Query genenetwork3 API for search.

genenetwork2 should be a thin wrapper web UI around the genenetwork3
API. Hence, this move.

* etc/default_settings.py (XAPIAN_DB_PATH): Delete variable.
* wqflask/wqflask/database.py: Remove xapian import.
(xapian_database, xapian_writable_database): Delete functions.
* wqflask/wqflask/gsearch.py: Do not import json, xapian, Nothing from
pymonad.maybe, base, utility.authentication_tools and
wqflask.database. Import MonadicDict from gn3.monads instead of
utility.monads and GN3_LOCAL_URL from utility.tools.
(GSearch.__init__): Query genenetwork3 search API instead of directly
reading a Xapian index.

3 files changed, 36 insertions, 86 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
index ab5a06cf..6d7ac063 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -35,8 +35,6 @@ GN2_PROXY = "http://localhost:8080"
 
 # GN PROXY
 GN_PROXY_URL="https://genenetwork.org/gn3-proxy/"
-# Xapian index
-XAPIAN_DB_PATH = "xapian"
 
 # ---- MySQL
 
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 7e03a000..663e2ebf 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -8,7 +8,6 @@ import contextlib
 
 #: type: ignore
 import MySQLdb
-import xapian
 
 
 class Connection(Protocol):
@@ -61,25 +60,3 @@ def database_connection() -> Iterator[Connection]:
         yield connection
     finally:
         connection.close()
-
-
-@contextlib.contextmanager
-def xapian_database():
-    """Open xapian database read-only."""
-    # pylint: disable-next=invalid-name
-    db = xapian.Database(get_setting("XAPIAN_DB_PATH"))
-    try:
-        yield db
-    finally:
-        db.close()
-
-
-@contextlib.contextmanager
-def xapian_writable_database():
-    """Open xapian database for writing."""
-    # pylint: disable-next=invalid-name
-    db = xapian.WritableDatabase(get_setting("XAPIAN_DB_PATH"))
-    try:
-        yield db
-    finally:
-        db.close()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 4efa6740..202d2670 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,13 +1,11 @@
-import json
+from urllib.parse import urlencode, urljoin
 
-from pymonad.maybe import Just, Maybe, Nothing
+from pymonad.maybe import Just, Maybe
 from pymonad.tools import curry
-import xapian
+import requests
 
-from base import webqtlConfig
-from utility.authentication_tools import check_resource_availability
-from utility.monads import MonadicDict
-from wqflask.database import xapian_database
+from gn3.monads import MonadicDict
+from utility.tools import GN3_LOCAL_URL
 
 # KLUDGE: Due to the lack of pagination, we hard-limit the maximum
 # number of search results.
@@ -20,22 +18,6 @@ class GSearch:
         self.type = kwargs["type"]
         self.terms = kwargs["terms"]
 
