Merge pull request #13 from refgenie/dev

Release v0.6.0
refgenie · Aug 9, 2024 · da9b527 · da9b527
2 parents 506f523 + b132525
commit da9b527
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Showing 11 changed files with 138 additions and 79 deletions.
diff --git a/frontend/src/components/ObjectLists.jsx b/frontend/src/components/ObjectLists.jsx
@@ -1,14 +1,16 @@
 import { Link } from "react-router-dom"
+import { useLoaderData } from "react-router-dom"
+
 
 // Basic list of Sequence Collections
 const CollectionList = ({collections}) => {
     const seqColList = collections || useLoaderData()[0]
-    console.log("CollectionList", CollectionList)
+    console.log("seqColList", seqColList)
 
     return (<>
       <div>
         <ul>
-          {seqColList.items.map((seqCol) => (
+          {seqColList.results.map((seqCol) => (
             <li key={seqCol}>
               Collection: <Link to={`/collection/${seqCol}`} className="font-monospace">{seqCol}</Link>
             </li>
@@ -18,6 +20,23 @@ const CollectionList = ({collections}) => {
     )
   }
 
+const AttributeList = ({attributes}) => {
+  const attrList = attributes || useLoaderData()[0]
+  console.log("attrList", attrList)
+
+  return (<>
+    <div>
+      <ul>
+        {attrList.results.map((attr) => (
+          <li key={attr}>
+            Attribute: <Link to={`/attribute/sorted_name_length_pairs/${attr}`}>{attr}</Link>
+          </li>
+        ))}
+      </ul>
+    </div></>
+  )
+}
+
 
 // Basic list of Pangenomes
 const PangenomeList = ({pangenomes}) => {
@@ -27,7 +46,7 @@ const PangenomeList = ({pangenomes}) => {
   return (<>
     <div>
       <ul>
-        {pangenomeList.items.map((pangenome) => (
+        {pangenomeList.results.map((pangenome) => (
           <li key={pangenome}>
             <Link to={`/pangenome/${pangenome}`}>{pangenome}</Link>
           </li>
@@ -39,5 +58,5 @@ const PangenomeList = ({pangenomes}) => {
 
 
 
-  export { CollectionList, PangenomeList }
+  export { AttributeList, CollectionList, PangenomeList }
 
diff --git a/frontend/src/main.jsx b/frontend/src/main.jsx
@@ -48,11 +48,13 @@ const fetchPangenomeLevels = async(digest, level="2", collated=true) => {
 }
 
 const fetchSeqColList = async() => {
-  const url = `${API_BASE}/list/collections?limit=10&offset=10`
-  const url2 = `${API_BASE}/list/pangenomes?limit=5`
+  const url = `${API_BASE}/list/collections?page_size=10&page=1`
+  const url2 = `${API_BASE}/list/pangenomes?page_size=5`
+  const url3 = `${API_BASE}/list/attributes/sorted_name_length_pairs?page_size=5`
   let resps = [
     fetch(url).then((response) => response.json()),
-    fetch(url2).then((response) => response.json())
+    fetch(url2).then((response) => response.json()),
+    fetch(url3).then((response) => response.json())
   ]
   return Promise.all(resps)
 }
@@ -79,8 +81,8 @@ const fecthComparison = async(digest1, digest2) => {
 }
 
 const fetchAttribute = async(attribute, digest) => {
-  const url = `${API_BASE}/attribute/${attribute}/${digest}/list`
-  const url2 = `${API_BASE}/attribute/${attribute}/${digest}`
+  const url = `${API_BASE}/list/collections/${attribute}/${digest}`
+  const url2 = `${API_BASE}/attribute/collection/${attribute}/${digest}`
   let resps = [
     fetch(url).then((response) => response.json()),
     fetch(url2).then((response) => response.json())
@@ -93,9 +95,9 @@ const fetchAttribute = async(attribute, digest) => {
 const Level1Collection = ({collection}) => {
   return (
     <div>
-      Names: <Link to={`/attribute/names/${collection.names}`}>{collection.names}</Link><br/>
-      Lengths: <Link to={`/attribute/lengths/${collection.lengths}`}>{collection.lengths}</Link><br/>
-      Sequences: <Link to={`/attribute/sequences/${collection.sequences}`}>{collection.sequences}</Link><br/>
+      Names: <Link to={`/attribute/collection/names/${collection.names}`}>{collection.names}</Link><br/>
+      Lengths: <Link to={`/attribute/collection/lengths/${collection.lengths}`}>{collection.lengths}</Link><br/>
+      Sequences: <Link to={`/attribute/collection/sequences/${collection.sequences}`}>{collection.sequences}</Link><br/>
     </div>
   )
 }
@@ -185,7 +187,7 @@ const CollectionTable = ({collections}) => {
       </tr>
     </thead>
     <tbody>
-    {seqColList["items"].map((collection) => (
+    {seqColList["results"].map((collection) => (
       <tr key={collection}>
         <td><LinkedCollectionDigest digest={collection.digest} clipboard={false}/></td>
         <td className="tiny mx-2"><LinkedAttributeDigest attribute="names" digest={collection.names_digest} clipboard={false}/></td>

