Update DatafileHandler default methods

   * Yield Packages and Dependencies before associating Packages to Resources

Signed-off-by: Jono Yang <jyang@nexb.com>

Author: JonoYang

src/packagedcode/models.py

@@ -938,14 +938,14 @@ def assemble(cls, package_data, resource, codebase, package_adder=add_to_package
             if not package.license_expression:
                 package.license_expression = cls.compute_normalized_license(package)
 
+            yield package
+
             cls.assign_package_to_resources(
                 package=package,
                 resource=resource,
                 codebase=codebase,
                 package_adder=package_adder,
             )
-
-            yield package
         else:
             # we have no package, so deps are not for a specific package uid
             package_uid = None
@@ -1047,6 +1047,12 @@ def assemble_from_many(cls, pkgdata_resources, codebase, package_adder=add_to_pa
 
         # process each package in sequence. The first item creates a package and
         # the other only update
+        # We are saving the Packages, Dependencies, and Resources in lists until
+        # after we go through `pkgdata_resources` for all Package data, then we
+        # yield Packages, then Dependencies, then Resources.
+        dependencies = []
+        resources = []
+        resources_from_package = []
         for package_data, resource in pkgdata_resources:
             if not base_resource:
                 base_resource = resource
@@ -1059,8 +1065,6 @@ def assemble_from_many(cls, pkgdata_resources, codebase, package_adder=add_to_pa
                         datafile_path=resource.path,
                     )
                     package_uid = package.package_uid
-                    if package_uid:
-                        package_adder(package_uid, resource, codebase)
             else:
                 # FIXME: What is the package_data is NOT for the same package as package?
                 # FIXME: What if the update did not do anything? (it does return True or False)
@@ -1069,31 +1073,40 @@ def assemble_from_many(cls, pkgdata_resources, codebase, package_adder=add_to_pa
                     package_data=package_data,
                     datafile_path=resource.path,
                 )
-                if package_uid:
-                    package_adder(package_uid, resource, codebase)
+
+            if package_uid:
+                resources_from_package.append((package_uid, resource,))
 
             # in all cases yield possible dependencies
             dependent_packages = package_data.dependencies
             if dependent_packages:
-                yield from Dependency.from_dependent_packages(
+                p_deps = Dependency.from_dependent_packages(
                     dependent_packages=dependent_packages,
                     datafile_path=resource.path,
                     datasource_id=package_data.datasource_id,
                     package_uid=package_uid,
                 )
+                dependencies.extend(list(p_deps))
 
             # we yield this as we do not want this further processed
-            yield resource
-
-        # the whole parent subtree of the base_resource is for this package
-        if package_uid:
-            for res in base_resource.walk(codebase):
-                package_adder(package_uid, res, codebase)
+            resources.append(resource)
 
+        # Yield Packages, Dependencies, and Resources
         if package:
             if not package.license_expression:
                 package.license_expression = cls.compute_normalized_license(package)
             yield package
+        yield from dependencies
+        yield from resources
+
+        # Associate Package to Resources once they have been yielded
+        for package_uid, resource in resources_from_package:
+            package_adder(package_uid, resource, codebase)
+
+        # the whole parent subtree of the base_resource is for this package
+        if package_uid:
+            for res in base_resource.walk(codebase):
+                package_adder(package_uid, res, codebase)
 
     @classmethod
     def assemble_from_many_datafiles(