From 9c7284e0293d15bf8b5d8c5a6217bc54e833f4aa Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 10:35:31 +0000
Subject: [PATCH 01/11] improve endpoints with pagination and queries

---
 Pipfile             |   2 +-
 Pipfile.lock        | 923 ++++++++++++++++++++++++--------------------
 app/routes/pride.py | 240 +++++++-----
 3 files changed, 636 insertions(+), 529 deletions(-)

diff --git a/Pipfile b/Pipfile
index 92d3d06..c4f9eed 100644
--- a/Pipfile
+++ b/Pipfile
@@ -4,7 +4,7 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-fastapi = ">=0.68.0,<0.69.0"
+fastapi = "*"
 uvicorn = "<0.16.0,>=0.15.0"
 lxml = ">=4.9.1"
 numpy = ">=1.14.3"
diff --git a/Pipfile.lock b/Pipfile.lock
index df38c9b..fd831ea 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "d02157feafbddd20dd8bb0dfa3f45d011ca9220de38435b868d67efd14dd9e60"
+            "sha256": "2451e061dd2f1c6e33f098c44c59acff9feaf52e924c4e4cd85ed0c5fc632138"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,6 +16,22 @@
         ]
     },
     "default": {
+        "annotated-types": {
+            "hashes": [
+                "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43",
+                "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==0.6.0"
+        },
+        "anyio": {
+            "hashes": [
+                "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee",
+                "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==4.2.0"
+        },
         "asgiref": {
             "hashes": [
                 "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e",
@@ -26,11 +42,11 @@
         },
         "certifi": {
             "hashes": [
-                "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1",
-                "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"
+                "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f",
+                "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2023.11.17"
+            "version": "==2024.2.2"
         },
         "charset-normalizer": {
             "hashes": [
@@ -154,74 +170,75 @@
         },
         "fastapi": {
             "hashes": [
-                "sha256:36bcdd3dbea87c586061005e4a40b9bd0145afd766655b4e0ec1d8870b32555c",
-                "sha256:38526fc46bda73f7ec92033952677323c16061e70a91d15c95f18b11895da494"
+                "sha256:2c9bab24667293b501cad8dd388c05240c850b58ec5876ee3283c47d6e1e3a4d",
+                "sha256:f3817eac96fe4f65a2ebb4baa000f394e55f5fccdaf7f75250804bc58f354f73"
             ],
             "index": "pypi",
-            "version": "==0.68.2"
+            "version": "==0.109.2"
         },
         "greenlet": {
             "hashes": [
-                "sha256:0a02d259510b3630f330c86557331a3b0e0c79dac3d166e449a39363beaae174",
-                "sha256:0b6f9f8ca7093fd4433472fd99b5650f8a26dcd8ba410e14094c1e44cd3ceddd",
-                "sha256:100f78a29707ca1525ea47388cec8a049405147719f47ebf3895e7509c6446aa",
-                "sha256:1757936efea16e3f03db20efd0cd50a1c86b06734f9f7338a90c4ba85ec2ad5a",
-                "sha256:19075157a10055759066854a973b3d1325d964d498a805bb68a1f9af4aaef8ec",
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-                "sha256:20107edf7c2c3644c67c12205dc60b1bb11d26b2610b276f97d666110d1b511d",
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+                "sha256:dd4f49ae60e10adbc94b45c0b5e6a179acc1736cf7a90160b404076ee283cf83",
+                "sha256:e1f145462f1fa6e4a4ae3c0f782e580ce44d57c8f2c7aae1b6fa88c0b2efdb41",
+                "sha256:e3391d1e16e2a5a1507d83e4a8b100f4ee626e8eca43cf2cadb543de69827c4c",
+                "sha256:fcd2469d6a2cf298f198f0487e0a5b1a47a42ca0fa4dfd1b6862c999f018ebbf",
+                "sha256:fd096eb7ffef17c456cfa587523c5f92321ae02427ff955bebe9e3c63bc9f0da",
+                "sha256:fe754d231288e1e64323cfad462fcee8f0288654c10bdf4f603a39ed923bef33"
             ],
             "markers": "platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))",
-            "version": "==3.0.1"
+            "version": "==3.0.3"
         },
         "h11": {
             "hashes": [
@@ -256,101 +273,87 @@
         },
         "lxml": {
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         },
         "networkx": {
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@@ -362,45 +365,45 @@
         },
         "numpy": {
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@@ -420,34 +423,38 @@
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@@ -459,11 +466,11 @@
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@@ -553,45 +560,96 @@
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@@ -604,19 +662,19 @@
         },
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@@ -636,112 +694,117 @@
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@@ -767,60 +830,68 @@
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+                "sha256:605b6b059f4b57b277f75ace81cc5bc6335efcbcc4ccb9066695e515dbdb3900",
+                "sha256:665f0a3954635b5b777a55111ababf44b4fc12b1f3ba0a435b602b6387ffd7cf",
+                "sha256:6f9e2e59cbcc6ba1488404aad43de005d05ca56e069477b33ff74e91b6319735",
+                "sha256:736ea78cd06de6c21ecba7416499e7236a22374561493b456a1f7ffbe3f6cdb4",
+                "sha256:74b080c897563f81062b74e44f5a72fa44c2b373741a9ade701d5f789a10ba23",
+                "sha256:75432b5b14dc2fff43c50435e248b45c7cdadef73388e5610852b95280ffd0e9",
