fixed html report key bug

kbaseapps · Oct 17, 2023 · 27c598d · 27c598d
1 parent a864f95
commit 27c598d
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -50,10 +50,10 @@ RUN pip install ete3==3.1.3 PyQt5==5.11.3
 
 # tree utils install
 WORKDIR /kb/module
-RUN git clone https://github.com/dcchivian/tree_utils \
-    && mkdir bin \
-    && mv tree_utils/gtdb/* bin/ \
-    && chmod +x bin/*
+RUN git clone https://github.com/dcchivian/tree_utils && \
+    mkdir bin && \
+    mv tree_utils/gtdb/* bin/ && \
+    chmod +x bin/*
 
 # -----------------------------------------
 

diff --git a/lib/kb_gtdbtk/core/genome_obj_update.py b/lib/kb_gtdbtk/core/genome_obj_update.py
@@ -19,9 +19,6 @@
 [OBJID_I, NAME_I, TYPE_I, SAVE_DATE_I, VERSION_I, SAVED_BY_I, WSID_I,
  WORKSPACE_I, CHSUM_I, SIZE_I, META_I] = range(11)  # object_info tuple    
 
-# global for tree html
-tree_key_taxon_seen = dict()
-
 
 # get_obj_info ()
 def get_obj_info (
@@ -339,18 +336,22 @@ def _write_gtdb_tree_html_file (out_dir, files_for_html):
         indent_cnt = 0
         key_box_size = '15px'
         key_font_size = key_box_size
-        table_buf += ['<td align=left valign=middle><table border=0>']
+        table_buf += ['<td align=left valign=top><table border=0>']
         #tax_level_order = ['d', 'p', 'c', 'o', 'f', 'g']
         tax_level_order = ['p', 'c', 'o', 'f', 'g']
         first_row = True
+        global tree_key_taxon_seen
         tree_key_taxon_seen = dict()  # need to reset in case multiple trees have same taxon
+
         for tax_level in tax_level_order:  # phylum -> genus
             for taxon in sorted (lineages.keys()):
                 if taxon[0] != tax_level:
                     continue
                 if taxon not in tree_key_taxon_seen:
                     if first_row:
                         first_row = False
+                        table_buf += ['<tr><td>&nbsp;</td></tr>']
+                        table_buf += ['<tr><td>&nbsp;</td></tr>']
                     else:
                         table_buf += ['<tr><td>&nbsp;</td></tr>']
                     table_buf += add_tree_key_row (taxon, lineages, taxon_color, indent_cnt, key_box_size, key_font_size)

diff --git a/test/kb_gtdbtk_server_test.py b/test/kb_gtdbtk_server_test.py
@@ -264,6 +264,7 @@ def prepare_data(cls):
         except Exception as e:
             raise ValueError ("ABORT: unable to save Bac AssemblySet object.\n"+str(e))
 
+
     @classmethod
     def clean_scratch_dir(cls):
         for inode in os.listdir(cls.scratch):