Added new report endpoint for user error reporting. This endpoint requires...

Added new report endpoint for user error reporting. This endpoint requires proper authentication through keycloak. Added additional checks to phonon data.

encyclopedia-gui @ 15cb97c9

-Subproject commit 134d89fc0a25ea367c454d299c8603af893b3b66
+Subproject commit 15cb97c9cf61fd59309a50f6700b99733fc6a659

nomad/app/api/encyclopedia.py

@@ -17,6 +17,7 @@ The encyclopedia API of the nomad@FAIRDI APIs.
 """
 import re
 import math
+import json
 import numpy as np
 
 from flask_restplus import Resource, abort, fields, marshal
@@ -24,12 +25,12 @@ from flask import request
 from elasticsearch_dsl import Search, Q, A
 from elasticsearch_dsl.utils import AttrDict
 
-from nomad import config, files
+from nomad import config, files, infrastructure
 from nomad.units import ureg
 from nomad.atomutils import get_hill_decomposition
 from nomad.datamodel.datamodel import EntryArchive
 from .api import api
-from .common import enable_gzip
+from .auth import authenticate
 
 ns = api.namespace("encyclopedia", description="Access encyclopedia metadata.")
 re_formula = re.compile(r"([A-Z][a-z]?)(\d*)")
@@ -791,7 +792,6 @@ calculations_result = api.model("calculations_result", {
 
 @ns.route("/materials/<string:material_id>/calculations")
 class EncCalculationsResource(Resource):
-    @enable_gzip()
     @api.response(404, "Suggestion not found")
     @api.response(400, "Bad request")
     @api.response(200, "Metadata send", fields.Raw)
@@ -1133,7 +1133,6 @@ calculation_property_result = api.model("calculation_property_result", {
 
 @ns.route("/materials/<string:material_id>/calculations/<string:calc_id>")
 class EncCalculationResource(Resource):
-    @enable_gzip()
     @api.response(404, "Material or calculation not found")
     @api.response(400, "Bad request")
     @api.response(200, "Metadata send", fields.Raw)
@@ -1283,6 +1282,63 @@ class EncCalculationResource(Resource):
         return result, 200
 
 
+report_query = api.model("report_query", {
+    "server": fields.String,
+    "username": fields.String,
+    "email": fields.String,
+    "first_name": fields.String,
+    "last_name": fields.String,
+    "category": fields.String,
+    "subcategory": fields.String(allow_null=True),
+    "representatives": fields.Raw(Raw=True),
+    "message": fields.String,
+})
+
+
+@ns.route("/materials/<string:material_id>/reports")
+class ReportsResource(Resource):
+    @api.response(500, "Error sending report")
+    @api.response(400, "Bad request")
+    @api.response(204, "Report succesfully sent", fields.Raw)
+    @api.expect(calculation_property_query, validate=False)
+    @api.marshal_with(calculation_property_result, skip_none=True)
+    @api.doc("enc_calculation")
+    @authenticate(required=True)
+    def post(self, material_id):
+
+        # Get query parameters as json
+        try:
+            query = marshal(request.get_json(), report_query)
+        except Exception as e:
+            abort(400, message=str(e))
+
+        # Send the report as an email
+        query["material_id"] = material_id
+        representatives = query["representatives"]
+        if representatives is not None:
+            representatives = "\n" + "\n".join(["  {}: {}".format(key, value) for key, value in representatives.items()])
+            query["representatives"] = representatives
+        mail = (
+            "Server: {server}\n\n"
+            "Username: {username}\n"
+            "First name: {first_name}\n"
+            "Last name: {last_name}\n"
+            "Email: {email}\n\n"
+            "Material id: {material_id}\n"
+            "Category: {category}\n"
+            "Subcategory: {subcategory}\n"
+            "Representative calculations: {representatives}\n\n"
+            "Message: {message}"
+        ).format(**query)
+        try:
+            infrastructure.send_mail(
+                name="webmaster", email="lauri.himanen@gmail.com", message=mail, subject='Encyclopedia error report')
+        except Exception as e:
+            abort(500, message="Error sending error report email.")
+        print(mail)
+        return "", 204
+
+
 def read_archive(upload_id: str, calc_id: str) -> EntryArchive:
     """Used to read data from the archive.
 

nomad/infrastructure.py

@@ -453,7 +453,6 @@ def send_mail(name: str, email: str, message: str, subject: str):
 
     msg = MIMEText(message)
     msg['Subject'] = subject
-    msg['From'] = 'The nomad team <%s>' % config.mail.from_address
     msg['To'] = name
     to_addrs = [email]
 

nomad/normalizing/encyclopedia/encyclopedia.py

@@ -207,6 +207,7 @@ class EncyclopediaNormalizer(Normalizer):
         """
         sec_enc = self.backend.entry_archive.section_metadata.m_create(EncyclopediaMetadata)
         status_enums = EncyclopediaMetadata.status.type
+        calc_enums = Calculation.calculation_type.type
 
         # Do nothing if section_run is not present
         if self.section_run is None:
@@ -261,7 +262,6 @@ class EncyclopediaNormalizer(Normalizer):
                     "unsupported method type for encyclopedia",
                     enc_status=status_enums.unsupported_method_type,
                 )
-                calc_enums = Calculation.calculation_type.type
                 if calc_type != calc_enums.phonon_calculation:
                     return
 
@@ -292,7 +292,7 @@ class EncyclopediaNormalizer(Normalizer):
             if functional_type is None:
                 sec_enc.status = status_enums.unsupported_method_type
                 self.logger.info(
-                    "unsupported functinoal type for encyclopedia",
+                    "unsupported functional type for encyclopedia",
                     enc_status=status_enums.unsupported_method_type,
                 )
                 return

nomad/processing/data.py

@@ -444,7 +444,7 @@ class Calc(Proc):
 
             # Get encyclopedia method information directly from the referenced calculation.
             ref_enc_method = ref_archive.section_metadata.encyclopedia.method
-            if ref_enc_method is None or len(ref_enc_method) == 0:
+            if ref_enc_method is None or len(ref_enc_method) == 0 or ref_enc_method.functional_type is None:
                 raise ValueError("No method information available in referenced calculation.")
             backend.entry_archive.section_metadata.encyclopedia.method = ref_enc_method
 
@@ -455,6 +455,7 @@ class Calc(Proc):
             self._entry_metadata.dft.xc_functional = ref_archive.section_metadata.dft.xc_functional
             self._entry_metadata.dft.basis_set = ref_archive.section_metadata.dft.basis_set
             self._entry_metadata.dft.update_group_hash()
+            self._entry_metadata.encyclopedia.status = EncyclopediaMetadata.status.type.success
         except Exception as e:
             logger.error("Could not retrieve method information for phonon calculation.", exception=e)
             if self._entry_metadata.encyclopedia is None:

tests/normalizing/test_encyclopedia.py

@@ -520,9 +520,9 @@ def test_phonon(phonon: EntryArchive):
     dos = prop.phonon_dos
     thermo_props = prop.thermodynamical_properties
     assert calc_type == Calculation.calculation_type.type.phonon_calculation
-    assert status == EncyclopediaMetadata.status.type.success
 
-    # TODO: Check method information
+    # The method information is filled after the whole upload has been processed.
+    assert status == EncyclopediaMetadata.status.type.unsupported_method_type
 
     # Check dos
     assert dos is not None