diff options
| -rw-r--r-- | wqflask/base/data_set.py | 7 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 3 | ||||
| -rw-r--r-- | wqflask/utility/authentication_tools.py | 61 | ||||
| -rw-r--r-- | wqflask/utility/redis_tools.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/export_traits.py | 119 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/search_results.js | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 28 |
10 files changed, 184 insertions, 65 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 21ace006..5d562871 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -959,7 +959,7 @@ class GenotypeDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2 + Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on @@ -1130,11 +1130,14 @@ class MrnaAssayDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2 + Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2 FROM (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) left join ProbeSetSE on (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) + left join NStrain on + (NStrain.DataId = ProbeSetData.Id AND + NStrain.StrainId = ProbeSetData.StrainId) WHERE ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index f9da7b87..7666348e 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -152,7 +152,7 @@ class GeneralTrait(object): '''Return a text formatted alias''' alias = 'Not available' - if self.alias: + if getattr(self, "alias", None): alias = string.replace(self.alias, ";", " ") alias = string.join(string.split(alias), ", ") @@ -412,6 +412,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): Phenotype.Id = PublishXRef.PhenotypeId AND Publication.Id = PublishXRef.PublicationId AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishXRef.InbredSetId = InbredSet.Id AND PublishFreeze.Id = %s """ % (trait.name, dataset.id) diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index f9028f32..ed7462d1 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -6,7 +6,7 @@ import requests from base import data_set, webqtlConfig from utility import hmac -from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id +from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource Redis = get_redis_conn() from flask import Flask, g, redirect, url_for @@ -16,13 +16,7 @@ logger = logging.getLogger(__name__ ) def check_resource_availability(dataset, trait_id=None): - #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy - if g.user_session.user_id in Redis.smembers("super_users"): - return webqtlConfig.SUPER_PRIVILEGES - - response = None - - #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible + #At least for now assume temporary entered traits are accessible if type(dataset) == str: return webqtlConfig.DEFAULT_PRIVILEGES if dataset.type == "Temp": @@ -33,9 +27,13 @@ def check_resource_availability(dataset, trait_id=None): if resource_id: resource_info = get_resource_info(resource_id) if not resource_info: - return webqtlConfig.DEFAULT_PRIVILEGES - else: - return response #ZS: Need to substitute in something that creates the resource in Redis later + resource_info = add_new_resource(dataset, trait_id) + + #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy + if g.user_session.user_id in Redis.smembers("super_users"): + return webqtlConfig.SUPER_PRIVILEGES + + response = None the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) try: @@ -43,10 +41,43 @@ def check_resource_availability(dataset, trait_id=None): except: response = resource_info['default_mask'] - if response: - return response - else: #ZS: No idea how this would happen, but just in case - return False + return response + +def add_new_resource(dataset, trait_id=None): + resource_ob = { + 'owner_id' : webqtlConfig.DEFAULT_OWNER_ID, + 'default_mask': webqtlConfig.DEFAULT_PRIVILEGES, + 'group_masks' : {} + } + + if dataset.type == "Publish": + resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id) + resource_ob['data'] = { + 'dataset': dataset.id, + 'trait' : trait_id + } + resource_ob['type'] = 'dataset-publish' + elif dataset.type == "Geno": + resource_ob['name'] = dataset.name + resource_ob['data'] = { + 'dataset': dataset.id + } + resource_ob['type'] = 'dataset-geno' + else: + resource_ob['name'] = dataset.name + resource_ob['data'] = { + 'dataset': dataset.id + } + resource_ob['type'] = 'dataset-probeset' + + resource_info = add_resource(resource_ob, update=False) + + return resource_info + +def get_group_code(dataset): + results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone() + + return results[0] def