Merge commit '555d93ff42af3d2468eb950ff0d2c8548b8b179e' 0.3.1 into no…

…te/dev
rki-mf1 · Nov 11, 2022 · 5a39726 · 5a39726
2 parents 7fc1420 + 555d93f
commit 5a39726
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Showing 4 changed files with 23 additions and 4 deletions.
diff --git a/libs/mpxsonar/.env.tmeplate → libs/mpxsonar/.env.template b/libs/mpxsonar/.env.tmeplate → libs/mpxsonar/.env.template
diff --git a/libs/mpxsonar/pyproject.toml b/libs/mpxsonar/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mpxsonar"
-version = "0.3.0"
+version = "0.3.1"
 description = "A database-driven system for handling genomic sequences and screening genomic profiles."
 authors = ["Stephan Fuchs <FuchsS@rki.de>", "Kunaphas Kongkitimanon <KongkitimanonK@rki.de>", "Matthew Huska <HuskaM@rki.de>"]
 license = "GPL3"

diff --git a/libs/mpxsonar/src/mpxsonar/dbm.py b/libs/mpxsonar/src/mpxsonar/dbm.py
@@ -811,12 +811,14 @@ def get_molecule_ids(self, reference_accession=None):
             "SELECT `molecule.accession`, `molecule.id` FROM referenceView WHERE "
             + condition
         )
+        # print(sql, val)
         self.cursor.execute(sql, val)
         output = {
             x["molecule.accession"]: x["molecule.id"]
             for x in self.cursor.fetchall()
             if x is not None
         }
+        # print(output)
         return output
 
     # Do we need this function?
@@ -888,6 +890,7 @@ def get_element_ids(self, reference_accession=None, type=None):
         if type:
             sql += " AND type = ?"
             molecule_ids.append(type)
+        # print(sql, molecule_ids)
         self.cursor.execute(sql, molecule_ids)
         row = self.cursor.fetchall()
         if not row:

diff --git a/libs/mpxsonar/src/mpxsonar/sonar.py b/libs/mpxsonar/src/mpxsonar/sonar.py
@@ -369,7 +369,7 @@ def parse_args(args):
         "-v",
         "--version",
         action="version",
-        version="mpxsonar " + VERSION,
+        version="MPXSonar " + VERSION,
         help="Show program's version number and exit.",
     )
 
@@ -400,7 +400,7 @@ def parse_args(args):
 
 def check_file(fname):
     if not os.path.isfile(fname):
-        sys.exit("iput error: " + fname + " is not a valid file.")
+        sys.exit("input error: " + fname + " is not a valid file.")
 
 
 def main(args):  # noqa: C901
@@ -629,6 +629,22 @@ def main(args):  # noqa: C901
         reserved_props = {}
 
         with sonarDBManager(args.db, readonly=False, debug=args.debug) as dbm:
+            # check reference
+            if args.reference:
+                if len(dbm.references) != 0 and args.reference not in [
+                    d["accession"] for d in dbm.references
+                ]:
+                    rows = dbm.references
+                    if not rows:
+                        print("*** no references ***")
+                    else:
+                        print("*** Available Reference***")
+                        print(tabulate(rows, headers="keys", tablefmt="fancy_grid"))
+                    sys.exit(
+                        "Input Error: "
+                        + str(args.reference)
+                        + " is not available in our database."
+                    )
             for pname in dbm.properties:
                 if hasattr(args, pname):
                     props[pname] = getattr(args, pname)
@@ -637,7 +653,7 @@ def main(args):  # noqa: C901
                     reserved_props["with_sublineage"] = args.with_sublineage
                 else:
                     sys.exit(
-                        "input error: "
+                        "Input Error: "
                         + args.with_sublineage
                         + " is mismatch to the available properties"
                     )