From 64880f86cdf67c963470098c2aa17d1598fe60e0 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Thu, 7 Nov 2024 15:21:26 -0500
Subject: [PATCH 1/3] G3-495 adding threshold value to the geneset detail view
 GW legacy

---
 pyproject.toml                 |  2 +-
 src/application.py             | 58 ++++++++++++++++++++++++++++++++++
 src/templates/genesetMeta.html | 11 +++++++
 3 files changed, 70 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index bf9abf73..1835fc5f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.4.7"
+version = "1.4.8"
 description = ""
 authors = ["Alexander Berger <alexander.berger@jax.org>"]
 readme = "README.md"
diff --git a/src/application.py b/src/application.py
index 16f5a80e..c83992b8 100644
--- a/src/application.py
+++ b/src/application.py
@@ -38,6 +38,7 @@
 from authlib.integrations.base_client.errors import OAuthError
 
 from decorators import login_required, create_guest, restrict_to_current_user
+from src.error import internal_server_error
 from tools import abbablueprint
 from tools import booleanalgebrablueprint
 from tools import combineblueprint
@@ -2745,6 +2746,9 @@ def render_viewgeneset_main(gs_id, curation_view=None, curation_team=None, curat
     for sp_id, sp_name in geneweaverdb.get_all_species().items():
         species.append([sp_id, sp_name])
 
+    # Try to get formated threshold value from geneset threshold
+    threshold_value = format_str_threshold_value(geneset)
+
     return render_template(
         'viewgenesetdetails.html',
         gs_id=gs_id,
@@ -2765,11 +2769,65 @@ def render_viewgeneset_main(gs_id, curation_view=None, curation_team=None, curat
         show_gene_list=show_gene_list,
         totalGenes=numgenes,
         uploaded_as=uploaded_as,
+        threshold_value=threshold_value,
         #SRP IMPLEMENTATION
         srp=srp
         #SRP IMPLEMENTATION END
     )
 
+def format_str_threshold_value(geneset: dict) -> str:
+    """
+    Formats the threshold value for a gene set to be displayed in the gene set
+    details page,
+    - if the threshold is set and the values are numbers a formatted string value is returned, otherwise None is returned.
+    - if the threshold is a single value, it is formatted as "< value"
+    - if the threshold is a range, it is formatted as "value1 < value2"
+    - if the threshold is binary type(3), None is returned
+    - if the threshold values are the same, None is returned
+
+    arguments
+        geneset: a GeneSet object
+
+    returns
+        a string representation of the threshold value
+    """
+    print (geneset)
+    response = None
+    type = geneset.threshold_type
+
+    ## if binary type return None
+    if type == 3:
+        return None
+
+    threshold = str(geneset.threshold)
+
+    if threshold is not None:
+        thresh = threshold.split(',')
+        if len(thresh) == 1:
+            if not is_number(thresh[0]):
+                response= None
+            else:
+                response= "< " + thresh[0]
+
+        elif len(thresh) > 1:
+            if not is_number(thresh[0]) or not is_number(thresh[1]):
+                response= None
+            elif thresh[0] == thresh[1]:
+                response= None
+            else:
+                response= thresh[0] + " < " + thresh[1]
+
+    return response
+
+def is_number(input):
+    """ Checks if the input is a number"""
+    try:
+        float(input)
+        return True
+    except ValueError:
+        return False
+
+
 @app.route('/viewgenesetoverlap/<list:gs_ids>', methods=['GET'])
 @login_required(allow_guests=True)
 def render_viewgenesetoverlap(gs_ids):
diff --git a/src/templates/genesetMeta.html b/src/templates/genesetMeta.html
index 9f17719b..f4697efa 100644
--- a/src/templates/genesetMeta.html
+++ b/src/templates/genesetMeta.html
@@ -34,6 +34,17 @@
                 </div>
             </div>
 
+            {% if threshold_value%}
+                <div class="row">
+                    <div class="col-md-2">
+                        <p class="text-right"><strong>THRESHOLD:</strong></p>
+                    </div>
+                    <div class="col-md-10">
+                        <p>{{ threshold_value }}</p>
+                    </div>
+                </div>
+            {% endif %}
+
             <div class="row">
                 <div class="col-md-2">
                     <p class="text-right"><strong>DATE ADDED:</strong></p>

From cc4d5a44dcfd8426541f74500d86abff958c96f5 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Thu, 7 Nov 2024 15:34:35 -0500
Subject: [PATCH 2/3] G3-495 version udpate

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1835fc5f..8612b405 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.4.8"
+version = "1.5.1"
 description = ""
 authors = ["Alexander Berger <alexander.berger@jax.org>"]
 readme = "README.md"

From 1201d21d1ded4000f465a446a69f808420d61acc Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Mon, 11 Nov 2024 09:50:17 -0500
Subject: [PATCH 3/3] G3-495 version udpate, clean up

---
 pyproject.toml     | 2 +-
 src/application.py | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8612b405..f28c6e09 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.5.1"
+version = "1.5.2"
 description = ""
 authors = ["Alexander Berger <alexander.berger@jax.org>"]
 readme = "README.md"
diff --git a/src/application.py b/src/application.py
index c83992b8..b73aa1f4 100644
--- a/src/application.py
+++ b/src/application.py
@@ -2791,7 +2791,6 @@ def format_str_threshold_value(geneset: dict) -> str:
     returns
         a string representation of the threshold value
     """
-    print (geneset)
     response = None
     type = geneset.threshold_type