Add NcbiTaxonomySQlite class to describe NCBI Taxonomy SQLite databases

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -367,6 +367,7 @@
     <datatype extension="chira.sqlite" type="galaxy.datatypes.binary:ChiraSQLite" mimetype="application/octet-stream" display_in_upload="true" />
     <datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
     <datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="ncbitaxonomy.sqlite" type="galaxy.datatypes.binary:NcbiTaxonomySQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/>
     <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
     <datatype extension="memepsp" type="galaxy.datatypes.sequence:MemePsp" display_in_upload="true" description="The MEME Position Specific Priors (PSP) format includes the name of the sequence for which a prior distribution corresponds." description_url="http://meme-suite.org/doc/psp-format.html"/>

lib/galaxy/datatypes/binary.py

@@ -1584,7 +1584,7 @@ class CuffDiffSQlite(SQlite):
         try:
             return dataset.peek
         except Exception:
-            return "CuffDiff SQLite Database, version %s" % (dataset.metadata.gemini_version or 'unknown')
+            return "CuffDiff SQLite Database, version %s" % (dataset.metadata.cuffdiff_version or 'unknown')
 
 
 class MzSQlite(SQlite):
@@ -1854,12 +1854,66 @@ class GAFASQLite(SQlite):
             log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
-        if super(IdpDB, self).sniff(filename):
+        if super(GAFASQLite, self).sniff(filename):
             table_names = frozenset({'gene', 'gene_family', 'gene_family_member', 'meta', 'transcript'})
             return self.sniff_table_names(filename, table_names)
         return False
 
 
+class NcbiTaxonomySQlite(SQlite):
+    """Class describing the NCBI Taxonomy database stored in SQLite as done by rust-ncbitaxonomy"""
+    MetadataElement(name='ncbitaxonomy_schema_version', default='20200501095116', param=MetadataParameter, desc='ncbitaxonomy schema version',
+                    readonly=True, visible=True, no_value='20200501095116')
+    MetadataElement(name="taxon_count", default=[], param=MetadataParameter, desc="Count of taxa in the taxonomy",
+                    readonly=True, visible=True, no_value=[])
+
+    file_ext = 'ncbitaxonomy.sqlite'
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(NcbiTaxonomySQlite, self).set_meta(dataset, overwrite=overwrite, **kwd)
+        try:
+            conn = sqlite.connect(dataset.file_name)
+            c = conn.cursor()
+            version_query = 'SELECT version FROM __diesel_schema_migrations ORDER BY run_on DESC LIMIT 1'
+            results = c.execute(version_query).fetchall()
+            if len(results) == 0:
+                raise Exception('version not found in __diesel_schema_migrations table')
+            dataset.metadata.ncbitaxonomy_schema_version = results[0][0]
+            taxons_query = 'SELECT count(name) FROM taxonomy'
+            results = c.execute(taxons_query).fetchall()
+            if len(results) == 0:
+                raise Exception('could not count size of taxonomy table')
+            dataset.metadata.taxon_count = results[0][0]
+        except Exception as e:
+            log.warning("%s, set_meta Exception: %s", self, e)
+
+    def sniff(self, filename):
+        if super(NcbiTaxonomySQlite, self).sniff(filename):
+            table_names = frozenset({'__diesel_schema_migrations', 'taxonomy'})
+            return self.sniff_table_names(filename, table_names)
+        return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = "NCBI Taxonomy SQLite Database, version {} ({} taxons)".format(
+                getattr(dataset.metadata, "ncbitaxonomy_schema_version", "unknown"),
+                getattr(dataset.metadata, "taxon_count", "unknown")
+            )
+            dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except Exception:
+            return "NCBI Taxonomy SQLite Database, version {} ({} taxons)".format(
+                getattr(dataset.metadata, "ncbitaxonomy_schema_version", "unknown"),
+                getattr(dataset.metadata, "taxon_count", "unknown")
+            )
+
+
 class Xlsx(Binary):
     """Class for Excel 2007 (xlsx) files"""
     file_ext = "xlsx"