check_admin(resource_id=None): the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 6c912a23..1377a564 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -264,17 +264,14 @@ def get_resources(): return resource_list def get_resource_id(dataset, trait_id=None): + resource_id = False if dataset.type == "Publish": if trait_id: resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id)) - else: - return False elif dataset.type == "ProbeSet": resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) elif dataset.type == "Geno": resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) - else: - return False return resource_id diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 2d96c05a..3272c03d 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -4,24 +4,30 @@ import csv import xlsxwriter import StringIO import datetime +import itertools + +from zipfile import ZipFile, ZIP_DEFLATED import simplejson as json +from base.trait import create_trait, retrieve_trait_info + from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + def export_search_results_csv(targs): table_data = json.loads(targs['export_data']) - table_headers = table_data['headers'] table_rows = table_data['rows'] - buff = StringIO.StringIO() - writer = csv.writer(buff) - + now = datetime.datetime.now() + time_str = now.strftime('%H:%M_%d%B%Y') if 'file_name' in targs: - file_name = targs['file_name'] + zip_file_name = targs['file_name'] + "_export_" + time_str else: - file_name = "table_export.csv" + zip_file_name = "export_" + time_str metadata = [] @@ -40,19 +46,98 @@ def export_search_results_csv(targs): if targs['filter_term'] != "None": metadata.append(["Search Filter Terms: " + targs['filter_term']]) metadata.append(["Exported Row Number: " + str(len(table_rows))]) + metadata.append(["Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)"]) + metadata.append([]) + + trait_list = [] + for trait in table_rows: + trait_name, dataset_name, _hash = trait.split(":") + trait_ob = create_trait(name=trait_name, dataset_name=dataset_name) + trait_ob = retrieve_trait_info(trait_ob, trait_ob.dataset, get_qtl_info=True) + trait_list.append(trait_ob) + + table_headers = ['Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] + + traits_by_group = sort_traits_by_group(trait_list) + + file_list = [] + for group in traits_by_group.keys(): + group_traits = traits_by_group[group] + buff = StringIO.StringIO() + writer = csv.writer(buff) + csv_rows = [] + + sample_headers = [] + for sample in group_traits[0].dataset.group.samplelist: + sample_headers.append(sample) + sample_headers.append(sample + "_SE") + + full_headers = table_headers + sample_headers + + for metadata_row in metadata: + writer.writerow(metadata_row) + + csv_rows.append(full_headers) + + for trait in group_traits: + if getattr(trait, "symbol", None): + trait_symbol = getattr(trait, "symbol") + elif getattr(trait, "abbreviation", None): + trait_symbol = getattr(trait, "abbreviation") + else: + trait_symbol = "N/A" + row_contents = [ + trait.dataset.group.species, + trait.dataset.group.name, + trait.dataset.name, + trait.name, + trait_symbol, + getattr(trait, "description_display", "N/A"), + getattr(trait, "probe_target_description", "N/A"), + getattr(trait, "pubmed_id", "N/A"), + getattr(trait, "chr", "N/A"), + getattr(trait, "mb", "N/A"), + trait.alias_fmt, + getattr(trait, "geneid", "N/A"), + getattr(trait, "homologeneid", "N/A"), + getattr(trait, "unigeneid", "N/A"), + getattr(trait, "strand_probe", "N/A"), + getattr(trait, "probe_set_specificity", "N/A"), + getattr(trait, "probe_set_blat_score", "N/A"), + getattr(trait, "probe_set_blat_mb_start", "N/A"), + getattr(trait, "probe_set_blat_mb_end", "N/A"), + getattr(trait, "locus_chr", "N/A"), + getattr(trait, "locus_mb", "N/A"), + getattr(trait, "locus", "N/A"), + getattr(trait, "lrs", "N/A"), + getattr(trait, "pvalue", "N/A"), + getattr(trait, "mean", "N/A") + ] + + for sample in trait.dataset.group.samplelist: + if sample in trait.data: + row_contents += [trait.data[sample].value, trait.data[sample].variance] + else: + row_contents += ["x", "x"] + + csv_rows.append(row_contents) + + csv_rows = map(list, itertools.izip_longest(*[row for row in csv_rows])) + writer.writerows(csv_rows) + csv_data = buff.getvalue() + buff.close() - for metadata_row in metadata: - writer.writerow(metadata_row) + file_name = group + "_traits.csv" + file_list.append([file_name, csv_data]) - writer.writerow([]) + return file_list - writer.writerow(table_headers) - for trait_info in table_rows: - writer.writerow(trait_info) +def sort_traits_by_group(trait_list=[]): + traits_by_group = {} + for