hybrid search

mpcontribs-api/mpcontribs/api/contributions/document.py

@@ -163,7 +163,26 @@ class Contributions(DynamicDocument):
         ReferenceField("Attachments", null=True), default=list, max_length=10
     )
     notebook = ReferenceField("Notebooks")
-    atlas = AtlasManager("formula_autocomplete")
+    atlas = AtlasManager(
+        "formula_autocomplete",
+        definition={
+            "analyzer": "lucene.whitespace",
+            "searchAnalyzer": "lucene.whitespace",
+            "mappings": {
+                "dynamic": False,
+                "fields": {
+                    "data": {"dynamic": True, "type": "document"},
+                    "formula": {"type": "string"},
+                    "identifier": {"type": "string"},
+                    "is_public": {"type": "boolean"},
+                    "last_modified": {"type": "date"},
+                    "needs_build": {"type": "boolean"},
+                    "project": [{"type": "stringFacet"}, {"type": "string"}],
+                },
+            },
+            "storedSource": True,
+        },
+    )
     meta = {
         "collection": "contributions",
         "indexes": [
@@ -192,31 +211,6 @@ def objects(doc_cls, queryset):
             "needs_build",
         )
 
-    @classmethod
-    def atlas_filter(cls, term):
-        try:
-            comp = Composition(term)
-        except Exception:
-            raise ValueError(f"{term} is not a valid composition")
-
-        try:
-            for element in comp.elements:
-                Element(element)
-        except Exception:
-            raise ValueError(f"{element} not a valid element")
-
-        ind_str = []
-
-        if len(comp) == 1:
-            d = comp.get_integer_formula_and_factor()
-            ind_str.append(d[0] + str(int(d[1])) if d[1] != 1 else d[0])
-        else:
-            for i, j in comp.reduced_composition.items():
-                ind_str.append(i.name + str(int(j)) if j != 1 else i.name)
-
-        final_terms = ["".join(entry) for entry in permutations(ind_str)]
-        return AtlasQ(formula=final_terms[0])  # TODO formula__in=final_terms
-
     @classmethod
     def post_init(cls, sender, document, **kwargs):
         # replace existing components with according ObjectIds

mpcontribs-api/mpcontribs/api/contributions/views.py

@@ -169,53 +169,3 @@ def has_add_permission(self, req, obj):
             raise Unauthorized(f"{obj.identifier} already added for {obj.project.id}")
 
         return True
-
-
-@contributions.route("/search")
-def search():
-    formula = request.args.get("formula")
-    if not formula:
-        abort(404, description="Missing formula param.")
-
-    try:
-        comp = Composition(formula)
-    except (CompositionError, ValueError):
-        abort(400, description="Invalid formula provided.")
-
-    ind_str = []
-
-    if len(comp) == 1:
-        d = comp.get_integer_formula_and_factor()
-        ind_str.append(d[0] + str(int(d[1])) if d[1] != 1 else d[0])
-    else:
-        for i, j in comp.reduced_composition.items():
-            ind_str.append(i.name + str(int(j)) if j != 1 else i.name)
-
-    final_terms = ["".join(entry) for entry in permutations(ind_str)]
-    limit = request.args.get("limit", ContributionsResource.default_limit)
-
-    pipeline = [
-        {
-            "$search": {
-                "index": "formula_autocomplete",
-                "text": {"path": "formula", "query": final_terms},
-            }
-        },
-        {"$project": {"formula": 1, "length": {"$strLenCP": "$formula"}, "project": 1}},
-        {"$match": {"length": {"$gte": len(final_terms[0])}}},
-        {"$limit": limit},
-        {"$sort": {"length": 1}},
-    ]
-
-    results = []
-
-    for contrib in Contributions.objects().aggregate(pipeline):
-        results.append(
-            {
-                "id": str(contrib["_id"]),
-                "formula": contrib["formula"],
-                "project": contrib["project"],
-            }
-        )
-
-    return jsonify(results)

mpcontribs-api/mpcontribs/api/core.py

@@ -2,7 +2,6 @@
 """Custom meta-class and MethodView for Swagger"""
 
 import os
-import logging
 import yaml
 
 from copy import deepcopy
@@ -581,8 +580,18 @@ def has_read_permission(self, request, qs):
                         return qs.none()
                 else:
                     names = None
-                    if q and "project" in q and "$in" in q["project"]:
-                        names = q.pop("project").pop("$in")
+                    if hasattr(qs._query_obj, "children"):
+                        children = deepcopy(qs._query_obj.children)
+                    else:
+                        children = [deepcopy(qs._query_obj)]
+
+                    qs._query_obj = Q()
+                    for node in children:
+                        for field, value in node.query.items():
+                            if field == "project__in":
+                                names = value
+                            else:
+                                qs = qs.filter(**{field: value})
 
