Nesting include settings in .shed.yml (source as list)? #180
Description
Consider a moderately complex include setting like this which is quite repetitive:
include:
- README.rst
- venn_list.py
- venn_list.xml
- tool_dependencies.xml
- source: ../../test-data/magic.pdf
strip_components: 2
- source: ../../test-data/venn_list.tabular
strip_components: 2
- source: ../../test-data/rhodopsin_proteins.fasta
strip_components: 2
It seems that currently include is a flat list of elements (defaulting to source entries if not a mini-dict), but allowing each source entry to be a list would allow this kind of bundling:
include:
- README.rst
- venn_list.py
- venn_list.xml
- tool_dependencies.xml
- strip_components: 2
source:
- ../../test-data/magic.pdf
- ../../test-data/venn_list.tabular
- ../../test-data/rhodopsin_proteins.fasta
e.g. Something like this hack:
$ git diff
diff --git a/planemo/shed/__init__.py b/planemo/shed/__init__.py
index 8bacfc8..e108bc6 100644
--- a/planemo/shed/__init__.py
+++ b/planemo/shed/__init__.py
@@ -882,7 +882,10 @@ class RealizedFile(object):
def realized_files_for(path, include_info):
if not isinstance(include_info, dict):
include_info = {"source": include_info}
- source = include_info.get("source")
+ source_list = include_info.get("source")
+ if not isinstance(source_list, list):
+ # A single filename or pattern
+ source_list = [source_list]
destination = include_info.get("destination", None)
strip_components = include_info.get("strip_components", 0)
if destination is None:
@@ -890,14 +893,16 @@ class RealizedFile(object):
destination_specified = False
else:
destination_specified = True
- abs_source = os.path.join(path, source)
- dest_is_file = destination_specified and os.path.isfile(abs_source)
realized_files = []
- for globbed_file in _glob(path, source):
- src = os.path.relpath(globbed_file, path)
- realized_files.append(
- RealizedFile(path, src, destination, dest_is_file, strip_components)
- )
+ for source in source_list:
+ abs_source = os.path.join(path, source)
+ dest_is_file = destination_specified and os.path.isfile(abs_source)
+ for globbed_file in _glob(path, source):
+ src = os.path.relpath(globbed_file, path)
+ realized_files.append(
+ RealizedFile(path, src, destination, dest_is_file, strip_components)
+ )
+ info("Found %i files from source %r" % (len(realized_files), source_list))
return realized_files
def __str__(self)
More work would be needed to preserve the work in #158 for spotting missing includes.
Also, harking back to #160 this would be possible too (but requires a few more tweaks to planemo/shed/__init__.py in realize_to to deal with implicit destinations of . being used internally):
include:
- strip_components: 2
source:
- ../../tools/venn_list/README.rst
- ../../tools/venn_list/venn_list.py
- ../../tools/venn_list/venn_list.xml
- ../../tools/venn_list/tool_dependencies.xml
- ../../test-data/magic.pdf
- ../../test-data/venn_list.tabular
- ../../test-data/rhodopsin_proteins.fasta
Having played with this a bit, it would be an alternative solution to my proposal in #160, and might have some other future usecases - but overall I think it is too complicated?