Fix test failures

EdinburghGenomics · Nov 20, 2024 · f16cc21 · f16cc21
1 parent d44e350
commit f16cc21
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Showing 5 changed files with 26 additions and 10 deletions.
diff --git a/compile_cell_info.py b/compile_cell_info.py
@@ -8,7 +8,6 @@
 from smrtino import load_yaml, dump_yaml
 from smrtino.ParseXML import get_metadata_info2
 import json
-from pprint import pprint
 
 """ The info needed to report on a SMRT cell consists of several YAML files:
         sc_data.yaml about the files in the upstream
@@ -73,7 +72,6 @@ def load_reports_zip(args_dict):
                               f" with {args_dict[f'{r}_report']}")
                 res[r] = json.load(jfh)
 
-    #pprint(res)
     return res
 
 def compile_json_reports(reports_dict, metadata_xml):

diff --git a/make_report.py b/make_report.py
@@ -270,12 +270,16 @@ def format_cell(cdict, cell_link=None):
 
     if 'reports' in cdict:
         # New version v2
-        rep("", "## SMRTLink Sample and Reports", "")
+        rep('<dl class="dl-horizontal">')
+        rep("<dt>Project</dt>", f"<dl>{projects_str}</dl>")
+        rep('</dl>', '')
+
+        rep("## SMRTLink Sample and Reports", "")
         rep('', *make_reports_table(cdict['reports']))
 
     else:
         # Old version
-        rep("", "## Basics", "")
+        rep("## Basics", "")
         rep('<dl class="dl-horizontal">')
         for k, v in sorted(cdict.items()):
             if k == 'cell_uuid' and cell_link:

diff --git a/test/revio_out_examples/r84140_20240116_162812/m84140_240116_163605_s1.info.yaml b/test/revio_out_examples/r84140_20240116_162812/m84140_240116_163605_s1.info.yaml
@@ -1,17 +1,21 @@
 _cstats:
 - Barcode: foo
   File: Fail_reads
+  Kinnex: '-'
   _dummy: 'FailCStats'
   _headings:
   - Barcode
   - File
+  - Kinnex
   - Dummy
 - Barcode: foo
   File: Hifi_reads
+  Kinnex: '-'
   _dummy: 'HifiCStats'
   _headings:
   - Barcode
   - File
+  - Kinnex
   - Dummy
 _filename: m84140_240116_163605_s1.hifi_reads.all.consensusreadset.xml
 _parts:

diff --git a/test/test_compile_bc_info.py b/test/test_compile_bc_info.py
@@ -7,14 +7,22 @@
 import logging
 import yaml
 
-from unittest.mock import Mock
+from unittest.mock import NonCallableMock
 from io import StringIO
 
 DATA_DIR = os.path.abspath(os.path.dirname(__file__) + '/revio_out_examples')
 VERBOSE = os.environ.get('VERBOSE', '0') != '0'
 
 from compile_bc_info import gen_info
 
+class NoneMock(NonCallableMock):
+    """A Mock where fetching undefined attributes returns None,
+       rather then a new Mock object. Useful for mocking command
+       line args.
+    """
+    def _get_child_mock(self, **kw):
+        return None
+
 class T(unittest.TestCase):
 
     @classmethod
@@ -34,16 +42,14 @@ def tearDown(self):
 
     ### THE TESTS ###
     def get_mock_args(self):
-        args = Mock()
+        args = NoneMock()
 
-        args.xmlfile = None
-        args.metaxml = None
         args.plots = []
         args.stats = []
-        args.taxon = None
-        args.binning = None
         args.debug = False
 
+        # For all other attributes, NoneMock returns None
+
         return args
 
     def test_revio_nobc(self):

diff --git a/test/test_make_report.py b/test/test_make_report.py
@@ -76,6 +76,8 @@ def test_format_cell(self):
            Again, test with minimal input for now.
         """
         expected = dd("""\
+                         ## Basics
+
                          <dl class="dl-horizontal">
                          <dt>bs_project</dt>
                          <dd><span style='color: Tomato;'>None</span></dd>
@@ -138,6 +140,8 @@ def test_format_report(self):
 
             # SMRT cell info
 
+            ## Basics
+
             <dl class="dl-horizontal">
             <dt>barcodes</dt>
             <dd>bc1</dd>