1 files changed, 129 insertions, 0 deletions
diff --git a/gn2/wqflask/external_tools/send_to_webgestalt.py b/gn2/wqflask/external_tools/send_to_webgestalt.py
new file mode 100644
index 00000000..9633e560
--- /dev/null
+++ b/gn2/wqflask/external_tools/send_to_webgestalt.py
@@ -0,0 +1,129 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from gn2.wqflask.database import database_connection
+
+from gn2.base.trait import retrieve_trait_info
+from gn2.utility import helper_functions
+from gn2.utility.tools import get_setting
+
+
+class SendToWebGestalt:
+    def __init__(self, start_vars):
+        trait_db_list = [trait.strip()
+                         for trait in start_vars['trait_list'].split(',')]
+        helper_functions.get_trait_db_obs(self, trait_db_list)
+
+        self.chip_name = test_chip(self.trait_list)
+
+        self.wrong_input = "False"
+        if self.chip_name == "mixed" or self.chip_name == "not_microarray" or '_NA' in self.chip_name:
+            self.wrong_input = "True"
+        else:
+            trait_name_list, gene_id_list = gen_gene_id_list(self.trait_list)
+
+            self.target_url = "https://www.webgestalt.org/option.php"
+
+            id_type = "entrezgene"
+
+            self.hidden_vars = {
+                'gene_list': "\n".join(gene_id_list),
+                             'id_type': "entrezgene",
+                             'ref_set': "genome",
+                             'enriched_database_category': "geneontology",
+                             'enriched_database_name': "Biological_Process",
+                             'sig_method': "fdr",
+                             'sig_value': "0.05",
+                             'enrich_method': "ORA",
+                             'fdr_method': "BH",
+                             'min_num': "2"
+            }
+
+            species = self.trait_list[0][1].group.species
+            if species == "rat":
+                self.hidden_vars['organism'] = "rnorvegicus"
+            elif species == "human":
+                self.hidden_vars['organism'] = "hsapiens"
+            elif species == "mouse":
+                self.hidden_vars['organism'] = "mmusculus"
+            else:
+                self.hidden_vars['organism'] = "others"
+
+
+def test_chip(trait_list):
+    final_chip_name = ""
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        for trait_db in trait_list:
+            dataset = trait_db[1]
+            cursor.execute(
+                "SELECT GeneChip.GO_tree_value "
+                "FROM GeneChip, ProbeFreeze, "
+                "ProbeSetFreeze WHERE "
+                "GeneChip.Id = ProbeFreeze.ChipId "
+                "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                "AND ProbeSetFreeze.Name = %s", (dataset.name,)
+            )
+
+            if result := cursor.fetchone():
+                chip_name = result[0]
+                if chip_name:
+                    if chip_name != final_chip_name:
+                        if final_chip_name:
+                            return "mixed"
+                        else:
+                            final_chip_name = chip_name
+                    else:
+                        pass
+                else:
+                    cursor.execute(
+                        "SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, "
+                        "ProbeSetFreeze WHERE "
+                        "GeneChip.Id = ProbeFreeze.ChipId AND "
+                        "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                        "AND ProbeSetFreeze.Name = %s", (dataset.name,)
+                    )
+                    result = cursor.fetchone()
+                    chip_name = f'{result[0]}_NA'
+                    return chip_name
+            else:
+                cursor.execute(
+                    "SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, "
+                    "ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId "
+                    "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+                    "ProbeSetFreeze.Name = %s", (dataset.name,)
+                )
+                result = cursor.fetchone()
+                if not result:
+                    return "not_microarray"
+                else:
+                    chip_name = f'{result[0]}_NA'
+                    return chip_name
+    return chip_name
+
+
+def gen_gene_id_list(trait_list):
+    trait_name_list = []
+    gene_id_list = []
+    for trait_db in trait_list:
+        trait = trait_db[0]
+        trait_name_list.append(trait.name)
+        retrieve_trait_info(trait, trait.dataset)
+        gene_id_list.append(str(trait.geneid))
+    return trait_name_list, gene_id_list