From bbe054c5263073e87e3695007bdb1b417f73c324 Mon Sep 17 00:00:00 2001
From: AAnzel <44969003+AAnzel@users.noreply.github.com>
Date: Tue, 21 Dec 2021 16:18:19 +0100
Subject: [PATCH] Changed: Changed some text. Started creating case study
 layout.

---
 Source/case_study.py | 21 +++++++++++++++++++--
 Source/example_1.py  |  3 +--
 Source/example_2.py  |  2 +-
 Source/upload.py     |  2 +-
 4 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/Source/case_study.py b/Source/case_study.py
index 082c4a5..c2f22ac 100644
--- a/Source/case_study.py
+++ b/Source/case_study.py
@@ -37,6 +37,8 @@
     path_case_study_genomics, 'MT_Depths')
 path_case_study_proteomics_fasta = os.path.join(
     path_case_study_proteomics, 'set_of_78')
+path_case_study_metabolomics_precalculated = os.path.join(
+    path_case_study_metabolomics, 'fig4.tsv')
 
 
 def upload_multiple(key_suffix):
@@ -49,7 +51,10 @@ def upload_multiple(key_suffix):
         'Metaproteomics': {
             'Raw FASTA files': 'FASTA'},
         'Metatranscriptomics': {
-            'Depth-of-coverage': 'DEPTH'}
+            'Depth-of-coverage': 'DEPTH'},
+        'Metabolomics': {
+            'Processed data set 1': 'PR1',
+            'Processed data set 2': 'PR2'}
     }
 
     selected_data_set_type = st.selectbox(
@@ -75,6 +80,17 @@ def upload_multiple(key_suffix):
     elif key_suffix == 'Metatranscriptomics':
         return_path = path_case_study_transcriptomics_depths
 
+    # TODO: Add calculated 1 and calculated 2 data sets here and maybe remove
+    # TODO: upload introand move everything here
+    elif key_suffix == 'Metabolomics':
+        if selected_data_set_type == 'Processed data set 1':
+            return_path = path_case_study_genomics_fasta
+
+        # elif selected_data_set_type == 'KEGG annotation files':
+        #     return_path = path_case_study_genomics_kegg
+        elif selected_data_set_type == 'Depth-of-coverage':
+            return_path = path_case_study_genomics_depths
+
     else:
         pass
 
@@ -188,7 +204,8 @@ def create_main_case_study():
     case_study_omics_list = ['Metagenomics', 'Metabolomics', 'Metaproteomics',
                              'Metatranscriptomics', 'Physico-chemical']
     choose_omics = st.multiselect(
-        'What kind of data set do you want to see?', case_study_omics_list)
+        'What kind of omic data do you want to explore?',
+        case_study_omics_list)
 
     num_of_columns = len(choose_omics)
 
diff --git a/Source/example_1.py b/Source/example_1.py
index 8fd0f38..d1e850b 100644
--- a/Source/example_1.py
+++ b/Source/example_1.py
@@ -61,7 +61,6 @@ def upload_multiple(key_suffix):
 
     if key_suffix == 'Metagenomics':
         if selected_data_set_type == 'Raw FASTA files':
-
             return_path = path_example_1_genomics_fasta
 
         # elif selected_data_set_type == 'KEGG annotation files':
@@ -192,7 +191,7 @@ def create_main_example_1():
     example_1_omics_list = ['Metagenomics', 'Metabolomics', 'Metaproteomics',
                             'Metatranscriptomics', 'Physico-chemical']
     choose_omics = st.multiselect(
-        'What kind of data set do you want to see?', example_1_omics_list)
+        'What kind of omic data do you want to explore?', example_1_omics_list)
 
     num_of_columns = len(choose_omics)
 
diff --git a/Source/example_2.py b/Source/example_2.py
index 36691ae..f3c945d 100644
--- a/Source/example_2.py
+++ b/Source/example_2.py
@@ -101,7 +101,7 @@ def create_main_example_2():
 
     example_2_omics_list = ['Transcriptomics']
     choose_omics = st.multiselect(
-        'What kind of data set do you want to see?', example_2_omics_list)
+        'What kind of omic data do you want to explore?', example_2_omics_list)
 
     charts = []  # An empty list to hold all pairs (visualizations, key)
 
diff --git a/Source/upload.py b/Source/upload.py
index 8018e03..66ba04f 100644
--- a/Source/upload.py
+++ b/Source/upload.py
@@ -259,7 +259,7 @@ def upload_multiple(key_suffix):
     }
 
     selected_data_set_type = st.selectbox(
-        'What kind of data set do you want to upload?',
+        'What kind of omic data do you want to upload?',
         list(available_data_set_types[key_suffix].keys())
     )