Merge pull request #542 from biolink/gocamgen

Gocamgen reporting changes and deleting gpad_extensions_mapper
biolink · Mar 24, 2021 · 0ec3aa6 · 0ec3aa6
2 parents 20dc806 + d30d7ea
commit 0ec3aa6
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Showing 4 changed files with 137 additions and 788 deletions.
diff --git a/ontobio/rdfgen/gocamgen/errors.py b/ontobio/rdfgen/gocamgen/errors.py
@@ -1,5 +1,8 @@
+from ontobio.rdfgen.gocamgen import collapsed_assoc
+
+
 class GocamgenException(Exception):
-    def __init__(self, message):
+    def __init__(self, message: str):
         self.message = message
 
     def __str__(self):
@@ -14,6 +17,15 @@ class ShexException(GocamgenException):
     pass
 
 
+class CollapsedAssocGocamgenException(GocamgenException):
+    def __init__(self, message: str, assoc: collapsed_assoc.CollapsedAssociation):
+        self.message = message
+        self.assoc = assoc
+
+    def __str__(self):
+        return "{}\n{}".format(self.message, "\n".join([l.source_line for l in self.assoc.lines]))
+
+
 class GeneErrorSet:
     def __init__(self):
         self.errors = {}

diff --git a/ontobio/rdfgen/gocamgen/gocam_builder.py b/ontobio/rdfgen/gocamgen/gocam_builder.py
@@ -76,6 +76,8 @@ def make_model(self, gene, annotations: List[GoAssociation], output_directory=No
                     model.write(out_filename)
                     logger.info("Model for {} written to {} in {} sec".format(gene, out_filename,
                                                                               (time.time() - start_time)))
+                for err in model.errors:
+                    self.errors.add_error(gene, err)
                 return model
             except GocamgenException as ex:
                 self.errors.add_error(gene, ex)
@@ -156,13 +158,13 @@ def parse_gpi(gpi_file):
 class AssocExtractor:
     def __init__(self, gpad_file, parser_config: AssocParserConfig):
         self.assocs = []
-        gpad_parser = gpadparser.GpadParser(config=parser_config)
+        self.gpad_parser = gpadparser.GpadParser(config=parser_config)
         with open(gpad_file) as sg:
             lines = sum(1 for line in sg)
 
         with open(gpad_file) as gf:
             click.echo("Making products...")
-            with click.progressbar(iterable=gpad_parser.association_generator(file=gf, skipheader=True),
+            with click.progressbar(iterable=self.gpad_parser.association_generator(file=gf, skipheader=True),
                                    length=lines) as associations:
                 self.assocs = list(associations)