fix: added missing files

scibec/init_scibec/scibec_tools.py

@@ -0,0 +1,35 @@
+from scihub.scibec import SciBec
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "--config",
+        default="./init_scibec/demo_config.yaml",
+        help="path to the config file",
+    )
+    parser.add_argument(
+        "--url",
+        default="http://localhost:3030",
+        help="scibec url",
+    )
+    parser.add_argument(
+        "--activeExperiment",
+        help="scibec url",
+    )
+    clargs = parser.parse_args()
+    config_path = clargs.config
+    scibec_url = clargs.url
+    active_experiment = clargs.activeExperiment
+
+    scibec = SciBec()
+    scibec.url = scibec_url
+
+    if active_experiment:
+        experiment = scibec.get_experiment_by_pgroup(active_experiment)
+        scibec.set_experiment_active(experiment_id=experiment[0]["id"])
+    # beamlines = scibec.get_beamlines()
+    # if not beamlines:
+    #     scibec.add_beamline("TestBeamline")
+    # scibec.update_session_with_file(config_path)

scibec/init_scibec/setup_scibec_db.py

@@ -0,0 +1,115 @@
+import datetime
+import getpass
+import json
+
+import requests
+from scihub.scibec import SciBec
+from tqdm import tqdm
+
+
+class SciBecSetup:
+    scibec_url = "http://localhost:3030"
+
+    def __init__(self) -> None:
+        self.scibec = SciBec()
+        self.scibec.url = self.scibec_url
+
+        self._scicat_proposals = []
+        self.proposal_storage = []
+        self.access_groups = set()
+        self.location_storage = {}
+
+    @staticmethod
+    def get_scicat_proposals() -> list:
+        """retrieve all proposals from scicat"""
+
+        pwd = getpass.getpass()
+        payload = {"username": "proposalIngestor", "password": pwd}
+        headers = {"Content-type": "application/json", "Accept": "application/json"}
+        res = requests.post(
+            "https://dacat.psi.ch/api/v3/Users/login", json=payload, headers=headers, timeout=10
+        )
+
+        res_json = json.loads(res.content)
+        access_token_scicat = res_json["id"]
+
+        headers = {
+            "Content-type": "application/json",
+            "Accept": "application/json",
+            "Authorization": access_token_scicat,
+        }
+        res = requests.get("https://dacat.psi.ch/api/v3/Proposals", headers=headers, timeout=100)
+        return json.loads(res.content)
+
+    def _update_storage_with_proposals(self, max_time: int = None) -> None:
+        current_time = datetime.datetime.now()
+
+        for prop in self._scicat_proposals:
+            if max_time is not None:
+                time_delta = current_time - datetime.datetime.strptime(
+                    prop["MeasurementPeriodList"][0]["start"][:-1], "%Y-%m-%dT%H:%M:%S.%f"
+                )
+
+                if time_delta.days > max_time:
+                    continue
+
+            self.location_storage[prop["MeasurementPeriodList"][0]["instrument"]] = {}
+
+            self.location_storage[prop["MeasurementPeriodList"][0]["instrument"]] = {}
+            self.proposal_storage.append(
+                {
+                    "ownerGroup": prop["ownerGroup"],
+                    "abstract": prop["abstract"],
+                    "title": prop["title"],
+                    "location": prop["MeasurementPeriodList"][0]["instrument"],
+                    "info": prop,
+                }
+            )
+            for access_group in prop["accessGroups"]:
+                self.access_groups.add(access_group)
+
+    def _update_beamlines(self):
+        existing_beamlines = {
+            beamline["name"]: beamline["id"] for beamline in self.scibec.get_beamlines()
+        }
+        for location in tqdm(self.location_storage, desc="Updating beamlines..."):
+            if not location.startswith("/PSI"):
+                continue
+            beamline_name = location.split("/")[-1]
+            if beamline_name in existing_beamlines:
+                target_id = existing_beamlines[beamline_name]
+            else:
+                res = self.scibec.add_beamline(beamline_name)
+                existing_beamlines[beamline_name] = target_id = res["id"]
+            self.location_storage[location] = target_id
+
+    def _update_experiments(self):
+        for proposal in tqdm(self.proposal_storage, desc="Updating proposals..."):
+            title = proposal["title"]
+            if not title:
+                title = proposal["ownerGroup"]
+            experiment = {
+                "name": title,
+                "readACL": [proposal["ownerGroup"]],
+                "createACL": [proposal["ownerGroup"]],
+                "updateACL": [proposal["ownerGroup"]],
+                "beamlineId": self.location_storage[proposal["location"]],
+                "writeAccount": proposal["ownerGroup"],
+                "experimentInfo": proposal["info"],
+            }
+
+            res = self.scibec.get_experiment(name=title)
+            if not res:
+                self.scibec.add_experiment(experiment)
+
+    def sync_proposals(self):
+        """update / sync SciBec with SciCat proposals"""
+        self._scicat_proposals = self.get_scicat_proposals()
+        self._update_storage_with_proposals()
+        self._update_beamlines()
+        self._update_experiments()
+
+
+if __name__ == "__main__":
+    scibec_setup = SciBecSetup()
+    scibec_setup.sync_proposals()