From 3bce1c9f3a687069738267e74ca8c093f629544d Mon Sep 17 00:00:00 2001
From: anmol thapar <mr.anmolthapar@gmail.com>
Date: Tue, 7 Jan 2025 10:49:10 +0000
Subject: [PATCH 1/3] Add info_csv parameter to createMicroreact for
 conditional map and timeline handling

---
 PopPUNK/data/microreact_example.pkl | Bin 38827 -> 39577 bytes
 PopPUNK/plot.py                     |  14 +++++++++++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/PopPUNK/data/microreact_example.pkl b/PopPUNK/data/microreact_example.pkl
index ec31f47ad7510451aba0ad7b1160e5a01856a051..648127a34d8c159f490f4b16f0d07da9f69069b3 100644
GIT binary patch
delta 846
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diff --git a/PopPUNK/plot.py b/PopPUNK/plot.py
index c8e5dd6b..f9ccf58b 100644
--- a/PopPUNK/plot.py
+++ b/PopPUNK/plot.py
@@ -836,7 +836,7 @@ def outputsForMicroreact(combined_list, clustering, nj_tree, mst_tree, accMat, p
 
     return outfiles
 
-def createMicroreact(prefix, microreact_files, api_key=None):
+def createMicroreact(prefix, microreact_files, api_key=None, info_csv=None):
     """Creates a .microreact file, and instance via the API
 
     Args:
@@ -852,6 +852,7 @@ def createMicroreact(prefix, microreact_files, api_key=None):
     import requests
     import json
     from datetime import datetime
+    import pandas as pd
 
     microreact_api_new_url = "https://microreact.org/api/projects/create"
     description_string = "PopPUNK run on " + datetime.now().strftime("%Y-%b-%d %H:%M")
@@ -859,6 +860,17 @@ def createMicroreact(prefix, microreact_files, api_key=None):
     with pkg_resources.resource_stream(__name__, 'data/microreact_example.pkl') as example_pickle:
         json_pickle = pickle.load(example_pickle)
     json_pickle["meta"]["name"] = description_string
+    
+    # remove maps and timelines if not present in csv columns
+    if info_csv is None:
+        json_pickle["maps"] = {}
+        json_pickle["timelines"] = {}
+    else:
+        info_df = pd.read_csv(info_csv)
+        if 'latitude' not in info_df.columns or 'longitude' not in info_df.columns:
+            json_pickle["maps"] = {}
+        if 'date' not in info_df.columns:
+            json_pickle["timelines"] = {}
 
     # Read data in
     with open(microreact_files[0]) as cluster_file:

From 23a92732a889cc4e21741bb678122b3cf3014254 Mon Sep 17 00:00:00 2001
From: anmol thapar <mr.anmolthapar@gmail.com>
Date: Tue, 7 Jan 2025 12:09:44 +0000
Subject: [PATCH 2/3] Bump version to 2.7.3 and refactor createMicroreact to
 use update_maps_timelines for handling maps and timelines based on info_csv

---
 PopPUNK/__init__.py |  2 +-
 PopPUNK/plot.py     | 37 ++++++++++++++++++++++++++-----------
 2 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/PopPUNK/__init__.py b/PopPUNK/__init__.py
index d7f9d184..c6757346 100644
--- a/PopPUNK/__init__.py
+++ b/PopPUNK/__init__.py
@@ -3,7 +3,7 @@
 
 '''PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'''
 
-__version__ = '2.7.2'
+__version__ = '2.7.3'
 
 # Minimum sketchlib version
 SKETCHLIB_MAJOR = 2
diff --git a/PopPUNK/plot.py b/PopPUNK/plot.py
index f9ccf58b..4ffafe48 100644
--- a/PopPUNK/plot.py
+++ b/PopPUNK/plot.py
@@ -846,6 +846,8 @@ def createMicroreact(prefix, microreact_files, api_key=None, info_csv=None):
             List of Microreact files [clusters, dot, tree, mst_tree]
         api_key (str)
             API key for your account
+        info_csv (str)
+            CSV file containing additional information for Microreact
     """
     import pkg_resources
     import pickle
@@ -861,17 +863,9 @@ def createMicroreact(prefix, microreact_files, api_key=None, info_csv=None):
         json_pickle = pickle.load(example_pickle)
     json_pickle["meta"]["name"] = description_string
     
-    # remove maps and timelines if not present in csv columns
-    if info_csv is None:
-        json_pickle["maps"] = {}
-        json_pickle["timelines"] = {}
-    else:
-        info_df = pd.read_csv(info_csv)
-        if 'latitude' not in info_df.columns or 'longitude' not in info_df.columns:
-            json_pickle["maps"] = {}
-        if 'date' not in info_df.columns:
-            json_pickle["timelines"] = {}
-
+    # Update maps and timelines
+    update_maps_timelines(json_pickle, info_csv)
+    
     # Read data in
     with open(microreact_files[0]) as cluster_file:
         csv_string = cluster_file.read()
@@ -910,6 +904,27 @@ def createMicroreact(prefix, microreact_files, api_key=None, info_csv=None):
 
     return url
 
+def update_maps_timelines(micoreact_sample_json, info_csv=None):
+    """
+    Update the maps and timelines in the Microreact JSON file.
+    Removes maps and timelines if the required columns are not present in the info CSV.
+    
+    Args:
+        micoreact_sample_json (dict)
+            Microreact JSON file
+        info_csv (str)
+            CSV file containing additional information for Microreact
+    """
+    if info_csv is None:
+        micoreact_sample_json["maps"] = {}
+        micoreact_sample_json["timelines"] = {}
+    else:
+        info_df = pd.read_csv(info_csv)
+        if 'latitude' not in info_df.columns or 'longitude' not in info_df.columns:
+            micoreact_sample_json["maps"] = {}
+        if 'year' not in info_df.columns:
+            micoreact_sample_json["timelines"] = {}
+            
 def outputsForPhandango(combined_list, clustering, nj_tree, mst_tree, outPrefix, epiCsv,
                         queryList = None, overwrite = False):
     """Generate files for Phandango

From ce87e8e5e57e837c47f7098e94ec499ad791eba6 Mon Sep 17 00:00:00 2001
From: anmol thapar <mr.anmolthapar@gmail.com>
Date: Tue, 7 Jan 2025 12:24:05 +0000
Subject: [PATCH 3/3] Remove unused pandas import from createMicroreact
 function

---
 PopPUNK/plot.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/PopPUNK/plot.py b/PopPUNK/plot.py
index 4ffafe48..2328c160 100644
--- a/PopPUNK/plot.py
+++ b/PopPUNK/plot.py
@@ -854,7 +854,6 @@ def createMicroreact(prefix, microreact_files, api_key=None, info_csv=None):
     import requests
     import json
     from datetime import datetime
-    import pandas as pd
 
     microreact_api_new_url = "https://microreact.org/api/projects/create"
     description_string = "PopPUNK run on " + datetime.now().strftime("%Y-%b-%d %H:%M")