DNA Segment Map - fix bug 13375 and enhancement 13382 (#600)

Fix dump when DNA Association data contains tab characters.

Add config option to include/exclude Citation Notes for parsing DNA data. Association Notes are always parsed. Currently Citations attached to an Association are parsed too. This makes them optional. 

Add config for character scale in Legend to allow more entries. Default fontsize is 12. This option lets user specify the fontsize for the Legend. This does not impact the chart size.

Author: GaryGriffin

DNA/dnasegmentmap.py

@@ -62,6 +62,8 @@
 CONFIG.register('map.paternal-background', (0.833, 0.845, 0.92, 1.0))
 CONFIG.register('map.legend-single-chromosome-y-offset', 25)
 CONFIG.register('map.show-centromere',0)
+CONFIG.register('map.legend-char-height',12)
+CONFIG.register('map.include-citation-notes',1)
 
 CONFIG.init()
 
@@ -116,6 +118,7 @@ def main(self):
             segmap.gender = active.gender
             segmap.active = active
             segmap.relationship = self.relationship
+            include_citation_notes = segmap._config.get('map.include-citation-notes')
 
             for assoc in active.get_person_ref_list():
                 if assoc.get_relation() == 'DNA':
@@ -142,13 +145,14 @@ def main(self):
                             assoc_handle = assoc.ref
                             self.write_chromo(line, side, rgb_color, assoc, note, segmap)
                     # Get Notes attached to Citation which is attached to the Association
-                    for citation_handle in assoc.get_citation_list():
-                        citation = self.dbstate.db.get_citation_from_handle(citation_handle)
-                        for handle in citation.get_note_list():
-                            note = self.dbstate.db.get_note_from_handle(handle)
-                            for line in note.get().split('\n'):
-                                assoc_handle = assoc.ref
-                                self.write_chromo(line, side, rgb_color, assoc, note, segmap)
+                    if include_citation_notes :
+                        for citation_handle in assoc.get_citation_list():
+                            citation = self.dbstate.db.get_citation_from_handle(citation_handle)
+                            for handle in citation.get_note_list():
+                                note = self.dbstate.db.get_note_from_handle(handle)
+                                for line in note.get().split('\n'):
+                                    assoc_handle = assoc.ref
+                                    self.write_chromo(line, side, rgb_color, assoc, note, segmap)
             if len(segmap.segments) > 0:
                 segmap.show()
                 self.vbox.pack_start(segmap, True, True, 0)
@@ -158,12 +162,17 @@ def write_chromo(self, line, side, rgb_color, assoc, note, segmap):
         if "\t" in line:
 # Tabs are the field separators. Now determine THOUSEP and RADIXCHAR. Use Field 2 (Stop Pos) to see if there are THOUSEP there. Use Field 3 (SNPs) to see if there is a radixchar
             field = line.split('\t')
-            if "," in field[2]:
-                line = line.replace(",", "")
-            elif "." in field[2]:
-                line = line.replace(".", "")
-            if "," in field[3]:
-                line = line.replace(",", ".")
+            if len(field) > 3:
+                if "," in field[2]:
+                    line = line.replace(",", "")
+                elif "." in field[2]:
+                    line = line.replace(".", "")
+                if "," in field[3]:
+                    line = line.replace(",", ".")
+            else:
+                associate = segmap.dbstate.db.get_person_from_handle(assoc.ref)
+                id_str = _(_nd.display(associate) )
+                print("Skipping: ",id_str,line)
             line = line.replace("\t", ",")
 # If Tab is not the field separator, then comma is. And point is the radixchar.
         field = line.split(',')
@@ -239,6 +248,7 @@ def __init__(self):
         self.paternal_background = self._config.get('map.paternal-background')
         self.legend_single_chromosome = self._config.get('map.legend-single-chromosome-y-offset')
         self.show_centromere = self._config.get('map.show-centromere')
+        self.legend_char_height = self._config.get('map.legend-char-height')
         self._config.save()
         self.chromosomesThirtySeven = (
             ('1', 249250621),
@@ -477,7 +487,7 @@ def do_draw(self, cr):
                     label_width = width
                 offset_x = -(len(label)-2)* 6
                 cr.move_to(offset_x, i * 2 * (chr_height + spacing) + offset+7)
-                self.__chrrects.append((offset_x, i * 2 * (chr_height + spacing) + offset+7, 12, chr_height))
+                self.__chrrects.append((offset_x, i * 2 * (chr_height + spacing) + offset+7, chr_height, chr_height))
                 PangoCairo.show_layout(cr, layout)
 