+                "sha256:75f99202324383d613ddd1f7455ac908dca9c2dd729ec8584c9541dd41822a2c",
+                "sha256:790f533fa5c8901a62b6fef5811d48980adeb2f51f1290ade8b5e7ba990ba3de",
+                "sha256:798f717ae7c806d67145f6ae94dc7c342d3222d3b9a311a784f371a4333212c7",
+                "sha256:7c88f0c7dcc5f99bdb34b4fd9b69b93c89f893f454f40219fe923a3a2fd11625",
+                "sha256:7d505815ac340568fd03f719446a589162d55c52f08abd77ba8964fbb7eb5b5f",
+                "sha256:84daa0a2055df9ca0f148a64fdde12ac635e30edbca80e87df9b3aaf419e144a",
+                "sha256:87d91043ea0dc65ee583026cb18e1b458d8ec5fc0a93637126b5fc0bc3ea68c4",
+                "sha256:87f6e732bccd7dcf1741c00f1ecf33797383128bd1c90144ac8adc02cbb98643",
+                "sha256:884272dcd3ad97f47702965a0e902b540541890f468d24bd1d98bcfe41c3f018",
+                "sha256:8b8cb63d3ea63b29074dcd29da4dc6a97ad1349151f2d2949495418fd6e48db9",
+                "sha256:91f7d9d1c4dd1f4f6e092874c128c11165eafcf7c963128f79e28f8445de82d5",
+                "sha256:a2c69a7664fb2d54b8682dd774c3b54f67f84fa123cf84dda2a5f40dcaa04e08",
+                "sha256:a3be4987e3ee9d9a380b66393b77a4cd6d742480c951a1c56a23c335caca4ce3",
+                "sha256:a86b4240e67d4753dc3092d9511886795b3c2852abe599cffe108952f7af7ac3",
+                "sha256:aa9373708763ef46782d10e950b49d0235bfe58facebd76917d3f5cbf5971aed",
+                "sha256:b64b183d610b424a160b0d4d880995e935208fc043d0302dd29fee32d1ee3f95",
+                "sha256:b801154027107461ee992ff4b5c09aa7cc6ec91ddfe50d02bca344918c3265c6",
+                "sha256:bb209a73b8307f8fe4fe46f6ad5979649be01607f11af1eb94aa9e8a3aaf77f0",
+                "sha256:bc8b7dabe8e67c4832891a5d322cec6d44ef02f432b4588390017f5cec186a84",
+                "sha256:c51db269513917394faec5e5c00d6f83829742ba62e2ac4fa5c98d58be91662f",
+                "sha256:c55731c116806836a5d678a70c84cb13f2cedba920212ba7dcad53260997666d",
+                "sha256:cf18ff7fc9941b8fc23437cc3e68ed4ebeff3599eec6ef5eebf305f3d2e9a7c2",
+                "sha256:d24f571990c05f6b36a396218f251f3e0dda916e0c687ef6fdca5072743208f5",
+                "sha256:db854730a25db7c956423bb9fb4bdd1216c839a689bf9cc15fada0a7fb2f4570",
+                "sha256:dc55990143cbd853a5d038c05e79284baedf3e299661389654551bd02a6a68d7",
+                "sha256:e607cdd99cbf9bb80391f54446b86e16eea6ad309361942bf88318bcd452363c",
+                "sha256:ecf6d4cda1f9f6cb0b45803a01ea7f034e2f1aed9475e883410812d9f9e3cfcf",
+                "sha256:f2a159111a0f58fb034c93eeba211b4141137ec4b0a6e75789ab7a3ef3c7e7e3",
+                "sha256:f37c0caf14b9e9b9e8f6dbc81bc56db06acb4363eba5a633167781a48ef036ed",
+                "sha256:f5693145220517b5f42393e07a6898acdfe820e136c98663b971906120549da5"
             ],
             "index": "pypi",
-            "version": "==2.0.23"
+            "version": "==2.0.25"
         },
         "sqlalchemy-utils": {
             "hashes": [
@@ -832,11 +903,11 @@
         },
         "starlette": {
             "hashes": [
-                "sha256:3c8e48e52736b3161e34c9f0e8153b4f32ec5d8995a3ee1d59410d92f75162ed",
-                "sha256:7d49f4a27f8742262ef1470608c59ddbc66baf37c148e938c7038e6bc7a998aa"
+                "sha256:13d429aa93a61dc40bf503e8c801db1f1bca3dc706b10ef2434a36123568f044",
+                "sha256:90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==0.14.2"
+            "markers": "python_version >= '3.8'",
+            "version": "==0.36.3"
         },
         "tomli": {
             "hashes": [
@@ -848,27 +919,27 @@
         },
         "typing-extensions": {
             "hashes": [
-                "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0",
-                "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"
+                "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783",
+                "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==4.8.0"
+            "version": "==4.9.0"
         },
         "tzdata": {
             "hashes": [
-                "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a",
-                "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"
+                "sha256:aa3ace4329eeacda5b7beb7ea08ece826c28d761cda36e747cfbf97996d39bf3",
+                "sha256:dd54c94f294765522c77399649b4fefd95522479a664a0cec87f41bebc6148c9"
             ],
             "markers": "python_version >= '2'",
-            "version": "==2023.3"
+            "version": "==2023.4"
         },
         "urllib3": {
             "hashes": [
-                "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3",
-                "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"
+                "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20",
+                "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"
             ],
             "index": "pypi",
-            "version": "==2.1.0"
+            "version": "==2.2.0"
         },
         "uvicorn": {
             "hashes": [
diff --git a/app/routes/pride.py b/app/routes/pride.py
index d751463..65770f5 100644
--- a/app/routes/pride.py
+++ b/app/routes/pride.py
@@ -1,6 +1,7 @@
 import configparser
 import os
 from typing import List, Annotated
+from math import ceil
 
 import requests
 from fastapi import APIRouter, Depends, status, Query, Path
@@ -358,6 +359,7 @@ async def update_metadata_by_project(project_id: str, session: Session = Depends
 
