diff options
| -rw-r--r-- | README.md | 2 | ||||
| -rw-r--r-- | wqflask/base/data_set/dataset.py | 90 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/rust_correlation.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 27 | ||||
| -rw-r--r-- | wqflask/wqflask/database.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/db_info.py | 128 | ||||
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/show_trait.css | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_select_menu.js | 169 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js | 253 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/edit_probeset.html | 33 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_metadata_details.html | 186 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 15 |
16 files changed, 406 insertions, 559 deletions
@@ -67,6 +67,7 @@ env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \ GENENETWORK_FILES=~/data/gn2_data/ \ GN_PROXY_URL="http://localhost:8080"\ GN3_LOCAL_URL="http://localhost:8081"\ + SPARQL_ENDPOINT=http://localhost:8892/sparql\ ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev ``` @@ -182,6 +183,7 @@ env HOME=/home/frederick \ GN2_PROFILE=~/opt/gn2-latest \ GN3_DEV_REPO_PATH=~/genenetwork/genenetwork3 \ SQL_URI="mysql://username:password@host-ip:host-port/db_webqtl" \ + SPARQL_ENDPOINT=http://localhost:8892/sparql\ SERVER_PORT=5001 \ bin/genenetwork2 ../gn2_settings.py \ -cli python3 -m scripts.profile_corrs \ 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">×</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">×</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',)) |