-        queryparser = xapian.QueryParser()
-        queryparser.set_stemmer(xapian.Stem("en"))
-        queryparser.set_stemming_strategy(queryparser.STEM_SOME)
-        queryparser.add_boolean_prefix("author", "A")
-        queryparser.add_boolean_prefix("species", "XS")
-        queryparser.add_boolean_prefix("group", "XG")
-        queryparser.add_boolean_prefix("tissue", "XI")
-        queryparser.add_boolean_prefix("dataset", "XDS")
-        queryparser.add_boolean_prefix("symbol", "XY")
-        queryparser.add_boolean_prefix("chr", "XC")
-        queryparser.add_boolean_prefix("peakchr", "XPC")
-        queryparser.add_prefix("description", "XD")
-        for i, prefix in enumerate(["mean:", "peak:", "mb:", "peakmb:", "additive:", "year:"]):
-            queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix))
-        querystring = self.terms
-        query = queryparser.parse_query(querystring)
         # FIXME: Handle presentation (that is, formatting strings for
         # display) in the template rendering, not when retrieving
         # search results.
@@ -44,41 +26,34 @@ class GSearch:
         hmac = curry(2, lambda dataset, dataset_fullname: f"{dataset_fullname}:{dataset}")
         convert_lod = lambda x: x / 4.61
         self.trait_list = []
-        # pylint: disable=invalid-name
-        with xapian_database() as db:
-            enquire = xapian.Enquire(db)
-            # Filter documents by type.
-            enquire.set_query(xapian.Query(xapian.Query.OP_FILTER,
-                                           query,
-                                           xapian.Query(f"XT{self.type}")))
-            for i, trait in enumerate(
-                    [MonadicDict(json.loads(xapian_match.document.get_data()))
-                     for xapian_match in enquire.get_mset(0, MAX_SEARCH_RESULTS)]):
-                trait["index"] = Just(i)
-                trait["location_repr"] = (Maybe.apply(chr_mb)
-                                          .to_arguments(trait.pop("chr"), trait.pop("mb")))
-                trait["LRS_score_repr"] = trait.pop("lrs").map(convert_lod).map(format3f)
-                trait["additive"] = trait["additive"].map(format3f)
-                trait["mean"] = trait["mean"].map(format3f)
-                trait["max_lrs_text"] = (Maybe.apply(chr_mb)
-                                         .to_arguments(trait.pop("geno_chr"), trait.pop("geno_mb")))
-                if self.type == "gene":
-                    trait["hmac"] = (Maybe.apply(hmac)
-                                     .to_arguments(trait["dataset"], trait["dataset_fullname"]))
-                elif self.type == "phenotype":
-                    trait["display_name"] = trait["name"]
-                    inbredsetcode = trait.pop("inbredsetcode")
-                    if inbredsetcode.map(len) == Just(3):
-                        trait["display_name"] = (Maybe.apply(
-                            curry(2, lambda inbredsetcode, name: f"{inbredsetcode}_{name}"))
-                                                 .to_arguments(inbredsetcode, trait["name"]))
-                    trait["hmac"] = (Maybe.apply(hmac)
-                                     .to_arguments(trait.pop("dataset_fullname"), trait["name"]))
-                    trait["authors_display"] = (trait.pop("authors").map(
-                        lambda authors:
-                        ", ".join(authors[:2] + ["et al."] if len(authors) >=2 else authors)))
-                    trait["pubmed_text"] = trait["year"].map(str)
-                    trait["pubmed_link"] = (trait["pubmed_id"].map(
-                        lambda pubmedid: webqtlConfig.PUBMEDLINK_URL % pubmedid))
-                self.trait_list.append(trait.data)
-            self.trait_count = len(self.trait_list)
+        for i, trait in enumerate(requests.get(
+                urljoin(GN3_LOCAL_URL, "/api/search?" + urlencode({"query": self.terms,
+                                                                   "type": self.type,
+                                                                   "per_page": MAX_SEARCH_RESULTS}))).json()):
+            trait = MonadicDict(trait)
+            trait["index"] = Just(i)
+            trait["location_repr"] = (Maybe.apply(chr_mb)
+                                      .to_arguments(trait.pop("chr"), trait.pop("mb")))
+            trait["LRS_score_repr"] = trait.pop("lrs").map(convert_lod).map(format3f)
+            trait["additive"] = trait["additive"].map(format3f)
+            trait["mean"] = trait["mean"].map(format3f)
+            trait["max_lrs_text"] = (Maybe.apply(chr_mb)
+                                     .to_arguments(trait.pop("geno_chr"), trait.pop("geno_mb")))
+            if self.type == "gene":
+                trait["hmac"] = (Maybe.apply(hmac)
+                                 .to_arguments(trait["dataset"], trait["dataset_fullname"]))
+            elif self.type == "phenotype":
+                trait["display_name"] = trait["name"]
+                inbredsetcode = trait.pop("inbredsetcode")
+                if inbredsetcode.map(len) == Just(3):
+                    trait["display_name"] = (Maybe.apply(
+                        curry(2, lambda inbredsetcode, name: f"{inbredsetcode}_{name}"))
+                                             .to_arguments(inbredsetcode, trait["name"]))
+                trait["hmac"] = (Maybe.apply(hmac)
+                                 .to_arguments(trait.pop("dataset_fullname"), trait["name"]))
+                trait["authors_display"] = (trait.pop("authors").map(
+                    lambda authors:
+                    ", ".join(authors[:2] + ["et al."] if len(authors) >=2 else authors)))
+                trait["pubmed_text"] = trait["year"].map(str)
+            self.trait_list.append(trait.data)
+        self.trait_count = len(self.trait_list)