diff --git a/frontend/src/pages/AttributeView.jsx b/frontend/src/pages/AttributeView.jsx
@@ -6,7 +6,7 @@ import { CollectionList } from '../components/ObjectLists.jsx'
 const AttributeView = () => { 
     const content = useLoaderData()
     const { attribute, digest } = useParams()
-    const api_url = `${API_BASE}/attribute/${attribute}/${digest}`
+    const api_url = `${API_BASE}/attribute/collection/${attribute}/${digest}`
     const api_url_list = `${API_BASE}/list/collections/${attribute}/${digest}`
     let results = content[0]
     let attribute_value = content[1]

diff --git a/frontend/src/pages/DemoPage.jsx b/frontend/src/pages/DemoPage.jsx
@@ -21,6 +21,7 @@ function DemoPage() {
             <th>digest</th>
           </tr>
         </thead>
+        <tbody>
         {Object.keys(demo_seqcol_digests).map((property) => {
           return (
             <tr key={demo_seqcol_digests[property]}>
@@ -29,6 +30,7 @@ function DemoPage() {
             </tr>
           )
         })}
+        </tbody>
       </table>
       <CompareTable seqColList={Object.values(demo_seqcol_digests)}/>
     </div>

diff --git a/frontend/src/pages/HomePage.jsx b/frontend/src/pages/HomePage.jsx
@@ -2,15 +2,18 @@ import { PangenomeList } from '../components/ObjectLists.jsx'
 import { CollectionList } from '../components/ObjectLists.jsx'
 import { Link } from "react-router-dom";
 import { useLoaderData } from "react-router-dom";
+import { AttributeList } from '../components/ObjectLists';
+
 
 const HomePage = () => {
     const loaderData = useLoaderData()
     console.log("HomePage loadData ", loaderData)
     const collections = loaderData[0]
     const pangenomes = loaderData[1]
+    const sorted_name_length_pairs = loaderData[2]
 
     const PangenomeExamplesList = () => {
-      if (pangenomes.items[0]) {
+      if (pangenomes.results[0]) {
         return <>
           <h3>Example Pangenomes:</h3>
           <PangenomeList pangenomes={pangenomes}/>
@@ -54,6 +57,14 @@ const HomePage = () => {
         </ul>
         <PangenomeExamplesList/>
 
+        <h5 className="mt-4">4. List of sorted_name_length_pairs on this server:</h5>
+        <p className="text-muted fs-6">
+        The <span className="font-monospace text-success">/list/attributes</span> endpoint lets you retrieve
+        a list of all the values of a particular attribute hosted by this server.
+        </p>
+        <AttributeList attributes={sorted_name_length_pairs}/>
+
+
       </div>
     )
   }

diff --git a/refget/_version.py b/refget/_version.py
@@ -1 +1 @@
-__version__ = "0.5.0"
+__version__ = "0.6.0"
diff --git a/refget/agents.py b/refget/agents.py
@@ -123,7 +123,7 @@ def list_by_offset(self, limit=50, offset=0):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"count": count, "limit": limit, "offset": offset, "items": seqcols}
+            return {"pagination": { "page": offset*limit, "page_size": limit, "total": count}, "results": seqcols}
 
     def list(self, page_size=100, cursor=None):
         with Session(self.engine) as session:
@@ -223,7 +223,7 @@ def list_by_offset(self, limit=50, offset=0):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"count": count, "limit": limit, "offset": offset, "items": seqcols}
+            return {"pagination": { "page": offset*limit, "page_size": limit, "total": count}, "results": seqcols}
 