     # add new record
     session.add(project_details)
+    # session.add_all(list_of_project_sub_details)
     session.commit()
     logger.info("Saving medatadata COMPLETED")
     return 0
@@ -459,68 +461,114 @@ async def delete_dataset(project_id: str, session: Session = Depends(get_session
         session.close()
 
 
-@pride_router.get("/projects", tags=["Projects"])
-async def list_all_projects(session: Session = Depends(get_session), page: int = 1, page_size: int = 10) -> list[
-    ProjectDetail]:
-    """
-    This gives the high-level view of list of projects
-    :param session: connection to database
-    :param page: page number
-    :param page_size: number of records per page
-    :return: List of ProjectDetails in JSON format
-    """
-    try:
-        offset = (page - 1) * page_size
-        projects = session.query(ProjectDetail).offset(offset).limit(page_size).all()
-    except Exception as e:
-        # Handle the exception here
-        logging.error(f"Error occurred: {str(e)}")
-        return []
-    if projects is None or projects == []:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Projects not found")
-
-    return projects
+# @pride_router.get("/projects", tags=["Projects"])
+# async def list_all_projects(session: Session = Depends(get_session), page: int = 1, page_size: int = 10) -> list[
+#     ProjectDetail]:
+#     """
+#     This gives the high-level view of list of projects
+#     :param session: connection to database
+#     :param page: page number
+#     :param page_size: number of records per page
+#     :return: List of ProjectDetails in JSON format
+#     """
+#     try:
+#         offset = (page - 1) * page_size
+#         projects = session.query(ProjectDetail).offset(offset).limit(page_size).all()
+#         total_elements = session.query(ProjectDetail).all().__len__()
+#     except Exception as e:
+#         # Handle the exception here
+#         logging.error(f"Error occurred: {str(e)}")
+#     if projects is None or projects == []:
+#         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Projects not found")
+#     response = {
+#         "projects": projects,
+#         "page": {
+#             "page_no": page,
+#             "page_size": page_size,
+#             "total_elements": total_elements,
+#             "total_pages": ceil(total_elements / page_size),
+#             "number": 0
+#         }
+#     }
+#
+#     return response
 
 
-@pride_router.get("/projects/search", tags=["Projects"])
-async def project_search(query: str = Query(...),
-                         page: int = 1,
-                         page_size: int = 10,
+@pride_router.get("/projects", tags=["Projects"])
+async def project_search(q: Annotated[str | None, Query(default=None,
+                                                        alias="query",
+                                                        max_length=20,
+                                                        title="query",
+                                                        description="Protein accession, protein name or gene name",
+                                                        example="PXD035 or PXD035519 or membrane")] = None,
+                         page: int = Query(1, description="Page number"),
+                         page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
                          session: Session = Depends(get_session)
                          ) -> list[ProjectDetail]:
     """
     This gives the high-level view of list of projects
-    :param session: connection to database
+    :param q: Query parameter
     :param page: page number
-    :param page_size: number of records per page
+    :param page_size: records per page
     :return: List of ProjectDetails in JSON format
+    :param session: connection to database
     """
-    project_search_sql = text("""
-        SELECT p.id FROM projectdetails p
-    JOIN public.projectsubdetails ps ON p.id = ps.project_detail_id
-    WHERE p.project_id = :query OR
-          p.title ILIKE '%' || :query || '%' OR
-          p.description ILIKE '%' || :query || '%' OR
-          p.organism ILIKE '%' || :query || '%' OR
+    projects = None
+    where_condition = ""
+
+    if q and q != '*':
+        where_condition += """ WHERE p.project_id LIKE '%' || :query || '%' OR
+          p.title LIKE '%' || :query || '%' OR
+          p.description LIKE '%' || :query || '%' OR
+          p.organism LIKE '%' || :query || '%' OR
           ps.protein_accession = :query OR
-          ps.protein_name ILIKE '%' || :query || '%' OR
-          ps.gene_name ILIKE '%' || :query || '%'
-      """)
-    matchig_ids = session.execute(project_search_sql, {"query": query}).fetchall()
-    list_of_ids = [id for (id,) in matchig_ids]
+          ps.protein_name LIKE '%' || :query || '%' OR
+          ps.gene_name LIKE '%' || :query || '%'
+               """
+
+    project_search_sql = text(f"""
+                SELECT p.id FROM projectdetails p
+                JOIN public.projectsubdetails ps ON p.id = ps.project_detail_id
+                {where_condition}
+               ORDER BY id
+           """)
 
