Improved: Changed visualization download functionality from built-in …

…to in-house method. Visualizations will now be downloaded using a button.

Dockerfile

@@ -11,14 +11,16 @@ RUN /opt/conda/bin/conda install --yes \
         scipy==1.6.2 \
         protobuf==3.14.0 \
         python-Levenshtein==0.12.2 \
+        reportlab==3.5.67 \
         nomkl
 
 RUN /opt/conda/bin/conda config --add channels conda-forge
 
 RUN /opt/conda/bin/conda install --yes \
         altair==4.1.0 \
         biopython==1.78 \
-        gensim==4.0.1
+        gensim==4.0.1 \
+        svglib==1.1.0
 
 RUN /opt/conda/bin/conda clean --all --yes
 

Source/common.py

@@ -16,6 +16,8 @@
 from Bio import SeqIO
 from Bio.SeqUtils.ProtParam import ProteinAnalysis
 from scipy.spatial.distance import jaccard, pdist, squareform
+from svglib.svglib import svg2rlg
+from reportlab.graphics import renderPDF
 
 
 __author__ = 'Aleksandar Anžel'
@@ -42,13 +44,24 @@
 alt.data_transformers.enable("default", max_rows=MAX_ROWS)
 
 
-# Functions below are shared among different omics Function that saves charts
-# from list_of_charts with names from list_of_names
-def save_charts(list_of_chart, list_of_names, folder_path):
 
-    for chart, name in zip(list_of_chart, list_of_names):
-        # altair_saver.save(chart, os.path.join (folder_path, name))
-        chart.save(os.path.join(folder_path, name))
+# Functions below are shared among different omics.
+def save_chart(chart, folder_path):
+
+    file_path = os.path.join(folder_path, 'result')
+    chart.save(file_path + '.png')
+    chart.save(file_path + '.svg')
+    drawing = svg2rlg(file_path + '.svg')
+    renderPDF.drawToFile(drawing, file_path + '.pdf')
+
+    # TODO: Create an archive, get the archive path and use it below
+
+    with open(zipped_file_path, 'rb') as zipped_file:
+        st.download_button(label='Download visualization', data=zipped_file,
+                           file_name='movis_visualization.zip',
+                           mime='application/zip')
+
+    return None
 
 
 # This function creates new dataframe with column that represent season

Source/example_1.py

@@ -24,6 +24,8 @@
     path_example_1_root_data, 'metabolomics')
 path_example_1_phy_che = os.path.join(
     path_example_1_root_data, 'phy_che')
+path_example_1_viz = os.path.join(
+    path_example_1_root_data, 'visualizations')
 
 path_example_1_genomics_fasta = os.path.join(
     path_example_1_genomics, 'rmags_filtered')
@@ -214,6 +216,7 @@ def create_main_example_1():
         with st.spinner('Visualizing...'):
             if 'altair' in str(type_of_chart):
                 st.altair_chart(i[0], use_container_width=True)
+                common.save_chart(i[0], path_example_1_viz)
             else:
                 pass
 

Source/example_2.py

@@ -48,6 +48,8 @@
 path_example_2_transcriptomics_final = os.path.join(
     path_example_2_transcriptomics, 'Final.csv')
 
+path_example_2_viz = os.path.join(
+    path_example_2_root_data, 'visualizations')
 
 def upload_intro(folder_path, key_suffix):
     df = None
@@ -114,6 +116,7 @@ def create_main_example_2():
         with st.spinner('Visualizing...'):
             if 'altair' in str(type_of_chart):
                 st.altair_chart(i[0], use_container_width=True)
+                common.save_chart(i[0], path_example_2_viz)
             else:
                 pass
 

Source/upload.py

@@ -27,6 +27,7 @@
 path_uploaded_transcriptomics = os.path.join(path_uploaded, 'transcriptomics')
 path_uploaded_metabolomics = os.path.join(path_uploaded, 'metabolomics')
 path_uploaded_phy_che = os.path.join(path_uploaded, 'phy_che')
+path_uploaded_viz = os.path.join(path_uploaded, 'visualizations')
 
 path_uploaded_dict = {
     'Genomics': path_uploaded_genomics,
@@ -464,6 +465,7 @@ def create_main_upload():
         with st.spinner('Visualizing...'):
             if 'altair' in str(type_of_chart):
                 st.altair_chart(i[0], use_container_width=True)
+                common.save_chart(i[0], path_uploaded_viz)
             else:
                 pass