diff options
Diffstat (limited to 'wqflask')
18 files changed, 111 insertions, 136 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index afffe780..2f1549ae 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -150,10 +150,12 @@ Publish or ProbeSet. E.g. "geno": "Geno", } + group_name = name if t in ['pheno', 'other_pheno']: - name = name.replace("Publish", "") + group_name = name.replace("Publish", "") - if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())): + results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + if results: self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) return True @@ -1173,40 +1175,6 @@ class TempDataSet(DataSet): self.fullname = 'Temporary Storage' self.shortname = 'Temp' - @staticmethod - def handle_pca(desc): - if 'PCA' in desc: - # Todo: Modernize below lines - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - return desc - - def get_desc(self): - query = 'SELECT description FROM Temp WHERE Name=%s' % self.name - logger.sql(query) - g.db.execute(query) - desc = g.db.fetchone()[0] - desc = self.handle_pca(desc) - return desc - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - """ % escape(trait.name) - - logger.sql(query) - results = g.db.execute(query).fetchall() - def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 819836b1..0f3d455c 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -17,8 +17,15 @@ class CorrScatterPlot(object): """Page that displays a correlation scatterplot with a line fitted to it""" def __init__(self, params): - self.dataset_1 = data_set.create_dataset(params['dataset_1']) - self.dataset_2 = data_set.create_dataset(params['dataset_2']) + if "Temp" in params['dataset_1']: + self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1]) + else: + self.dataset_1 = data_set.create_dataset(params['dataset_1']) + if "Temp" in params['dataset_2']: + self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1]) + else: + self.dataset_2 = data_set.create_dataset(params['dataset_2']) + #self.dataset_3 = data_set.create_dataset(params['dataset_3']) self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1) self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 0ac94139..3beee84f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -147,7 +147,7 @@ class CorrelationMatrix(object): if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap - if num_overlap == 0: + if num_overlap < 2: corr_result_row.append([target_trait, 0, num_overlap]) pca_corr_result_row.append(0) else: diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 78407e22..9fad1cf1 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -11,7 +11,7 @@ class Docs(object): def __init__(self, entry, start_vars={}): sql = """ - SELECT Docs.title, Docs.content + SELECT Docs.title, CAST(Docs.content AS BINARY) FROM Docs WHERE Docs.entry LIKE %s """ @@ -22,7 +22,7 @@ class Docs(object): self.content = "" else: self.title = result[0] - self.content = result[1].encode("latin1") + self.content = result[1] self.editable = "false" # ZS: Removing option to edit to see if text still gets vandalized diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 39a07310..14ff2183 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -25,16 +25,16 @@ def manage_resource(): group_masks_with_names = get_group_names(group_masks) default_mask = resource_info['default_mask']['data'] owner_id = resource_info['owner_id'] - owner_info = get_user_by_unique_column("user_id", owner_id) - - if 'name' in owner_info: - owner_display_name = owner_info['full_name'] - elif 'user_name' in owner_info: - owner_display_name = owner_info['user_name'] - elif 'email_address' in owner_info: - owner_display_name = owner_info['email_address'] - else: - owner_display_name = None + + owner_display_name = None + if owner_id != "none": + owner_info = get_user_by_unique_column("user_id", owner_id) + if 'name' in owner_info: + owner_display_name = owner_info['full_name'] + elif 'user_name' in owner_info: + owner_display_name = owner_info['user_name'] + elif 'email_address' in owner_info: + owner_display_name = owner_info['email_address'] return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 338302af..92deab20 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -46,4 +46,9 @@ table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { table.dataTable.cell-border tbody tr th:first-child, table.dataTable.cell-border tbody tr td:first-child { border-left: 1px solid #ccc; +} + +.glyphicon { + position: relative; + top: 2px; }
\ 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 685d6291..86660126 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -93,7 +93,7 @@ $(function() { }); - add = function() { + add_to_collection = function() { var traits; traits = $("#trait_table input:checked").map(function() { return $(this).val(); @@ -250,7 +250,7 @@ $(function() { $("#select_all").click(select_all); $("#deselect_all").click(deselect_all); $("#invert").click(invert); - $("#add").click(add); + $("#add").click(add_to_collection); $("#submit_bnw").click(submit_bnw); $("#export_traits").click(export_traits); $('.trait_checkbox, .btn').click(change_buttons); @@ -261,6 +261,12 @@ $(function() { let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A + function extract_inner_text(the_string){ + var span = document.createElement('span'); + span.innerHTML = the_string; + return span.textContent || span.innerText; + } + function sort_NAs(a, b, sort_function){ if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { return 0; @@ -276,10 +282,10 @@ $(function() { $.extend( $.fn.dataTableExt.oSort, { "natural-minus-na-asc": function (a, b) { - return sort_NAs(a, b, naturalAsc) + return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc) }, "natural-minus-na-desc": function (a, b) { - return sort_NAs(a, b, naturalDesc) + return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc) } }); diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index e6802cc4..b44538cf 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -21,6 +21,14 @@ {% block css %} {% endblock %} + <style> + table.dataTable thead .sorting_asc { + background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }}); + } + table.dataTable thead .sorting_desc { + background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }}); + } + </style> </head> <body style="width: 100%"> diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index 825dfb84..62b6abb5 100644 --- a/wqflask/wqflask/templates/collections/add.html +++ b/wqflask/wqflask/templates/collections/add.html @@ -5,7 +5,7 @@ or add to an existing collection.