Merge pull request #13 from colin-combe/sql_timing

Sql timing

app/routes/xiview.py

@@ -126,7 +126,7 @@ async def get_data_object(ids, pxid):
         data["matches"] = await get_matches(cur, ids)
         # data["peptides"] = await get_peptides(cur, data["matches"], ids)
         # data["proteins"] = await get_proteins(cur, data["peptides"])
-        data["peptides"] = await get_all_peptides(cur, ids)
+        data["peptides"] = await get_peptides2(cur, ids)
         data["proteins"] = await get_all_proteins(cur, ids)
         cur.close()
     except (Exception, psycopg2.DatabaseError) as e:
@@ -224,7 +224,7 @@ async def get_results_metadata(cur, ids):
 async def get_matches(cur, ids):
     # todo - check whats going on with this rank =1 and pass_threshold = True in mascot data, rank =1 condition seems to speeds things up (but should be redundant)
     # todo - rename 'si' to 'm'
-    query = """WITH submodpep AS (SELECT * FROM modifiedpeptide WHERE upload_id = ANY(%s))
+    query = """WITH submodpep AS (SELECT * FROM modifiedpeptide WHERE upload_id = ANY(%s) AND link_site1 > -1)
 SELECT si.id AS id, si.pep1_id AS pi1, si.pep2_id AS pi2,
                 si.scores AS sc,
                 cast (si.upload_id as text) AS si,
@@ -241,9 +241,8 @@ async def get_matches(cur, ids):
             INNER JOIN submodpep mp2 ON si.pep2_id = mp2.id AND si.upload_id = mp2.upload_id
             WHERE si.upload_id = ANY(%s) 
             AND si.pass_threshold = TRUE 
-            AND si.rank = 1
-            AND mp1.link_site1 > 0
-            AND mp2.link_site1 > 0;"""
+            AND mp1.link_site1 > -1
+            AND mp2.link_site1 > -1;"""
     cur.execute(query, [ids, ids])
     return cur.fetchall()
 
@@ -435,6 +434,69 @@ async def get_all_peptides(cur, ids):
     cur.execute(query, [ids, ids])
     return cur.fetchall()
 
+@log_execution_time_async
+@xiview_data_router.get('/get_xiview_peptides2', tags=["xiVIEW"])
+async def get_xiview_peptides2(project, file=None):
+    """
+    Get all the peptides.
+    URLs have the following structure:
+    https: // www.ebi.ac.uk / pride / archive / xiview / get_xiview_peptides?project=PXD020453&file=Cullin_SDA_1pcFDR.mzid
+    Users may provide only projects, meaning we need to have an aggregated view.
+    https: // www.ebi.ac.uk / pride / archive / xiview / get_xiview_peptides?project=PXD020453
+
+    :return: json of the peptides
+    """
+    logger.info(f"get_xiview_peptides for {project}, file: {file}")
+    most_recent_upload_ids = await get_most_recent_upload_ids(project, file)
+
+    conn = None
+    data = {}
+    error = None
+
+    try:
+        conn = await get_db_connection()
+        cur = conn.cursor(cursor_factory=RealDictCursor)
+        data = await get_peptides2(cur, most_recent_upload_ids)
+        cur.close()
+    except (Exception, psycopg2.DatabaseError) as e:
+        logger.error(e)
+        return {"error": "Database error"}, 500
+    finally:
+        if conn is not None:
+            conn.close()
+
+    start_time = time.time()
+    json_bytes = orjson.dumps(data)
+    logger.info(f'peptides json dump time: {time.time() - start_time}')
+    log_json_size(json_bytes, "peptides")  # slows things down a little
+    return Response(json_bytes, media_type='application/json')
+
+
+@log_execution_time_async
+async def get_peptides2(cur, ids):
+    query = """with submatch as (select pep1_id, pep2_id, upload_id from match where upload_id = ANY(%s) and pass_threshold = true), 
+pep_ids as (select pep1_id, upload_id from submatch  union select pep2_id, upload_id from submatch),
+subpp AS (select * from peptideevidence WHERE upload_id = ANY(%s))
+select mp.id,
+                cast(mp.upload_id as text) AS u_id,
+                mp.base_sequence AS seq,
+                array_agg(pp.dbsequence_id) AS prt,
+                array_agg(pp.pep_start) AS pos,
+                array_agg(pp.is_decoy) AS dec,
+                mp.link_site1 AS ls1,
+                mp.link_site2 AS ls2,
+                mp.mod_accessions as m_as,
+                mp.mod_positions as m_ps,
+                mp.mod_monoiso_mass_deltas as m_ms,
+                mp.crosslinker_modmass as cl_m from pep_ids pi
+inner join modifiedpeptide mp on mp.upload_id = pi.upload_id and pi.pep1_id = mp.id
+                    JOIN subpp AS pp
+                    ON mp.id = pp.peptide_id AND mp.upload_id = pp.upload_id
+                    GROUP BY mp.id, mp.upload_id, mp.base_sequence;"""
+
+    cur.execute(query, [ids, ids])
+    return cur.fetchall()
+
 
 @log_execution_time_async
 @xiview_data_router.get('/get_xiview_proteins', tags=["xiVIEW"])