Merge pull request #277 from dgasmith/mol

Client: Removes ids when printing

qcf_0_6_to_0_7_migration.py

@@ -0,0 +1,104 @@
+import pymongo
+import tqdm
+import qcelemental as qcel
+import qcfractal.interface as ptl
+
+client = pymongo.MongoClient("localhost:27017")
+client.drop_database("qcarchive2")
+client.admin.command("copydb", fromdb="qcarchive", todb="qcarchive2")
+
+db = client.qcarchive2
+
+print("\nUpdating Molecule hashes:")
+mol_query = db.molecule.find(limit=1000)
+total = mol_query.count()
+
+updates = 0
+
+# First update molecules
+for raw_mol in tqdm.tqdm(mol_query, total=total):
+
+    tmpdata = raw_mol.copy()
+    tmpdata.pop("_id", None)
+    tmpdata.pop("molecular_formula", None)
+    tmpdata.pop("molecule_hash", None)
+
+    conupd = False
+    if ("connectivity" in tmpdata) and (tmpdata["connectivity"] == []):
+        tmpdata["connectivity"] = None
+        conupd = True
+
+    mol = qcel.models.Molecule(**tmpdata, validate=False)
+
+    mhash = mol.get_hash()
+    if mhash == raw_mol["molecule_hash"]:
+        if conupd:
+            print(raw_mol)
+            raise Exception()
+        continue 
+
+
+    upd_data = {"molecule_hash": mhash, "identifiers": tmpdata["identifiers"]}
+    upd_data["identifiers"]["molecule_hash"] = mhash
+    if conupd:
+        upd_data["connectivity"] = None
+
+    upd = db.molecule.update_one({"_id": raw_mol["_id"]}, {"$set": upd_data}) 
+    if upd.modified_count != 1:
+        print(upd)
+        print(upd_data)
+        break
+    else:
+        updates += 1
+
+print(f"Total number of result updates: {updates}")
+
+
+## Result updates
+print("\nUpdating Result Fields:")
+
+upd = db.result.update_many({}, {"$rename": {"extras.local_qcvars": "extras.qcvars", "properties.mp2_total_correlation_energy": "properties.mp2_correlation_energy"}})
+print(f"Total number of result updates: {upd.modified_count}")
+
+## Procedure updates
+
+## Result updates
+print("\nUpdating TorsionDrive Hashes:")
+
+td_query = db.procedure.find({"procedure": "torsiondrive"}, limit=1000)
+total = td_query.count()
+
+updates = 0
+
+# First update molecules
+for raw_td in tqdm.tqdm(td_query, total=total):
+
+    tmpdata = raw_td.copy()
+    tmpdata.pop("_id")
+    tmpdata.pop("_cls")
+    tmpdata.pop("hash_index")
+    td = ptl.models.TorsionDriveRecord(**tmpdata)
+
+    upd = db.molecule.update_one({"_id": raw_td["_id"]}, {"$set": {"hash_index": td.hash_index}}) 
+    if upd.modified_count != 1:
+        print(upd)
+        print(upd_data)
+        break
+    else:
+        updates += 1
+
+print("\nUpdating TorsionDriveDataset Fields:")
+
+td_query = db.collection.find({"collection": "torsiondrivedataset"}, limit=1000)
+
+for raw_col in td_query:
+
+    new_records = {}
+    for key, record in raw_col["records"].items():
+        tmp = record.copy()
+        tmp["object_map"] = tmp.pop("torsiondrives")
+        new_records[key] = tmp
+
+    db.collection.update_one({"_id": raw_col["_id"]}, {"records": new_records})
+
+

qcfractal/interface/client.py

@@ -429,6 +429,7 @@ def list_collections(self, collection_type: Optional[str] = None, aslist: bool =
         # Rename collection names
         repl_name_map = collections_name_map()
         for item in response:
+            item.pop("id", None)
             if item["collection"] in repl_name_map:
                 item["collection"] = repl_name_map[item["collection"]]
 

qcfractal/snowflake.py

@@ -109,8 +109,13 @@ def __init__(self,
         if storage_uri is None:
             mongod_port = _find_port()
             self._mongod_tmpdir = tempfile.TemporaryDirectory()
+
+            mongod_path = shutil.which("mongod")
+            if mongod_path is None:
+                raise OSError("Could not find `mongod` in PATH, please `conda install mongodb`.")
+
             self._mongod_proc = _background_process(
-                [shutil.which("mongod"), f"--port={mongod_port}", f"--dbpath={self._mongod_tmpdir.name}"])
+                [mongod_path, f"--port={mongod_port}", f"--dbpath={self._mongod_tmpdir.name}"])
             storage_uri = f"mongodb://localhost:{mongod_port}"
         else:
             self._mongod_tmpdir = None