropdown, items) {
- var item, _i, _len, _results;
- console.log("in redo:", dropdown, items);
- dropdown.empty();
- _results = [];
-
- if (dropdown.attr('id') == "group"){
- group_family_list = [];
- for (_i = 0, _len = items.length; _i < _len; _i++) {
- item = items[_i];
- group_family = item[2].toString().split(":")[1]
- group_family_list.push([item[0], item[1], group_family])
- }
-
- current_family = ""
- this_opt_group = null
- for (_i = 0, _len = group_family_list.length; _i < _len; _i++) {
- item = group_family_list[_i];
- if (item[2] != "None" && current_family == ""){
- current_family = item[2]
- this_opt_group = $("<optgroup label=\"" + item[2] + "\">")
- this_opt_group.append($("<option />").val(item[0]).text(item[1]));
- } else if (current_family != "" && item[2] == current_family){
- this_opt_group.append($("<option />").val(item[0]).text(item[1]));
- if (_i == group_family_list.length - 1){
- _results.push(dropdown.append(this_opt_group))
- }
- } else if (current_family != "" && item[2] != current_family && item[2] != "None"){
- current_family = item[2]
- _results.push(dropdown.append(this_opt_group))
- this_opt_group = $("<optgroup label=\"" + current_family + "\">")
- this_opt_group.append($("<option />").val(item[0]).text(item[1]));
- if (_i == group_family_list.length - 1){
- _results.push(dropdown.append(this_opt_group))
- }
- } else if (current_family != "" && this_opt_group != null && item[2] == "None"){
- _results.push(dropdown.append(this_opt_group))
- current_family = ""
- _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
- } else {
- _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
- }
- }
- } else if (dropdown.attr('id') == "type"){
- type_family_list = [];
- for (_i = 0, _len = items.length; _i < _len; _i++) {
- item = items[_i];
- type_family_list.push([item[0], item[1], item[2]])
- }
-
- current_family = ""
- this_opt_group = null
- for (_i = 0, _len = type_family_list.length; _i < _len; _i++) {
- item = type_family_list[_i];
- if (item[2] != "None" && current_family == ""){
- current_family = item[2]
- this_opt_group = $("<optgroup label=\"" + item[2] + "\">")
- this_opt_group.append($("<option />").val(item[0]).text(item[1]));
- if (_i == type_family_list.length - 1){
- _results.push(dropdown.append(this_opt_group))
- }
- } else if (current_family != "" && item[2] == current_family){
- this_opt_group.append($("<option />").val(item[0]).text(item[1]));
- if (_i == type_family_list.length - 1){
- _results.push(dropdown.append(this_opt_group))
- }
- } else if (current_family != "" && item[2] != current_family && item[2] != "None"){
- current_family = item[2]
- _results.push(dropdown.append(this_opt_group))
- this_opt_group = $("<optgroup label=\"" + current_family + "\">")
- this_opt_group.append($("<option />").val(item[0]).text(item[1]));
- if (_i == type_family_list.length - 1){
- _results.push(dropdown.append(this_opt_group))
- }
- } else {
- _results.push(dropdown.append(this_opt_group))
- current_family = ""
- _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
- }
- }
- } else {
- for (_i = 0, _len = items.length; _i < _len; _i++) {
- item = items[_i];
- if (item.length > 2){
- _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2])));
- } else {
- _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
- }
- }
- }
-
- return _results;
-};
-$('#species').change((function(_this) {
- return function() {
- return populate_group();
- };
-})(this));
-$('#group').change((function(_this) {
- return function() {
- if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option)
- return populate_type();
- }
- else {
- return false
- }
- };
-})(this));
-$('#type').change((function(_this) {
- return function() {
- return populate_dataset();
- };
-})(this));
-open_window = function(url, name) {
- var options;
- options = "menubar=yes,toolbar=yes,titlebar=yes,location=yes,resizable=yes,status=yes,scrollbars=yes,directories=yes,width=900";
- return open(url, name, options).focus();
-};
-group_info = function() {
- var group, species, url;
- species = $('#species').val();
- group = $('#group').val();
- url = "http://gn1.genenetwork.org/" + species + "Cross.html#" + group;
- return open_window(url, "Group Info");
-};
-$('#group_info').click(group_info);
-dataset_info = function() {
- var dataset, url;
- accession_id = $('#dataset option:selected').data("id");
- name = $('#dataset option:selected').val();
- if (accession_id != "None") {
- url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + accession_id + "&InfoPageName=" + name;
- } else {
- url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + name;
- }
- return open_window(url, "Dataset Info");
-};
-$('#dataset_info').click(dataset_info);
-make_default = function() {
- var holder, item, jholder, _i, _len, _ref;
- alert("The current settings are now your default.")