+    sql_values = {"query": q}
+
+    # project_search_sql = text("""
+    #     SELECT p.id FROM projectdetails p
+    # JOIN public.projectsubdetails ps ON p.id = ps.project_detail_id
+    # WHERE p.project_id = :query OR
+    #       p.title ILIKE '%' || :query || '%' OR
+    #       p.description ILIKE '%' || :query || '%' OR
+    #       p.organism ILIKE '%' || :query || '%' OR
+    #       ps.protein_accession = :query OR
+    #       ps.protein_name ILIKE '%' || :query || '%' OR
+    #       ps.gene_name ILIKE '%' || :query || '%'
+    #   """)
+    matchig_ids = set(session.execute(project_search_sql, sql_values).fetchall())
+    list_of_ids = [id for (id,) in matchig_ids]
     try:
         offset = (page - 1) * page_size
         projects = session.query(ProjectDetail).filter(ProjectDetail.id.in_(list_of_ids)).offset(offset).limit(
             page_size).all()
+        total_elements = session.query(ProjectDetail).filter(ProjectDetail.id.in_(list_of_ids)).all().__len__()
     except Exception as e:
         # Handle the exception here
         logging.error(f"Error occurred: {str(e)}")
-        return []
     if projects is None or projects == []:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Projects not found")
-
-    return projects
+    response = {
+        "projects": projects,
+        "page": {
+            "page_no": page,
+            "page_size": page_size,
+            "total_elements": total_elements,
+            "total_pages": ceil(total_elements / page_size),
+            "number": 0
+        }
+    }
+    return response
 
 
 @pride_router.get("/projects/{project_id}", tags=["Projects"])
@@ -546,33 +594,6 @@ def project_detail_view(project_id: str, session: Session = Depends(get_session)
     return project_detail
 
 
-#
-# @pride_router.get("/projects/{project_id}/proteins", tags=["Projects"])
-# def project_detail_view(project_id: str, session: Session = Depends(get_session), page: int = 1, page_size: int = 10) -> \
-#         list[ProjectSubDetail]:
-#     """
-#     Retrieve protein detail by px_accession.
-#     """
-#     try:
-#         project_detail = session.query(ProjectDetail) \
-#             .options(joinedload(ProjectDetail.project_sub_details)) \
-#             .filter(ProjectDetail.project_id == project_id).scalar()
-#
-#         offset = (page - 1) * page_size
-#         project_sub_details = session.query(ProjectSubDetail).filter(
-#             ProjectSubDetail.project_detail_id == project_detail.id) \
-#             .offset(offset).limit(page_size).all()
-#
-#     except Exception as e:
-#         logging.error(f"Error occurred: {str(e)}")
-#         project_sub_details = None
-#
-#     if project_sub_details is None or project_sub_details == []:
-#         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Project detail not found")
-#
-#     return project_sub_details
-
-
 @pride_router.get("/projects/{project_id}/proteins", tags=["Projects"])
 async def protein_search(project_id: Annotated[str, Path(...,
                                                          title="Project ID",
@@ -595,40 +616,44 @@ async def protein_search(project_id: Annotated[str, Path(...,
     :return: List of ProjectDetails in JSON format
     """
     try:
-        if q is None or q == '*':
-            sql = text("""
-                                  SELECT * FROM projectsubdetails 
-                                  WHERE project_detail_id IN (SELECT id 
-                                                              FROM projectdetails 
-                                                              WHERE project_id = :project_id)
-                                  ORDER BY id
-                                  LIMIT :limit OFFSET :offset
-                              """)
-            sql_values = {
-                "project_id": project_id,
-                "limit": page_size,
-                "offset": (page - 1) * page_size
-            }
-        else:
-            sql = text("""
-                                  SELECT * FROM projectsubdetails 
-                                  WHERE (protein_accession LIKE '%' || :query || '%' OR
-                                         gene_name LIKE '%' || :query || '%' OR
-                                         protein_name LIKE '%' || :query || '%') 
-                                         AND project_detail_id IN (SELECT id 
-                                                                   FROM projectdetails 
-                                                                   WHERE project_id = :project_id)
-                                  ORDER BY id
-                                  LIMIT :limit OFFSET :offset
-                              """)
-            sql_values = {
-                "project_id": project_id,
-                "query": q,
-                "limit": page_size,
-                "offset": (page - 1) * page_size
-            }
+        where_condition = """project_detail_id IN (SELECT id FROM projectdetails WHERE project_id = :project_id)"""
+
+        if q and q != '*':
+            where_condition += """ AND (protein_accession LIKE '%' || :query || '%' 
+                     OR gene_name LIKE '%' || :query || '%' 
+                     OR protein_name LIKE '%' || :query || '%')
+            """
+
+        sql = text(f"""
+            SELECT * FROM projectsubdetails 
+            WHERE {where_condition}
+            ORDER BY id
+            LIMIT :limit OFFSET :offset
+        """)
 
+        # Set the SQL values
+        sql_values = {
+            "project_id": project_id,
+            "query": q,
+            "limit": page_size,
+            "offset": (page - 1) * page_size
+        }
+
+        sql_total_count = text(f"""
+                  SELECT id FROM projectsubdetails 
+                  WHERE {where_condition}
+              """)
+
+        # Set the SQL values
+        sql_values_total_count = {
+            "project_id": project_id,
+            "query": q
+        }
+
+        # Execute the SQL query
         result = session.execute(sql, sql_values)
+        result_total = session.execute(sql_total_count, sql_values_total_count)
+        total_elements = result_total.all().__len__()
         proteins = result.fetchall()
 
         # Convert rows to a list of ProjectSubDetail objects
@@ -656,7 +681,18 @@ async def protein_search(project_id: Annotated[str, Path(...,
     if not proteins_list:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="proteins not found")
 
