diff options
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/demo_correlation_page.html | 6 |
2 files changed, 27 insertions, 21 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index f1137c0e..1cd1b332 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -63,6 +63,7 @@ def compute_correlation(start_vars, method="pearson"): if corr_type == "sample": corr_input_data = { + "target": target_dataset, "target_dataset": target_dataset.trait_data, "target_samplelist": target_dataset.samplelist, "trait_data": { @@ -80,16 +81,17 @@ def compute_correlation(start_vars, method="pearson"): corr_input_data = { "primary_tissue": primary_tissue_data, - "target_tissues": target_tissue_data + "target_tissues_dict": target_tissue_data } requests_url = f"{GN3_CORRELATION_API}/tissue_corr/{method}" - else: - pass - # lit correlation/literature - # to fetch values from the database + elif corr_type == "lit": + (this_trait_geneid, geneid_dict, species) = do_lit_correlation( + this_trait, this_dataset, target_dataset) + requests_url = f"{GN3_CORRELATION_API}/lit_corr/{species}/{this_trait_geneid}" + corr_input_data = geneid_dict corr_results = requests.post(requests_url, json=corr_input_data) data = corr_results.json() @@ -97,6 +99,18 @@ def compute_correlation(start_vars, method="pearson"): return data +def do_lit_correlation(this_trait, this_dataset, target_dataset): + geneid_dict = this_dataset.retrieve_genes("GeneId") + species = this_dataset.group.species.lower() + + this_trait_geneid = this_trait.geneid + this_trait_gene_data = { + this_trait.name: this_trait_geneid + } + + return (this_trait_geneid, geneid_dict, species) + + 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( @@ -108,23 +122,15 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict): 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", + "this_id": this_trait.name, "tissue_values": primary_trait_tissue_values } + target_tissue_data = { + "trait_symbol_dict": trait_symbol_dict, + "symbol_tissue_vals_dict": corr_result_tissue_vals_dict + } return (primary_tissue_data, target_tissue_data) diff --git a/wqflask/wqflask/templates/demo_correlation_page.html b/wqflask/wqflask/templates/demo_correlation_page.html index ddcdf38d..a8651067 100644 --- a/wqflask/wqflask/templates/demo_correlation_page.html +++ b/wqflask/wqflask/templates/demo_correlation_page.html @@ -10,11 +10,11 @@ {% endblock %} {% block content %} <div class="container"> - <!-- {{correlation_results}} --> - + {{correlation_results}} +<!-- {% for corr in correlation_results %} <div>{{corr}}</div> - {% endfor %} + {% endfor %} --> </div> {% endblock %} |