- holder = {};
- _ref = ['species', 'group', 'type', 'dataset'];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- item = _ref[_i];
- holder[item] = $("#" + item).val();
- }
- jholder = JSON.stringify(holder);
- return $.cookie('search_defaults', jholder, {
- expires: 365
- });
-};
-apply_default = function() {
- var defaults, item, populate_function, _i, _len, _ref, _results;
- defaults = $.cookie('search_defaults');
- if (defaults) {
- defaults = $.parseJSON(defaults);
- } else {
- defaults = {
- species: "mouse",
- group: "BXD",
- type: "Hippocampus mRNA",
- dataset: "HC_M2_0606_P"
- };
- }
-
- _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- item = _ref[_i];
- $("#" + item[0]).val(defaults[item[0]]);
- if (item[1]) {
- populate_function = "populate_" + item[1];
- console.log("Calling:", populate_function);
- _results.push(window[populate_function]());
- } else {
- _results.push(void 0);
- }
- }
- return _results;
-};
-check_search_term = function() {
- var or_search_term, and_search_term;
- or_search_term = $('#or_search').val();
- and_search_term = $('#and_search').val();
- console.log("or_search_term:", or_search_term);
- console.log("and_search_term:", and_search_term);
- if (or_search_term === "" && and_search_term === "") {
- alert("Please enter one or more search terms or search equations.");
- return false;
- }
-};
-$("#make_default").click(make_default);
-$("#btsearch").click(check_search_term);
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 8d83d1a6..29fdc5f1 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -17,8 +17,8 @@
<hr style="height: 1px; background-color: #A9A9A9;">
</div>
<div style="max-width: 100%;">
- <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if this_dataset.accession_id != 'None' %}GN_AccessionId={{ this_dataset.accession_id }}{% else %}InfoPageName={{ this_dataset.name }}{% endif %}">{{ this_dataset.fullname }}</a>
- dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if target_dataset.accession_id != 'None' %}GN_AccessionId={{ target_dataset.accession_id }}{% else %}InfoPageName={{ target_dataset.name }}{% endif %}">{{ target_dataset.fullname }}</a>
+ <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if this_dataset.accession_id %}GN_AccessionId={{ this_dataset.accession_id }}{% else %}InfoPageName={{ this_dataset.name }}{% endif %}">{{ this_dataset.fullname }}</a>
+ dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if target_dataset.accession_id %}GN_AccessionId={{ target_dataset.accession_id }}{% else %}InfoPageName={{ target_dataset.name }}{% endif %}">{{ target_dataset.fullname }}</a>
dataset. The top {{ return_results }} correlations ranked by the {{ formatted_corr_type }} are displayed.