-    return proteins_list
+    response = {
+        "proteins": proteins_list,
+        "page": {
+            "page_no": page,
+            "page_size": page_size,
+            "total_elements": total_elements,
+            "total_pages": ceil(total_elements / page_size),
+            "number": 0
+        }
+    }
+
+    return response
 
 
 @pride_router.get("/statistics-count", tags=["Statistics"])

From 005f0fb08d66d311e5b0fd27366bd51d4f98bb19 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 10:55:10 +0000
Subject: [PATCH 02/11] improve endpoints with pagination and queries

---
 app/routes/pride.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/app/routes/pride.py b/app/routes/pride.py
index 65770f5..05bfcf6 100644
--- a/app/routes/pride.py
+++ b/app/routes/pride.py
@@ -564,8 +564,7 @@ async def project_search(q: Annotated[str | None, Query(default=None,
             "page_no": page,
             "page_size": page_size,
             "total_elements": total_elements,
-            "total_pages": ceil(total_elements / page_size),
-            "number": 0
+            "total_pages": ceil(total_elements / page_size)
         }
     }
     return response
@@ -688,7 +687,6 @@ async def protein_search(project_id: Annotated[str, Path(...,
             "page_size": page_size,
             "total_elements": total_elements,
             "total_pages": ceil(total_elements / page_size),
-            "number": 0
         }
     }
 

From 552feaf2103f0d0dbd86cf4d7bec0d7a867834b1 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 12:19:46 +0000
Subject: [PATCH 03/11] Bug fix

---
 app/routes/pride.py | 38 ++++++++++++++++++++++++++------------
 1 file changed, 26 insertions(+), 12 deletions(-)

diff --git a/app/routes/pride.py b/app/routes/pride.py
index 05bfcf6..419f00c 100644
--- a/app/routes/pride.py
+++ b/app/routes/pride.py
@@ -1,6 +1,6 @@
 import configparser
 import os
-from typing import List, Annotated
+from typing import List, Annotated, Union
 from math import ceil
 
 import requests
@@ -495,12 +495,26 @@ async def delete_dataset(project_id: str, session: Session = Depends(get_session
 
 
 @pride_router.get("/projects", tags=["Projects"])
-async def project_search(q: Annotated[str | None, Query(default=None,
-                                                        alias="query",
-                                                        max_length=20,
-                                                        title="query",
-                                                        description="Protein accession, protein name or gene name",
-                                                        example="PXD035 or PXD035519 or membrane")] = None,
+async def project_search(q: Union[str | None] = Query(default="",
+                                                      alias="query",
+                                                      max_length=20,
+                                                      title="query",
+                                                      description="Project accession, protein name or gene name",
+                                                      examples={
+                                                          "Project accession pattern": {
+                                                              "value": "PXD035",
+                                                              "description": "Project accession pattern"
+                                                          },
+                                                          "Project accession": {
+                                                              "value": "PXD035519",
+                                                              "description": "Protein accession"
+                                                          },
+                                                          "protein": {
+                                                              "value": "membrane",
+                                                              "description": "protein name"
+                                                          }
+                                                      }
+                                                      ),
                          page: int = Query(1, description="Page number"),
                          page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
                          session: Session = Depends(get_session)
@@ -598,11 +612,11 @@ async def protein_search(project_id: Annotated[str, Path(...,
                                                          title="Project ID",
                                                          pattern="^PXD\d{6}$",
                                                          example="PXD036833")],
-                         q: Annotated[str | None, Query(default=None,
-                                                        alias="query",
-                                                        max_length=20,
-                                                        title="query",
-                                                        description="Protein accession, protein name or gene name")] = None,
+                         q: Union[str | None] = Query(default=None,
+                                                      alias="query",
+                                                      max_length=20,
+                                                      title="query",
+                                                      description="Protein accession, protein name or gene name"),
                          page: int = Query(1, description="Page number"),
                          page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
                          session: Session = Depends(get_session)) -> list[ProjectSubDetail]:

From 4e27ee49764798a6e13265dfb6f4939fba825189 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 12:27:42 +0000
Subject: [PATCH 04/11] Bug fix

---
 app/routes/pride.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/routes/pride.py b/app/routes/pride.py
index 419f00c..36ef119 100644
--- a/app/routes/pride.py
+++ b/app/routes/pride.py
@@ -518,7 +518,7 @@ async def project_search(q: Union[str | None] = Query(default="",
                          page: int = Query(1, description="Page number"),
                          page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
                          session: Session = Depends(get_session)
-                         ) -> list[ProjectDetail]:
+                         ):
     """
     This gives the high-level view of list of projects
     :param q: Query parameter
@@ -619,7 +619,7 @@ async def protein_search(project_id: Annotated[str, Path(...,
                                                       description="Protein accession, protein name or gene name"),
                          page: int = Query(1, description="Page number"),
                          page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
-                         session: Session = Depends(get_session)) -> list[ProjectSubDetail]:
+                         session: Session = Depends(get_session)):
     """
     This gives the high-level view of a list of projects
     - **project_id**: PXD****** accession

From 3bfe78699c590760141f7429866ac3b717cf812f Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 12:34:53 +0000
Subject: [PATCH 05/11] Bug fix

---
 app/routes/pride.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/app/routes/pride.py b/app/routes/pride.py
index 36ef119..cbf2107 100644
--- a/app/routes/pride.py
+++ b/app/routes/pride.py
@@ -494,7 +494,7 @@ async def delete_dataset(project_id: str, session: Session = Depends(get_session
 #     return response
 
