diff options
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 89 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/demo_correlation_page.html | 22 |
2 files changed, 38 insertions, 73 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 7e269e41..7e865bf3 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -10,59 +10,6 @@ from wqflask.base.trait import retrieve_sample_data GN3_CORRELATION_API = "http://127.0.0.1:8080/api/correlation" -def compute_sample(target_dataset, trait_data, target_samplelist, method="pearson"): - """integration for integrating sample_r api correlation""" - data = { - "target_dataset": target_dataset, - "target_samplelist": target_samplelist, - "trait_data": { - "trait_sample_data": trait_data, - "trait_id": "HC_Q" - } - } - requests_url = f"http://127.0.0.1:8080/api/correlation/sample_x/{method}" - - results = requests.post(requests_url, json=data) - - data = results.json() - - return data - - -def get_tissue_correlation_input(this_trait, trait_symbol_dict): - """Gets tissue expression values for the primary trait and target tissues values""" - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=[this_trait.symbol]) - - if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( - )] - - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=list(trait_symbol_dict.values())) - - target_tissue_data = [] - for trait, symbol in list(trait_symbol_dict.items()): - if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( - )] - - this_trait_data = {"trait_id": trait, - "tissue_values": this_trait_tissue_values} - - target_tissue_data.append(this_trait_data) - - primary_tissue_data = { - "this_id": "TT", - "tissue_values": primary_trait_tissue_values - - } - - return (primary_tissue_data, target_tissue_data) - - return None - - def process_samples(start_vars, sample_names, excluded_samples=None): """process samples method""" sample_data = {} @@ -81,7 +28,7 @@ def process_samples(start_vars, sample_names, excluded_samples=None): def create_target_this_trait(start_vars): - """this function prefetch required data for correlation""" + """this function creates the required trait and target dataset for correlation""" this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset']) target_dataset = data_set.create_dataset( @@ -148,3 +95,37 @@ def compute_correlation(start_vars, method="pearson"): data = corr_results.json() return data + + +def get_tissue_correlation_input(this_trait, trait_symbol_dict): + """Gets tissue expression values for the primary trait and target tissues values""" + primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list=[this_trait.symbol]) + + if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: + primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( + )] + + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list=list(trait_symbol_dict.values())) + + target_tissue_data = [] + for trait, symbol in list(trait_symbol_dict.items()): + if symbol and symbol.lower() in corr_result_tissue_vals_dict: + this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( + )] + + this_trait_data = {"trait_id": trait, + "tissue_values": this_trait_tissue_values} + + target_tissue_data.append(this_trait_data) + + primary_tissue_data = { + "this_id": "TT", + "tissue_values": primary_trait_tissue_values + + } + + return (primary_tissue_data, target_tissue_data) + + return None diff --git a/wqflask/wqflask/templates/demo_correlation_page.html b/wqflask/wqflask/templates/demo_correlation_page.html index 4d310051..ddcdf38d 100644 --- a/wqflask/wqflask/templates/demo_correlation_page.html +++ b/wqflask/wqflask/templates/demo_correlation_page.html @@ -10,27 +10,11 @@ {% endblock %} {% block content %} <div class="container"> - {{correlation_results}} + <!-- {{correlation_results}} --> - <!-- {% for corr in correlation_results %} + {% for corr in correlation_results %} <div>{{corr}}</div> {% endfor %} - --> - </div> -{% endblock %} -{% block js %} - <script 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='js_alt/underscore.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> - <script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> - + </div> {% endblock %} |