Shortened reader pages

openworm · Jul 2, 2024 · 048c7f0 · 048c7f0
1 parent a853833
commit 048c7f0
Show file tree

Hide file tree

Showing 10 changed files with 173 additions and 69 deletions.
diff --git a/cect/Comparison.py b/cect/Comparison.py
@@ -3,8 +3,12 @@
 from cect.ConnectomeReader import analyse_connections
 from cect.ConnectomeReader import check_neurons
 
+import sys
+
 all_data = {}
 
+quick = len(sys.argv)>1 and eval(sys.argv[1])
+
 reader_pages = {"Varshney":"Varshney_data",
                 "White_A":"White_A_data",
                 "White_L4":"White_L4_data",
@@ -26,25 +30,26 @@
                      "N->N neurotrans.", 
                      "N->M neurotrans."]
 
-
-readers = {"SSData": "cect.SpreadsheetDataReader", 
-           "UpdSSData": "cect.UpdatedSpreadsheetDataReader",
-           "UpdSSData2": "cect.UpdatedSpreadsheetDataReader2",
-           "Varshney": "cect.VarshneyDataReader",
-           "White_L4": "cect.White_L4", 
-          }
-readers = {"SSData": "cect.SpreadsheetDataReader", 
-           "UpdSSData": "cect.UpdatedSpreadsheetDataReader",
-           "UpdSSData2": "cect.UpdatedSpreadsheetDataReader2",
-           "White_A": "cect.White_A", 
-           "White_L4": "cect.White_L4", 
-           "White_whole": "cect.White_whole",
-           "Varshney": "cect.VarshneyDataReader",
-           "Witvliet1": "cect.WitvlietDataReader1",
-           "Witvliet2": "cect.WitvlietDataReader2",
-           "WormNeuroAtlas": "cect.WormNeuroAtlasReader",
-           "Cook2019Herm": "cect.Cook2019HermReader",
-          }
+if quick:
+    readers = {"SSData": "cect.SpreadsheetDataReader", 
+            "UpdSSData": "cect.UpdatedSpreadsheetDataReader",
+            "UpdSSData2": "cect.UpdatedSpreadsheetDataReader2",
+            "Varshney": "cect.VarshneyDataReader",
+            "White_L4": "cect.White_L4", 
+            }
+else:
+    readers = {"SSData": "cect.SpreadsheetDataReader", 
+            "UpdSSData": "cect.UpdatedSpreadsheetDataReader",
+            "UpdSSData2": "cect.UpdatedSpreadsheetDataReader2",
+            "White_A": "cect.White_A", 
+            "White_L4": "cect.White_L4", 
+            "White_whole": "cect.White_whole",
+            "Varshney": "cect.VarshneyDataReader",
+            "Witvliet1": "cect.WitvlietDataReader1",
+            "Witvliet2": "cect.WitvlietDataReader2",
+            "WormNeuroAtlas": "cect.WormNeuroAtlasReader",
+            "Cook2019Herm": "cect.Cook2019HermReader",
+            }
 
 
 def shorten_neurotransmitter(nt):
@@ -53,7 +58,7 @@ def shorten_neurotransmitter(nt):
 
 
 # TODO: move elsewhere and make more generic
-def get_cell_link(cell_name):
+def get_cell_link(cell_name, html=False):
 
     url = None
 
@@ -71,7 +76,10 @@ def get_cell_link(cell_name):
         url = 'https://www.wormatlas.org/neurons/Individual Neurons/%sframeset.html'%cell_name
 
     if url is not None:
-        return '[%s](%s)'%(cell_name, url)
+        if html:
+            return '<a href="%s">%s</a>'%(url, cell_name)
+        else:
+            return '[%s](%s)'%(cell_name, url)
     else:
         return cell_name
 