                     qfilter = self.get_projects_filter(
                         username, groups, filter_names=names
@@ -610,15 +619,20 @@ def has_read_permission(self, request, qs):
                 qfilter = self.get_projects_filter(username, groups)
                 component = component[:-1] if component == "notebooks" else component
                 qfilter &= Q(**{f"{component}__in": ids})
-                contribs = Contributions.objects(qfilter).only(component).limit(len(ids))
+                contribs = (
+                    Contributions.objects(qfilter).only(component).limit(len(ids))
+                )
                 # return new queryset using "ids__in"
-                readable_ids = [
-                    getattr(contrib, component).id for contrib in contribs
-                ] if component == "notebook" else [
-                    dbref.id for contrib in contribs
-                    for dbref in getattr(contrib, component)
-                    if dbref.id in ids
-                ]
+                readable_ids = (
+                    [getattr(contrib, component).id for contrib in contribs]
+                    if component == "notebook"
+                    else [
+                        dbref.id
+                        for contrib in contribs
+                        for dbref in getattr(contrib, component)
+                        if dbref.id in ids
+                    ]
+                )
                 if not readable_ids:
                     return qs.none()
 

mpcontribs-api/tests/test_contributions_anon.tavern.yaml

@@ -0,0 +1,71 @@
+test_name: anonymous retrieval of contributions
+
+stages:
+  - name: get a contribution from a private project with all fields
+    skip: True
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/"
+      method: GET
+      headers:
+        accept: application/json
+      params:
+        project: periodic_band_structures
+        per_page: 1
+        _limit: 1
+        _fields: _all
+    response:
+      status_code: 200
+      json:
+        data: []
+        has_more: false
+        total_count: 0
+        total_pages: 0
+
+  - name: get a contribution with all fields
+    skip: True
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/"
+      method: GET
+      headers:
+        accept: application/json
+      params:
+        per_page: 1
+        _limit: 1
+        _fields: _all
+    response:
+      strict: false
+      status_code: 200
+      save:
+        json:
+          contrib_anon: "data[0]"
+
+  - name: retrieve single contribution with default fields
+    skip: True
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/{contrib_anon.id:s}/"
+      method: GET
+      headers:
+        accept: application/json
+    response:
+      status_code: 200
+      json:
+        id: "{contrib_anon.id}"
+        project: "{contrib_anon.project}"
+        identifier: "{contrib_anon.identifier}"
+        formula: "{contrib_anon.formula}"
+        is_public: !bool "{contrib_anon.is_public}"
+        last_modified: "{contrib_anon.last_modified}"
+        needs_build: !bool "{contrib_anon.needs_build}"
+
+  - name: retrieve single contribution with all fields
+    skip: True
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/{contrib_anon.id:s}/"
+      params:
+        _fields: _all
+      method: GET
+      headers:
+        accept: application/json
+    response:
+      status_code: 200
+      json: !force_original_structure "{contrib_anon}"

mpcontribs-api/tests/test_contributions_auth.tavern.yaml

@@ -0,0 +1,51 @@
+test_name: authenticated retrieval of contributions
+
+stages:
+  - name: get a contribution with all fields
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/"
+      method: GET
+      headers:
+        accept: application/json
+        X-API-KEY: "{tavern.env_vars.MP_API_KEY}"
+      params:
+        per_page: 1
+        _limit: 1
+        _fields: _all
+    response:
+      strict: false
+      status_code: 200
+      save:
+        json:
+          contrib_auth: "data[0]"
+
+  - name: retrieve single contribution with default fields
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/{contrib_auth.id:s}/"
+      method: GET
+      headers:
+        accept: application/json
+        X-API-KEY: "{tavern.env_vars.MP_API_KEY}"
+    response:
+      status_code: 200
+      json:
+        id: "{contrib_auth.id}"
+        project: "{contrib_auth.project}"
+        identifier: "{contrib_auth.identifier}"
+        formula: "{contrib_auth.formula}"
+        is_public: !bool "{contrib_auth.is_public}"
+        last_modified: "{contrib_auth.last_modified}"
+        needs_build: !bool "{contrib_auth.needs_build}"
+
+  - name: retrieve single contribution with all fields
+    request:
+      url: "{tavern.env_vars.MP_CONTRIBS_API_URL}/contributions/{contrib_auth.id:s}/"
+      params:
+        _fields: _all
+      method: GET
+      headers:
+        accept: application/json
+        X-API-KEY: "{tavern.env_vars.MP_API_KEY}"
+    response:
+      status_code: 200
+      json: !force_original_structure "{contrib_auth}"