</p> </div> <div class="modal-body" style="margin-left: 20px;"> - <form action="/collections/new" data-validate="parsley" id="add_form"> + <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form"> {% if traits is defined %} <input type="hidden" name="traits" value="{{ traits }}" /> {% else %} diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index dce814dd..bc487a59 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -16,8 +16,6 @@ </h1> <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3> - <!--<hr style="height: 1px; background-color: #A9A9A9;">--> - <div> <form id="collection_form" action="/delete" method="post"> <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> @@ -77,7 +75,7 @@ <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> <input type="hidden" name="file_name" id="file_name" value="collection_table"> - <button class="btn btn-default" id="export_traits">Download CSV</button> + <button class="btn btn-default" id="export_traits">Download</button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> @@ -99,9 +97,9 @@ <th data-export="Description">Description</th> <th data-export="Location">Location</th> <th data-export="Mean">Mean</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th> - <th data-export="Max LRS Location">Max LRS Location</th> - <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> + <th data-export="Peak Location">Peak Location</th> + <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> </tr> </thead> @@ -144,7 +142,7 @@ <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD> {% endif %} <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD> - {% if this_trait.additive|float > 0 %} + {% if this_trait.additive|float != 0 %} <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD> {% else %} <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD> @@ -166,13 +164,13 @@ {% block js %} <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> - <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script> + <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript"> @@ -187,10 +185,14 @@ console.time("Creating table"); $('#trait_table').dataTable( { "columns": [ - { "type": "natural", "width": 10 }, + { + "orderDataType": "dom-checkbox", + "orderSequence": [ "desc", "asc"], + "width": 10 + }, { "type": "natural", "width": 50 }, { "type": "natural" }, - { "type": "natural", "width": 120 }, + { 'type': "natural-minus-na", "width": 120 }, { "type": "natural" }, { "type": "natural" }, { "type": "natural", "width": 130 }, @@ -199,10 +201,6 @@ { "type": "natural", "width": 130 }, { "type": "natural" } ], - "columnDefs": [ { - "targets": 0, - "orderable": false - } ], "order": [[1, "asc" ]], buttons: [ { diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 9b96de1c..d556f31a 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -51,7 +51,7 @@ {% if result[0].name == trait.name and result[0].dataset == trait.dataset %} <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td> {% else %} - <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> {% endif %} {% endfor %} </tr> diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index e597bea9..fb218e29 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -144,7 +144,7 @@ <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD> <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td> <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %} @@ -164,22 +164,26 @@ <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Publish" %} {% if trait.abbreviation %} - <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD> + <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td> {% else %} - <TD data-export="N/A">N/A</TD> + <td data-export="N/A">N/A</td> {% endif %} <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td> {% if trait.authors %} <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td> {% else %} - <TD data-export="N/A">N/A</TD> + <td data-export="N/A">N/A</td> {% endif %} <td data-export="{{ trait.pubmed_text }}"> + {% if trait.pubmed_text != "N/A" %} <a href="{{ trait.pubmed_link }}"> {{ trait.pubmed_text }} </a> + {% else %} + {{ trait.pubmed_text }} + {% endif %} </td> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td> @@ -187,7 +191,7 @@ <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Geno" %} <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> {% endif %} @@ -365,9 +369,9 @@ { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, { "type": "scientific" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" } + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" } ], "createdRow": function ( row, data, index ) { $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); @@ -419,13 +423,13 @@ { "type": "natural" }, { "type": "natural", "width": "20%" }, { "type": "natural", "width": "12%" }, - { "orderDataType": "dom-innertext" }, + { "type": "natural-minus-na" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, { "type": "natural" }, { "type": "scientific" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" } + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" } ], "order": [[9, "asc" ]], "sDom": "Btir", @@ -461,7 +465,7 @@ { "type": "natural" }, { "type": "natural" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, - { "type": "natural" }, + { "type": "natural-minus-na" }, { "type": "scientific" } ], "order": [[6, "asc" ]], diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 06b71f53..6b3bec9a 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -17,13 +17,13 @@ </header> --> - <div class="container-fluid" style="min-width: 1200px;"> + <div class="container-fluid" style="min-width: 1210px;"> {{ flash_me() }} <div class="row" style="width: 100%;"> - <div class="col-xs-5" style="min-width: 530px; max-width: 550px;"> + <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> <section id="search"> <div> <h1>Select and search</h1> @@ -84,7 +84,7 @@ <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea> + <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> </div> </div> </div> @@ -105,7 +105,7 @@ <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea> + <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> </div> </div> </div> @@ -184,7 +184,7 @@ </section> </div> - <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;"> + <div class="col-xs-4" style="width: 600px !important;"> <section id="affiliates"> <div class="page-header"> <h1>Affiliates</h1> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 282e752d..e2e1aa46 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -127,7 +127,7 @@ <input type="hidden" name="export_data" id="export_data" value=""> <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button> <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> - <button class="btn btn-default" id="export_traits">Download CSV</button> + <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> @@ -274,10 +274,9 @@ }, { 'title': "Record", - 'type': "natural", + 'type': "natural-minus-na", 'data': null, 'width': "60px", - 'orderDataType': "dom-inner-text", 'render': function(data, type, row, meta) { return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>' } @@ -315,20 +314,20 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "lrs_score", 'width': "80px", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", + 'title': "Peak Location", 'type': "natural-minus-na", - 'width': "150px", + 'width': "120px", 'data': "lrs_location" }, { - 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "additive", 'width': "120px", @@ -367,17 +366,11 @@ author_string = data.authors } return author_string - // try { - // return decodeURIComponent(escape(author_string)) - // } catch(err){ - // return author_string - // } } }, { 'title': "Year", 'type': "natural-minus-na", - 'orderDataType': "dom-inner-text", 'data': null, 'width': "80px", 'render': function(data, type, row, meta) { @@ -390,20 +383,20 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "lrs_score", 'width': "80px", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", + 'title': "Peak Location", 'type': "natural-minus-na", - 'width': "150px", + 'width': "120px", 'data': "lrs_location" }, { - 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'width': "120px", 'data': "additive", @@ -412,7 +405,7 @@ { 'title': "Location", 'type': "natural-minus-na", - 'width': "140px", + 'width': "120px", 'data': "location" }{% endif %} ], diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 8b3e4907..4aced50c 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -215,43 +215,27 @@ <div style="margin-bottom:15px;" class="btn-toolbar"> <div class="btn-group"> - <a href="#redirect"> - <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button> - </a> + <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button> {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %} {% if this_trait.symbol != None %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}"> - <button type="button" class="btn btn-default" title="Find similar expression data">Find</button> - </a> + <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}', '_blank')">Find</button> {% endif %} {% if UCSC_BLAT_URL != "" %} - <a target="_blank" href="{{ UCSC_BLAT_URL }}"> - <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button> - </a> + <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button> {% endif %} {% if this_trait.symbol != None %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}"> - <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button> - </a> + <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button> {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %} - <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on"> - <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button> - </a> + <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button> {% endif %} {% endif %} {% if show_probes == "True" %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON"> - <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button> - </a> + <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button> {% endif %} {% endif %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}"> - <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button> - </a> + <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button> {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} - <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}"> - <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button> - </a> + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button> {% endif %} </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index 05a2be73..a8ed91b1 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -5,7 +5,7 @@ <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ..."> </div> <div style="padding-left: 10px; display: inline;"> - <input type="button" class="btn btn-default export" value="Export"> + <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button> <select class="select optional span2 export_format"> <option value="excel">Excel</option> <option value="csv">CSV</option> diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 974081d3..7bdb3ef9 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -76,11 +76,13 @@ <i class="icon-signal"></i> Sort By Value </button> </div> + <!-- <div class="btn-group"> - <button type="button" class="btn btn-default" id="color_by_trait"> + <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;"> <i class="icon-tint"></i> Color by Trait </button> </div> + --> <div id="bar_chart_container"> <div id="bar_chart"></div> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 42a10c7a..94ec7137 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -50,7 +50,7 @@ from wqflask.search_results import SearchResultPage from wqflask.export_traits import export_search_results_csv from wqflask.gsearch import GSearch from wqflask.update_search_results import GSearch as UpdateGSearch -from wqflask.docs import Docs +from wqflask.docs import Docs, update_text from wqflask.db_info import InfoPage from utility import temp_data @@ -350,7 +350,7 @@ def environments(): @app.route("/update_text", methods=('POST',)) def update_page(): - docs.update_text(request.form) + update_text(request.form) doc = Docs(request.form['entry_type'], request.form) return render_template("docs.html", **doc.__dict__) |