@@ -119,7 +127,8 @@ def get_cell_link(cell_name):
     ref = '[%s](%s.md)'%(name,reader_pages[name]) if name in reader_pages else name
 
     if name in reader_pages:
-        with open('docs/%s.md'%reader_pages[name], 'w') as f:
+        filename = 'docs/%s.md'%reader_pages[name]
+        with open(filename, 'w') as f:
             f.write('## %s\n'%name)
 
             cells = {'Neurons': preferred, 
@@ -128,9 +137,18 @@ def get_cell_link(cell_name):
                      "Other cells": not_in_preferred}
 
             for t in cells:
-                f.write('\n### %s (%i)\n| '%(t,len(cells[t])))
-                for n in sorted(cells[t]):
-                    f.write('%s | '%(get_cell_link(n)))
+                f.write('\n### %s (%i)\n'%(t,len(cells[t])))
+                if len(cells[t])>0:
+                    f.write('<details><summary>Full list of %s</summary>\n'%t)
+                    ss = sorted(cells[t])
+                    for n in ss:
+                        f.write('%s'%(get_cell_link(n, True)))
+                        if n is not ss[-1]:
+                            f.write(' | ')
+
+                    f.write('\n</details>\n')
+
+        print('Written page: %s'%filename)
 
 
     all_data[ref] =[len(preferred),
@@ -156,6 +174,8 @@ def get_cell_link(cell_name):
 
 mk = df_all.to_markdown()
 
-with open('docs/Comparison.md', 'w') as f:
+filename = 'docs/Comparison.md'
+with open(filename, 'w') as f:
     f.write(mk)
 
+print('Written page: %s'%filename)
diff --git a/docs/Cook2019Herm_data.md b/docs/Cook2019Herm_data.md
diff --git a/docs/Varshney_data.md b/docs/Varshney_data.md
diff --git a/docs/White_A_data.md b/docs/White_A_data.md
diff --git a/docs/White_L4_data.md b/docs/White_L4_data.md
diff --git a/docs/White_whole_data.md b/docs/White_whole_data.md
diff --git a/docs/Witvliet1_data.md b/docs/Witvliet1_data.md
diff --git a/docs/Witvliet2_data.md b/docs/Witvliet2_data.md
diff --git a/docs/WormNeuroAtlas_data.md b/docs/WormNeuroAtlas_data.md
diff --git a/test.sh b/test.sh
@@ -2,28 +2,39 @@ set -ex
 
 pip install .
 
+quick_test=false
+
+if [[ ($# -eq 1) && ($1 == '-q') ]]; then
+    quick_test=true
+fi
+
 ##   Test readers
 
 python -m cect.SpreadsheetDataReader 
 python -m cect.UpdatedSpreadsheetDataReader                                                                                                                                                                      
 python -m cect.UpdatedSpreadsheetDataReader2                                                                                                                                                                  
 #python -m cect.OpenWormReader                                                                                                                                                            
 python -m cect.VarshneyDataReader
-python -m cect.Cook2019DataReader
-python -m cect.Cook2019HermReader
-python -m cect.WormNeuroAtlasReader
-python -m cect.W_SpreadsheetDataReader
-python -m cect.WitvlietDataReader1
-python -m cect.WitvlietDataReader2
-python -m cect.WhiteDataReader
-python -m cect.White_A
-python -m cect.White_L4
-python -m cect.White_whole
 
+if [ "$quick_test" == false ]; then
+
+    python -m cect.Cook2019DataReader
+    python -m cect.Cook2019HermReader
+    python -m cect.WormNeuroAtlasReader
+    python -m cect.W_SpreadsheetDataReader
+    python -m cect.WitvlietDataReader1
+    python -m cect.WitvlietDataReader2
+    python -m cect.WhiteDataReader
+    python -m cect.White_A
+    python -m cect.White_L4
+    python -m cect.White_whole
+fi
 
+python cect/Comparison.py $quick_test
+mkdocs build
 
 echo
-echo "  Successfully completed all cect tests!"
+echo "  Successfully completed all cect tests (quick run: $quick_test)!"
 echo