 
-@pride_router.get("/projects", tags=["Projects"])
+@pride_router.get("/projects", tags=["Projects"], response_model=None)
 async def project_search(q: Union[str | None] = Query(default="",
                                                       alias="query",
                                                       max_length=20,
@@ -518,7 +518,7 @@ async def project_search(q: Union[str | None] = Query(default="",
                          page: int = Query(1, description="Page number"),
                          page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
                          session: Session = Depends(get_session)
-                         ):
+                         ) -> list[ProjectDetail]:
     """
     This gives the high-level view of list of projects
     :param q: Query parameter
@@ -584,7 +584,7 @@ async def project_search(q: Union[str | None] = Query(default="",
     return response
 
 
-@pride_router.get("/projects/{project_id}", tags=["Projects"])
+@pride_router.get("/projects/{project_id}", tags=["Projects"], response_model=None)
 def project_detail_view(project_id: str, session: Session = Depends(get_session)) -> List[ProjectDetail]:
     """
     Retrieve project detail by px_accession.
@@ -607,7 +607,7 @@ def project_detail_view(project_id: str, session: Session = Depends(get_session)
     return project_detail
 
 
-@pride_router.get("/projects/{project_id}/proteins", tags=["Projects"])
+@pride_router.get("/projects/{project_id}/proteins", tags=["Projects"], response_model=None)
 async def protein_search(project_id: Annotated[str, Path(...,
                                                          title="Project ID",
                                                          pattern="^PXD\d{6}$",
@@ -619,7 +619,7 @@ async def protein_search(project_id: Annotated[str, Path(...,
                                                       description="Protein accession, protein name or gene name"),
                          page: int = Query(1, description="Page number"),
                          page_size: int = Query(10, gt=5, lt=100, description="Number of items per page"),
-                         session: Session = Depends(get_session)):
+                         session: Session = Depends(get_session)) -> list[ProjectSubDetail]:
     """
     This gives the high-level view of a list of projects
     - **project_id**: PXD****** accession

From cb294637f356e423e3e7e8ee02adc8073ed78ec2 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 13:17:46 +0000
Subject: [PATCH 06/11] Bug fix

---
 app/routes/parse.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/routes/parse.py b/app/routes/parse.py
index 5501b98..eac8300 100644
--- a/app/routes/parse.py
+++ b/app/routes/parse.py
@@ -42,7 +42,7 @@ class TableNamesEnum(str, Enum):
     projectsubdetail = "projectsubdetail"
 
 
-@parser_router.post("/write_data", tags=["Parser"])
+@parser_router.post("/write_data", tags=["Parser"], response_model=None)
 async def write_data(
         table: TableNamesEnum = Body(..., description="table name", embeded=True),
         data=Body(..., description="table data", embeded=True),
@@ -82,7 +82,7 @@ async def write_data(
     return result
 
 
-@parser_router.post("/write_new_upload", tags=["Parser"])
+@parser_router.post("/write_new_upload", tags=["Parser"], response_model=None)
 def write_new_upload(
         table: TableNamesEnum = Body(..., description="table name", embeded=True),
         data: dict = Body(..., description="table data", embeded=True),
@@ -99,7 +99,7 @@ def write_new_upload(
         raise HTTPException(status_code=500, detail="Internal Server Error")
 
 
-@parser_router.post("/write_mzid_info", tags=["Admin"])
+@parser_router.post("/write_mzid_info", tags=["Admin"], response_model=None)
 def write_mzid_info(analysis_software_list=Body(..., embeded=True),
                     spectra_formats=Body(..., embeded=True),
                     provider=Body(..., embeded=True),
@@ -136,7 +136,7 @@ def write_mzid_info(analysis_software_list=Body(..., embeded=True),
         conn.commit()
 
 
-@parser_router.post("/write_other_info", tags=["Parser"])
+@parser_router.post("/write_other_info", tags=["Parser"], response_model=None)
 def write_other_info(contains_crosslinks=Body(..., description="contains_crosslinks", embeded=True),
                      upload_warnings=Body(..., description="upload_warnings", embeded=True),
                      upload_id: int = None,

From 629e199cbc6f4879c69c3e454a3c3170a0c3a738 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 14:31:13 +0000
Subject: [PATCH 07/11] Bug fix

---
 app/routes/parse.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/app/routes/parse.py b/app/routes/parse.py
index eac8300..0ef0faf 100644
--- a/app/routes/parse.py
+++ b/app/routes/parse.py
@@ -1,17 +1,20 @@
 import base64
 import configparser
 import traceback
+from enum import Enum
+from typing import Annotated, Union
+from typing_extensions import Doc
 
-from fastapi import APIRouter, Depends, Query
+from fastapi import APIRouter, Depends, Query, Body
 from fastapi import HTTPException, Security
-from fastapi.params import Body
 from fastapi.security import APIKeyHeader
+from pydantic import BaseModel
 from sqlalchemy.orm import Session
 from app.models.upload import Upload
 from app.routes.shared import get_api_key
 from db_config_parser import get_conn_str
 from index import get_session
-from sqlalchemy import Table, Enum, MetaData, create_engine
+from sqlalchemy import Table, MetaData, create_engine
 import logging.config
 
 from parser.writer import Writer
@@ -47,7 +50,7 @@ async def write_data(
         table: TableNamesEnum = Body(..., description="table name", embeded=True),
         data=Body(..., description="table data", embeded=True),
         api_key: str = Security(get_api_key),
-        session: Session = Depends(get_session)):
+        session: Session = Depends(get_session)) -> None:
     """
         Insert data into table.
 
