fix: fix source retrieval during between workflow caching and report …

…generation
snakemake · Sep 29, 2021 · 2394ca4 · 2394ca4
1 parent b6b9b4b
commit 2394ca4
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/snakemake/caching/hash.py b/snakemake/caching/hash.py
@@ -52,6 +52,7 @@ def _get_provenance_hash(self, job: Job):
         elif job.is_script:
             _, source, _ = script.get_source(
                 job.rule.script,
+                job.rule.workflow.sourcecache,
                 basedir=job.rule.basedir,
                 wildcards=job.wildcards,
                 params=job.params,
@@ -60,6 +61,7 @@ def _get_provenance_hash(self, job: Job):
         elif job.is_notebook:
             _, source, _ = script.get_source(
                 job.rule.notebook,
+                job.rule.workflow.sourcecache,
                 basedir=job.rule.basedir,
                 wildcards=job.wildcards,
                 params=job.params,
@@ -68,6 +70,7 @@ def _get_provenance_hash(self, job: Job):
         elif job.is_wrapper:
             _, source, _ = script.get_source(
                 wrapper.get_script(job.rule.wrapper, prefix=workflow.wrapper_prefix),
+                job.rule.workflow.sourcecache,
                 basedir=job.rule.basedir,
                 wildcards=job.wildcards,
                 params=job.params,

diff --git a/snakemake/report/__init__.py b/snakemake/report/__init__.py
@@ -261,7 +261,7 @@ def code(self):
         elif self._rule.script is not None and not contains_wildcard(self._rule.script):
             logger.info("Loading script code for rule {}".format(self.name))
             _, source, language = script.get_source(
-                self._rule.script, self._rule.basedir
+                self._rule.script, self._rule.workflow.sourcecache, self._rule.basedir
             )
             sources = [source.decode()]
         elif self._rule.wrapper is not None and not contains_wildcard(
@@ -270,15 +270,17 @@ def code(self):
             logger.info("Loading wrapper code for rule {}".format(self.name))
             _, source, language = script.get_source(
                 wrapper.get_script(
-                    self._rule.wrapper, prefix=self._rule.workflow.wrapper_prefix
+                    self._rule.wrapper,
+                    self._rule.workflow.sourcecache,
+                    prefix=self._rule.workflow.wrapper_prefix,
                 )
             )
             sources = [source.decode()]
         elif self._rule.notebook is not None and not contains_wildcard(
             self._rule.notebook
         ):
             _, source, language = script.get_source(
-                self._rule.notebook, self._rule.basedir
+                self._rule.notebook, self._rule.workflow.sourcecache, self._rule.basedir
             )
             language = language.split("_")[1]
             sources = notebook.get_cell_sources(source)