Address BEP031 macro requests

src/04-modality-specific-files/10-microscopy.md

@@ -35,7 +35,7 @@ The current MACRO list ".ome.btf", ".png" and ".tif[.ome]", is it possible to ha
 If not, ".tif" and ".ome.tif" should be 2 separate lines but are concatenated as ".tif[.ome]"
 -->
 {{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
-"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"]) }}
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=3) }}
 
 Microscopy data MUST be stored in the `micr` directory.
 
@@ -459,7 +459,7 @@ sub-<label>/
 ```
 The current MACRO list ".jpg", ".png" and ".tif", is it possible to have one line with "<extension>" instead?
 -->
-{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"]) }}
+{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
 
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
 

tools/schemacode/schema.py

@@ -226,15 +226,17 @@ def _add_entity(filename_template, entity_pattern, requirement_level):
     return filename_template
 
 
-def make_filename_template(schema, **kwargs):
-    """Create codeblocks containing example filename patterns for a given
-    datatype.
+def make_filename_template(schema, n_dupes_to_combine=6, **kwargs):
+    """Create codeblocks containing example filename patterns for a given datatype.
 
     Parameters
     ----------
     schema : dict
         The schema object, which is a dictionary with nested dictionaries and
         lists stored within it.
+    n_dupes_to_combine : int
+        The minimum number of suffixes/extensions to combine in the template as
+        <suffix>/<extension>.
     kwargs : dict
         Keyword arguments used to filter the schema.
         Example kwargs that may be used include: "suffixes", "datatypes",
@@ -298,7 +300,7 @@ def make_filename_template(schema, **kwargs):
 
             # In cases of large numbers of suffixes,
             # we use the "suffix" variable and expect a table later in the spec
-            if len(group["suffixes"]) > 5:
+            if len(group["suffixes"]) >= n_dupes_to_combine:
                 suffix = "_<suffix>"
                 string += suffix
                 strings = [string]
@@ -314,7 +316,7 @@ def make_filename_template(schema, **kwargs):
                 ext if ext != "*" else ".<extension>" for ext in extensions
             ]
             extensions = utils.combine_extensions(extensions)
-            if len(extensions) > 5:
+            if len(extensions) >= n_dupes_to_combine:
                 # Combine exts when there are many, but keep JSON separate
                 if ".json" in extensions:
                     extensions = [".<extension>", ".json"]

tools/schemacode/utils.py

@@ -23,29 +23,35 @@ def get_schema_path():
 def combine_extensions(lst):
     """Combine extensions with their compressed versions in a list.
 
-    This is a basic solution to combining extensions with their
-    compressed versions in a list. Something more robust could
-    be written in the future.
+    Valid combinations are hardcoded in the function,
+    since some extensions look like compressed versions of one another, but are not.
 
     Parameters
     ----------
     lst : list of str
+        Raw list of extensions.
+
+    Returns
+    -------
+    new_lst : list of str
+        List of extensions, with compressed and uncompressed versions of the same extension
+        combined.
     """
+    COMPRESSION_EXTENSIONS = [".gz"]
+
     new_lst = []
-    # First, sort by length
-    lst = sorted(lst, key=len)
+    items_to_remove = []
     for item in lst:
-        temp_lst = new_lst[:]
-
-        item_found = False
-        for j, new_item in enumerate(temp_lst):
-            if new_item in item:
-                temp_item = new_item + "[" + item.replace(new_item, "", 1) + "]"
-                new_lst[j] = temp_item
-                item_found = True
-
-        if not item_found:
-            new_lst.append(item)
+        for ext in COMPRESSION_EXTENSIONS:
+            if item.endswith(ext) and item.replace(ext, "") in lst:
+                temp_item = item.replace(ext, "") + "[" + ext + "]"
+                new_lst.append(temp_item)
+                items_to_remove.append(item)
+                items_to_remove.append(item.replace(ext, ""))
+                continue
+
+    items_to_add = [item for item in lst if item not in items_to_remove]
+    new_lst += items_to_add
 
     return new_lst