@@ -72,19 +75,19 @@ async def write_data(
             result = conn.execute(statement)
             conn.commit()
             conn.close()
-        return result
+        return None
 
     except Exception as e:
         print(f"Caught an exception: {e}")
         traceback.print_exc()
     finally:
         session.close()
-    return result
+    return None
 
 
-@parser_router.post("/write_new_upload", tags=["Parser"], response_model=None)
+@parser_router.post("/write_new_upload", tags=["Parser"])
 def write_new_upload(
-        table: TableNamesEnum = Body(..., description="table name", embeded=True),
+        table: Annotated[TableNamesEnum, Body(..., description="table name", embeded=True)],
         data: dict = Body(..., description="table data", embeded=True),
         api_key: str = Security(get_api_key),
         session: Session = Depends(get_session)):
@@ -99,7 +102,7 @@ def write_new_upload(
         raise HTTPException(status_code=500, detail="Internal Server Error")
 
 
-@parser_router.post("/write_mzid_info", tags=["Admin"], response_model=None)
+@parser_router.post("/write_mzid_info", tags=["Admin"])
 def write_mzid_info(analysis_software_list=Body(..., embeded=True),
                     spectra_formats=Body(..., embeded=True),
                     provider=Body(..., embeded=True),
@@ -136,7 +139,7 @@ def write_mzid_info(analysis_software_list=Body(..., embeded=True),
         conn.commit()
 
 
-@parser_router.post("/write_other_info", tags=["Parser"], response_model=None)
+@parser_router.post("/write_other_info", tags=["Parser"])
 def write_other_info(contains_crosslinks=Body(..., description="contains_crosslinks", embeded=True),
                      upload_warnings=Body(..., description="upload_warnings", embeded=True),
                      upload_id: int = None,

From 97dff8298ee358866bd5fb6aa169d89aff9252f3 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 15:21:58 +0000
Subject: [PATCH 08/11] increase timeout

---
 main.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/main.py b/main.py
index 01ac7ec..8e7beca 100644
--- a/main.py
+++ b/main.py
@@ -6,6 +6,7 @@
     uvicorn.run(app,
                 host="0.0.0.0",
                 port=3000,
+                channel_timeout=300,
                 log_level="info",  # Set the desired log level ("debug", "info", "warning", etc.)
                 log_config="logging.ini"  # Specify the path to your logging configuration file
                 )

From b154ec9f1b2823d351769eec5c99c8a197232d2f Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 15:30:41 +0000
Subject: [PATCH 09/11] increase timeout

---
 main.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/main.py b/main.py
index 8e7beca..01ac7ec 100644
--- a/main.py
+++ b/main.py
@@ -6,7 +6,6 @@
     uvicorn.run(app,
                 host="0.0.0.0",
                 port=3000,
-                channel_timeout=300,
                 log_level="info",  # Set the desired log level ("debug", "info", "warning", etc.)
                 log_config="logging.ini"  # Specify the path to your logging configuration file
                 )

From 9fb6c7cd06dbaef3ae01d80285b26307ef794f04 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 21:29:00 +0000
Subject: [PATCH 10/11] adding more validations

---
 app/routes/pdbdev.py | 53 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 41 insertions(+), 12 deletions(-)

diff --git a/app/routes/pdbdev.py b/app/routes/pdbdev.py
index 5ff2d33..fed1b9a 100644
--- a/app/routes/pdbdev.py
+++ b/app/routes/pdbdev.py
@@ -1,13 +1,15 @@
 import json
 
 import psycopg2
-from fastapi import APIRouter, Depends
+from fastapi import APIRouter, Depends, Path
 from psycopg2.extras import RealDictCursor
 import logging
 from sqlalchemy import text
 from sqlalchemy.orm import Session
 from index import get_session
 from typing import List
+from enum import Enum
+from typing import Annotated
 
 from app.routes.shared import get_db_connection, get_most_recent_upload_ids
 
@@ -16,13 +18,13 @@
 app_logger = logging.getLogger(__name__)
 
 
-
 @pdbdev_router.get("/projects/{protein_id}", response_model=List[str], tags=["PDB-Dev"])
 async def get_projects_by_protein(protein_id: str, session: Session = Depends(get_session)):
     """
      Get the list of all the datasets in PRIDE crosslinking for a given protein.
     """
-    project_list_sql = text("""select distinct project_id from upload where id in (select upload_id from dbsequence where accession = :query)""")
+    project_list_sql = text(
+        """select distinct project_id from upload where id in (select upload_id from dbsequence where accession = :query)""")
     try:
         project_list = session.execute(project_list_sql, {"query": protein_id}).fetchall()
         # Convert the list of tuples into a list of strings
@@ -33,6 +35,7 @@ async def get_projects_by_protein(protein_id: str, session: Session = Depends(ge
         app_logger.error(error)
     return project_list
 
+
 @pdbdev_router.get('/projects/{project_id}/sequences', tags=["PDB-Dev"])
 async def sequences(project_id):
     """
@@ -52,21 +55,19 @@ async def sequences(project_id):
         conn = await get_db_connection()
         cur = conn.cursor(cursor_factory=RealDictCursor)
 