You can resort this list by clicking the headers. Select the Record ID to open the trait data
and analysis page.
diff --git a/wqflask/wqflask/templates/edit_probeset.html b/wqflask/wqflask/templates/edit_probeset.html
index 6c068e63..c5ef992e 100644
--- a/wqflask/wqflask/templates/edit_probeset.html
+++ b/wqflask/wqflask/templates/edit_probeset.html
@@ -3,6 +3,31 @@
{% block content %}
<!-- Start of body -->
<div class="container">
+ {% with messages = get_flashed_messages(category_filter=["warning"]) %}
+ {% if messages %}
+ {% for message in messages %}
+ <div class="alert alert-warning alert-dismissible" role="alert">
+ <button class="close" type="button" data-dismiss="alert" aria-label="Close">
+ <span aria-hidden="true">&times;</span>
+ </button>
+ {{ message }}
+ </div>
+ {% endfor %}
+ {% endif %}
+ {% endwith %}
+
+ {% with messages = get_flashed_messages(category_filter=["success"]) %}
+ {% if messages %}
+ {% for message in messages %}
+ <div class="alert alert-success alert-dismissible" role="alert">
+ <button class="close" type="button" data-dismiss="alert" aria-label="Close">
+ <span aria-hidden="true">&times;</span>
+ </button>
+ {{ message|safe }}
+ </div>
+ {% endfor %}
+ {% endif %}
+ {% endwith %}
<div class="page-header text-left">
<h1>Probeset Editing Form: {{ probeset.name }}</h1>
<small><a href="{{url_for('metadata_edit.show_history', name=name)}}" target="_blank">[View History]</a></small>
@@ -71,7 +96,7 @@
</div>
<div class="form-group">
<label for="homologeneid" class="col-sm-3 col-lg-2 control-label text-left">
- Homolegene Id:
+ Homologene Id:
</label>
<div class="col-sm-4">
<textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea>
@@ -188,6 +213,12 @@
{% block js %}
<script>
gn_server_url = "{{ gn_server_url }}";
+ spans = document.querySelectorAll("[data-message-id]")
+ spans.forEach((span) => {
+ span.innerHTML = $("[for='" + span.getAttribute("data-message-id") + "']").text();
+ });
+ $("[data-message-id]").lead
+
function MarkAsChanged(){
$(this).addClass("changed");
}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5bcd17b8..3a6f6e91 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -17,7 +17,7 @@
<div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
<!-- Need to customize text more for other types of searches -->
- <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
+ <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if metadata.accession_id %}GN_AccessionId={{ metadata.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
<br>
to find all records
{% if go_term is not none %}
@@ -97,8 +97,8 @@
<input type="hidden" name="database_name" id="database_name" value="{{ dataset.fullname }}">
<input type="hidden" name="file_name" id="file_name" value="search_results">
<input type="hidden" name="filter_term" id="filter_term" value="None">
- {% if dataset.accession_id is defined %}
- <input type="hidden" name="accession_id" id="accession_id" value="{{ dataset.accession_id }}">
+ {% if metadata.accession_id %}
+ <input type="hidden" name="accession_id" id="accession_id" value="{{ metadata.accession_id }}">
{% endif %}
<input type="hidden" name="export_data" id="export_data" value="">
<input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search For...">
diff --git a/wqflask/wqflask/templates/show_metadata_details.html b/wqflask/wqflask/templates/show_metadata_details.html
new file mode 100644
index 00000000..ffb197e2
--- /dev/null
+++ b/wqflask/wqflask/templates/show_metadata_details.html
@@ -0,0 +1,186 @@
+<table class="table metadata">
+ {% if metadata.accession_id %}
+ <tr>
+ <td><b>Title:</b></td>
+ <td><div>{{ metadata.accession_id }} {% if metadata.title %}: {{ metadata.title }} {% endif %}</div></td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.geo_series %}
+ <tr>
+ <td><b>Geo Series:</b></td>
+ <td><div>{{ metadata.geo_series|safe }}</div></td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.dataset_group %}
+ <tr>
+ <td><b>Dataset Group:</b></td>
+ <td><div>{{ metadata.dataset_group }}</div></td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.species_name %}
+ <tr>
+ <td><b>Species:</b></td>
+ <td><div>{{ metadata.species_name }}</div></td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.inbred_set_name %}
+ <tr>
+ <td><b>Group:</b></td>
+ <td><div>{{ metadata.inbred_set_name }}</div></td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.investigators %}
+ <tr>
+ <td><b>Investigator(s):</b></td>