trait in trait_list: + if trait.dataset.group.name not in traits_by_group.keys(): + traits_by_group[trait.dataset.group.name] = [] - writer.writerow([]) - writer.writerow(["Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)"]) - csv_data = buff.getvalue() - buff.close() + traits_by_group[trait.dataset.group.name].append(trait) - return csv_data, file_name \ No newline at end of file + return traits_by_group \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 39aae113..b3ed06fc 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -161,23 +161,11 @@ $(function() { trait_table.find('tbody tr').each(function (i, tr) { if (trait_table.find('input[name="searchResult"]:checked').length > 0) { if ($(this).find('input[name="searchResult"]').is(':checked')){ - this_row = []; - $(tr).find('td').each(function(j, td){ - if ($(td).data('export')){ - this_row.push($(td).data('export')); - } - }); - rows.push(this_row); + rows.push($(this).find('input[name="searchResult"]:checked').val()) } } else { - this_row = []; - $(tr).find('td').each(function(j, td){ - if ($(td).data('export')){ - this_row.push($(td).data('export')); - } - }); - rows.push(this_row); + rows.push($(this).find('input[name="searchResult"]').val()) } }); table_dict['rows'] = rows; diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 1879e075..50562200 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -96,7 +96,11 @@ </li> {% if g.user_session.logged_in %} <li class=""> - <a id="manage_groups" title="Manage Groups" href="/groups/manage">Manage Groups</a> + <a href="/edit_account_settings" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">User Account Settings<span class="caret"></a> + <ul class="dropdown-menu"> + <li><a id="manage_user" title="User Options" href="/user/manage">User Options</a></li> + <li><a id="manage_groups" title="Manage Groups" href="/groups/manage">Manage Groups</a></li> + </ul> </li> {% endif %} {% endif %} diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 132d5249..81803deb 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -333,6 +333,7 @@ {% block js %} <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> + <script type="text/javascript" src="/static/new/js_external/md5.min.js"></script> <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script> <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script> <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 94885f26..acee6724 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -21,8 +21,7 @@ {% endif %} </div> - <form method="post" action="" target="_blank" name="trait_page" id="trait_data_form" - class="form-horizontal"> + <form method="post" action="" target="_blank" name="trait_page" id="trait_data_form" class="form-horizontal"> <div id="hidden_inputs"> <input type="hidden" name="trait_hmac" value="{{ data_hmac('{}:{}'.format(this_trait.name, dataset.name)) }}"> {% for key in hddn %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 131345d3..57183eed 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -11,24 +11,24 @@ import datetime # for errors import time # for errors import sys import csv +import simplejson as json +import yaml import xlsxwriter import StringIO # Todo: Use cStringIO? +from zipfile import ZipFile, ZIP_DEFLATED + import gc import numpy as np - import cPickle as pickle import uuid -import simplejson as json -import yaml - import flask import base64 import array import sqlalchemy from wqflask import app -from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for +from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file from wqflask import group_manager from wqflask import resource_manager from wqflask import search_results @@ -421,11 +421,21 @@ def export_traits_csv(): logger.info("In export_traits_csv") logger.info("request.form:", request.form) logger.info(request.url) - csv_data, file_name = export_traits.export_search_results_csv(request.form) + file_list = export_traits.export_search_results_csv(request.form) - return Response(csv_data, - mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + if len(file_list) > 1: + memory_file = StringIO.StringIO() + with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf: + for the_file in file_list: + zf.writestr(the_file[0], the_file[1]) + + memory_file.seek(0) + + return send_file(memory_file, attachment_filename=filename + ".zip", as_attachment=True) + else: + return Response(file_list[0][1], + mimetype='text/csv', + headers={"Content-Disposition":"attachment;filename=" + file_list[0][0]}) @app.route('/export_perm_data', methods=('POST',)) def export_perm_data(): |