             self.set_axis(_('Chr'))
@@ -625,6 +635,7 @@ def do_draw(self, cr):
         cr.set_source_rgba(*fg_color)
         PangoCairo.show_layout(cr, layout)
         legend_offset_y += chr_height + 2 * spacing
+        legend_chr_height = self.legend_char_height
         chromo_count = -1
         row_num = 0
         maximum = self.maximum
@@ -706,21 +717,21 @@ def do_draw(self, cr):
                     cr.set_source_rgba(*fg_color)
                     cr.stroke()
 # Legend
-                cr.rectangle(legend_offset_x - chr_height - 2 * spacing,
+                cr.rectangle(legend_offset_x - legend_chr_height - 2 * spacing,
                              legend_offset_y + self.legend_swatch_offset_y,
-                             chr_height,
-                             chr_height)
+                             legend_chr_height,
+                             legend_chr_height)
                 cr.set_source_rgba(rgb_color[0], rgb_color[1], rgb_color[2], 1)
                 cr.fill_preserve()
                 cr.stroke()
                 layout = self.create_pango_layout(last_name)
                 cr.move_to(legend_offset_x, legend_offset_y)
-                self.__legendrects.append((legend_offset_x, legend_offset_y,len(assoc_name) * 6, chr_height))
+                self.__legendrects.append((legend_offset_x, legend_offset_y,len(assoc_name) * 6, legend_chr_height))
                 self.__associates.append(associate)
                 self.__assoc_handle.append(handle)
                 self.__legend_str.append(last_name)
                 cr.set_source_rgba(*fg_color)
-                legend_offset_y += chr_height + 2 * spacing
+                legend_offset_y += legend_chr_height + 2 * spacing
                 PangoCairo.show_layout(cr, layout)
 # Segment Info
               chr_offset = row_num * 2 * (chr_height + spacing) + offset
@@ -748,22 +759,22 @@ def do_draw(self, cr):
               if last_name != assoc_name:
                 last_name = assoc_name
 
-                cr.rectangle(legend_offset_x - chr_height - 2 * spacing,
+                cr.rectangle(legend_offset_x - legend_chr_height - 2 * spacing,
                              legend_offset_y,
-                             chr_height,
-                             chr_height)
+                             legend_chr_height,
+                             legend_chr_height)
                 cr.set_source_rgba(rgb_color[0], rgb_color[1], rgb_color[2], 1/chr_mult)
                 cr.fill_preserve()
                 cr.stroke()
 
                 layout = self.create_pango_layout(last_name)
                 cr.move_to(legend_offset_x, legend_offset_y)
-                self.__legendrects.append((legend_offset_x, legend_offset_y,len(assoc_name) * 6, chr_height))
+                self.__legendrects.append((legend_offset_x, legend_offset_y,len(assoc_name) * 6, legend_chr_height))
                 self.__associates.append(associate)
                 self.__assoc_handle.append(handle)
                 self.__legend_str.append(last_name)
                 cr.set_source_rgba(*fg_color)
-                legend_offset_y += chr_height + 2 * spacing
+                legend_offset_y += legend_chr_height + 2 * spacing
                 PangoCairo.show_layout(cr, layout)
         else: # Drawing all chromosome segments
           for chromo, start, stop, side, cms, snp, assoc_name, rgb_color, associate, handle, note in self.segments:
@@ -796,22 +807,22 @@ def do_draw(self, cr):
 # Legend entry
             if last_name != assoc_name:
                 last_name = assoc_name
-                cr.rectangle(legend_offset_x - chr_height - 2 * spacing,
+                cr.rectangle(legend_offset_x - legend_chr_height - 2 * spacing,
                              legend_offset_y + self.legend_swatch_offset_y,
-                             chr_height,
-                             chr_height)
+                             legend_chr_height,
+                             legend_chr_height)
                 cr.set_source_rgba(rgb_color[0], rgb_color[1], rgb_color[2], 1/chr_mult)
                 cr.fill_preserve()
                 cr.stroke()
 
                 layout = self.create_pango_layout(last_name)
                 cr.move_to(legend_offset_x, legend_offset_y)
-                self.__legendrects.append((legend_offset_x, legend_offset_y,len(assoc_name) * 6, chr_height))
+                self.__legendrects.append((legend_offset_x, legend_offset_y,len(assoc_name) * 6, legend_chr_height))
                 self.__associates.append(associate)
                 self.__assoc_handle.append(handle)
                 self.__legend_str.append(last_name)
                 cr.set_source_rgba(*fg_color)
-                legend_offset_y += chr_height + 2 * spacing
+                legend_offset_y += legend_chr_height + 2 * spacing
                 PangoCairo.show_layout(cr, layout)
 
         self.set_size_request(-1, bottom + height + 5)