+ <td><div>{{ metadata.investigators.name }}, {{ metadata.investigators.city }}, {{ metadata.investigators.country }} </div></td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.tissue_name %}
+ <tr>
+ <td><b>Tissue:</b></td>
+ <td>
+ {% if metadata.about_tissue %}
+ <div></div>
+ <details>
+ <summary><b title="Click to view tissue information">{{ metadata.tissue_name }}</b></summary>
+ <b>About the tissue used to generate this set of data:</b>
+ <div>{{ metadata.about_tissue|safe }}</div>
+ </details>
+ {% else %}
+ {{ metadata.tissue_name }}
+ {% endif %}
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.platform_name %}
+ <tr>
+ <td><b>Platforms:</b></td>
+ <td>
+ {% if metadata.about_platform %}
+ <details>
+ <summary><b title="Click to view platform information">{{ metadata.platform_name }}</b></summary>
+ <b>About the array platform:</b>
+ {{ metadata.about_platform|safe }}
+ </details>
+ {% else %}
+ {{ metadata.platform_name }}
+ {% endif %}
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.normalization_name %}
+ <tr>
+ <td><b>Normalization:</b></td>
+ <td>
+ {{ metadata.normalization_name }}
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.summary %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b title="Click to view summary">Summary</b></summary>
+ {{ metadata.summary|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+
+ {% if metadata.about_cases %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b title="Click to view case information">About the cases used to generate this set of data</b></summary>
+ {{ metadata.about_cases|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.about_data_processing %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b title="Click to view data values and processing">About Data Values and Data Processing</b></summary>
+ {{ metadata.about_data_processing|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.notes %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b>Notes</b></summary>
+ {{ metadata.notes|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.experiment_design %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b>Experiment Type</b></summary>
+ {{ metadata.experiment_design|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.contributors %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b>Contributor(s)</b></summary>
+ {{ metadata.contributors|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.citation %}
+ <tr>
+ <td>
+ <td>
+ <details>
+ <summary><b>Citation</b></summary>
+ {{ metadata.citation|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.acknowledgment %}
+ <tr>
+ <td></td>
+ <td>
+ <details>
+ <summary><b>Data source acknowledgment</b></summary>
+ {{ metadata.acknowledgment|safe }}
+ </details>
+ </td>
+ </tr>
+ {% endif %}
+
+
+</table>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 0f93188b..4b92545c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -51,8 +51,20 @@
<div class="panel-body">
{% include 'show_trait_details.html' %}
</div>
+ </div>
+ {% if metadata.accession_id %}
+ <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseMeta">
+ <h3 class="panel-title">
+ <span class="glyphicon glyphicon-chevron-down"></span> Data Set Group: {{ dataset.fullname }}
+ </h3>
</div>
- </div>
+ <div id="collapseMeta" class="panel-collapse collapse in">
+ <div class="panel-body">
+ {% include 'show_metadata_details.html' %}
+ </div>
+ </div>
+ {% endif %}
+ </div>
<div class="panel panel-default">
<div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
<h3 class="panel-title">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 211a8f13..1b34e2f8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -83,12 +83,14 @@ from utility.helper_functions import get_species_groups
from utility.redis_tools import get_redis_conn
import utility.hmac as hmac
+from gn3.db.rdf import get_dataset_metadata
from base.webqtlConfig import TMPDIR
from base.webqtlConfig import GENERATED_IMAGE_DIR
from wqflask.database import database_connection
+from wqflask.database import sparql_connection
import jobs.jobs as jobs
@@ -487,7 +489,18 @@ def show_trait_page():
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")
- return render_template("show_trait.html", **template_vars.__dict__)
+ metadata = (
+ template_vars.dataset.accession_id
+ .bind(
+ lambda idx: get_dataset_metadata(
+ sparql_connection(),
+ f"GN{idx}"
+ )
+ )
+ ).data
+
+ return render_template("show_trait.html",
+ metadata=metadata, **template_vars.__dict__)
@app.route("/heatmap", methods=('POST',))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 17:57:08 +0000