-        sql = """SELECT dbseq.id, u.identification_file_name, dbseq.sequencel, dbseq.accession
+        sql = text("""SELECT dbseq.id, u.identification_file_name, dbseq.sequencel, dbseq.accession
                     FROM upload AS u
                     JOIN dbsequence AS dbseq ON u.id = dbseq.upload_id
                     INNER JOIN peptideevidence pe ON dbseq.id = pe.dbsequence_ref AND dbseq.upload_id = pe.upload_id
                  WHERE u.id = ANY (%s)
                  AND pe.is_decoy = false
-                 GROUP by dbseq.id, dbseq.sequence, u.identification_file_name;"""
+                 GROUP by dbseq.id, dbseq.sequence, u.identification_file_name;""")
 
         print(sql)
         cur.execute(sql, [most_recent_upload_ids])
         mzid_rows = cur.fetchall()
 
         print("finished")
-        # close the communication with the PostgreSQL
-        cur.close()
     except (Exception, psycopg2.DatabaseError) as error:
         print(error)
     finally:
@@ -76,8 +77,37 @@ async def sequences(project_id):
         return {"data": mzid_rows}
 
 
-@pdbdev_router.get('/projects/{project_id}/residue-pairs/based-on-reported-psm-level/{passing_threshold}', tags=["PDB-Dev"])
-async def get_psm_level_residue_pairs(project_id, passing_threshold):
+class Threshold(str, Enum):
+    passing = "passing"
+    all = "all"
+
+    def is_valid_enum(value: str) -> bool:
+        try:
+            getattr(Threshold, value)
+            return True
+        except AttributeError:
+            return False
+
+@pdbdev_router.get('/projects/{project_id}/residue-pairs/based-on-reported-psm-level/{passing_threshold}',
+                   tags=["PDB-Dev"])
+async def get_psm_level_residue_pairs(project_id: Annotated[str, Path(...,
+                                                                      title="Project ID",
+                                                                      pattern="^PXD\d{6}$",
+                                                                      example="PXD036833")],
+                                      passing_threshold: Annotated[Threshold, Path(...,
+                                                                                   title="Threshold",
+                                                                                   description="Threshold passing or all the values",
+                                                                                   examples={
+                                                          "Passing": {
+                                                              "value": "passing",
+                                                              "description": "passing threshold"
+                                                          },
+                                                          "All": {
+                                                              "value": "all",
+                                                              "description": "all threshold"
+                                                          }
+                                                      })]
+                                      ):
     """
     Get all residue pairs (based on PSM level data) belonging to a project.
 
@@ -90,7 +120,7 @@ async def get_psm_level_residue_pairs(project_id, passing_threshold):
         if 'all' return all residue pairs
     :return:
     """
-    if passing_threshold not in ['passing', 'all']:
+    if not Threshold.is_valid_enum(passing_threshold):
         return f"Invalid value for passing_threshold: {passing_threshold}. " \
                f"Valid values are: passing, all", 400
 
@@ -119,10 +149,9 @@ async def get_psm_level_residue_pairs(project_id, passing_threshold):
 """
         # problem above in u.project_id
 
-        if passing_threshold.lower() == 'passing':
+        if passing_threshold.lower() == Threshold.passing:
             sql += " AND si.pass_threshold = true"
         sql += ";"
-        print(sql)
         cur.execute(sql, [most_recent_upload_ids])
         mzid_rows = cur.fetchall()
         data["data"] = mzid_rows

From d1681bed6dec4a39317a62afa16c52d7f895d6df Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 8 Feb 2024 21:29:12 +0000
Subject: [PATCH 11/11] adding more validations

---
 Pipfile      |  2 +-
 Pipfile.lock | 16 ++++------------
 2 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/Pipfile b/Pipfile
index c4f9eed..f084a58 100644
--- a/Pipfile
+++ b/Pipfile
@@ -5,7 +5,7 @@ name = "pypi"
 
 [packages]
 fastapi = "*"
-uvicorn = "<0.16.0,>=0.15.0"
+uvicorn = "*"
 lxml = ">=4.9.1"
 numpy = ">=1.14.3"
 pandas = ">=0.21.0"
diff --git a/Pipfile.lock b/Pipfile.lock
index fd831ea..ef4c5c8 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "2451e061dd2f1c6e33f098c44c59acff9feaf52e924c4e4cd85ed0c5fc632138"
+            "sha256": "3cfead865413a6c799afd11a370c4d406dbf6018330dbfd29e48558d07dc7cf3"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -32,14 +32,6 @@
             "markers": "python_version >= '3.8'",
             "version": "==4.2.0"
         },
-        "asgiref": {
-            "hashes": [
-                "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e",
-                "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==3.7.2"
-        },
         "certifi": {
             "hashes": [
                 "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f",
@@ -943,11 +935,11 @@
         },
         "uvicorn": {
             "hashes": [
-                "sha256:17f898c64c71a2640514d4089da2689e5db1ce5d4086c2d53699bf99513421c1",
-                "sha256:d9a3c0dd1ca86728d3e235182683b4cf94cd53a867c288eaeca80ee781b2caff"
+                "sha256:4b85ba02b8a20429b9b205d015cbeb788a12da527f731811b643fd739ef90d5f",
+                "sha256:54898fcd80c13ff1cd28bf77b04ec9dbd8ff60c5259b499b4b12bb0917f22907"
             ],
             "index": "pypi",
-            "version": "==0.15.0"
+            "version": "==0.27.0.post1"
         }
     },
     "develop": {}