adding command check

src/phlorest/commands/check.py

@@ -0,0 +1,57 @@
+"""
+Checks datasets for compliance
+"""
+import sys
+from cldfbench.cli_util import add_dataset_spec, get_dataset
+
+# values in metadata.json that should be present and should not be empty
+METAKEYS = [
+    'id', 'title', 'license', 'citation', 'name', 'author',
+    'scaling', 'analysis', 'family'
+]
+
+
+def register(parser):
+    add_dataset_spec(parser)
+
+
+def run(args):
+    try:
+        d = get_dataset(args)
+    except Exception as e:
+        print("Error: unable to load %s - %s" % (args.dataset, e))
+        return
+
+    # check metadata
+    for mdkey in METAKEYS:
+        if not getattr(d.metadata, mdkey, ''):
+            print("Error: %s metadata missing value for `%s`" % (d.id, mdkey))
+
+    # check title follows required format
+    if not getattr(d.metadata, 'title', '').startswith("Phlorest phylogeny derived from"):
+        print("Error: %s title does not follow `Phlorest phylogeny derived from`" % d.id)
+
+    # we don't have a summary tree file, and it's not flagged as missing
+    if not (d.cldf_dir / 'summary.trees').exists() and not d.metadata.missing.get('summary'):
+        print("Error: %s summary tree file missing" % d.id)
+
+    # we don't have a posterior tree file, and it's not flagged as missing
+    if not (d.cldf_dir / 'posterior.trees').exists() and not d.metadata.missing.get('posterior'):
+        print("Error: %s posterior tree file missing" % d.id)
+
+    # we don't have a nexus data file, and it's not flagged as missing
+    if not (d.cldf_dir / 'data.nex').exists() and not d.metadata.missing.get('nexus'):
+        print("Error: %s nexus data file missing" % d.id)
+
+    # do we have characters?
+    if not d.characters and not d.metadata.missing.get('characters'):
+        print("Error: %s characters.csv file missing" % d.id)
+
+    # check characters has the right columns
+    for char in d.characters:
+        if 'concepticonReference' in char:
+            print("Error: %s characters.csv uses `concepticonReference` rather than `Concepticon_ID`" % d.id)
+            break
+
+    # is the cldf valid?
+    d.cldf_reader().validate()