 
 class AttributeAgent(object):
@@ -250,7 +250,7 @@ def list(self, attribute_type, offset=0, limit=50):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"count": count, "limit": limit, "offset": offset, "items": seqcols}
+            return {"pagination": { "page": offset*limit, "page_size": limit, "total": count}, "results": seqcols}
 
     def search(self, attribute_type, digest, offset=0, limit=50):
         Attribute = ATTR_TYPE_MAP[attribute_type]
@@ -268,7 +268,7 @@ def search(self, attribute_type, digest, offset=0, limit=50):
             list_res = session.exec(list_stmt)
             count = cnt_res.one()
             seqcols = list_res.all()
-            return {"count": count, "limit": limit, "offset": offset, "items": seqcols}
+            return {"pagination": { "page": offset*limit, "page_size": limit, "total": count}, "results": seqcols}
 
 
 class RefgetDBAgent(object):

diff --git a/refget/examples.py b/refget/examples.py
@@ -12,6 +12,15 @@
     examples="a6748aa0f6a1e165f871dbed5e54ba62",
 )
 
+example_attribute_digest = Path(
+    ...,
+    description="Attribute digest",
+    pattern=r"^[-\w]+$",
+    max_length=64,
+    min_length=16,
+    examples="cGRMZIb3AVgkcAfNv39RN7hnT5Chk7RXCopy",
+)
+
 example_collection_digest = Path(
     ...,
     description="Sequence collection digest",

diff --git a/refget/seqcol_router.py b/refget/seqcol_router.py
@@ -30,6 +30,8 @@ async def get_schenge(request: Request):
     return request.app.state.schenge
 
 
+# dbagent is a RefgetDBAgent
+
 async def get_dbagent(request: Request):
     return request.app.state.dbagent
 
@@ -49,17 +51,6 @@ async def refget(request: Request, sequence_digest: str = example_sequence):
     return Response(content=schenge.refget(sequence_digest))
 
 
-@seqcol_router.get(
-    "/attribute/{attribute}/{attribute_digest}",
-    summary="Retrieve a single attribute of a sequence collection",
-    tags=["Retrieving data"],
-)
-async def attribute(
-    dbagent=Depends(get_dbagent), attribute: str = "names", attribute_digest: str = example_digest
-):
-    return JSONResponse(dbagent.attribute.get(attribute, attribute_digest))
-
-
 @seqcol_router.get(
     "/collection/{collection_digest}",
     summary="Retrieve a sequence collection",
@@ -92,6 +83,18 @@ async def collection(
             detail=str(e),
         )
 
+@seqcol_router.get(
+    "/attribute/collection/{attribute}/{attribute_digest}",
+    summary="Retrieve a single attribute of a sequence collection",
+    tags=["Retrieving data"],
+)
+async def attribute(
+    dbagent=Depends(get_dbagent), attribute: str = "names", attribute_digest: str = example_digest
+):
+    return JSONResponse(dbagent.attribute.get(attribute, attribute_digest))
+
+
+
 
 @seqcol_router.get(
     "/pangenome/{pangenome_digest}",
@@ -133,28 +136,6 @@ async def pangenome(
         )
 
 
-@seqcol_router.get(
-    "/attribute/{attribute}/{attribute_digest}/list",
-    summary="List sequence collections that contain a given attribute",
-    tags=["Discovering data"],
-)
-@seqcol_router.get(
-    "/list/collections/{attribute}/{attribute_digest}",
-    summary="List sequence collections that contain a given attribute",
-    tags=["Discovering data"],
-)
-async def attribute_search(
-    dbagent=Depends(get_dbagent),
-    attribute: str = "names",
-    attribute_digest: str = example_digest,
-    limit: int = 100,
-    offset: int = 0,
-):
-    # attr = dbagent.attribute.get(attribute, digest)
-    res = dbagent.attribute.search(attribute, attribute_digest, limit=limit, offset=offset)
-    res["items"] = [x.digest for x in res["items"]]
-    return JSONResponse(res)
-
 
 @seqcol_router.get(
     "/collection2/{collection_digest}",
@@ -268,34 +249,64 @@ async def compare_1_digest(
     return JSONResponse(schenge.compat_all(A, B))
 
 
+
 @seqcol_router.get(
-    "/list",
-    summary="List sequence collections on the server, paged by offset",
+    "/list/collections",
+    summary="List sequence collections on the server",
     tags=["Discovering data"],
 )
+async def list_collections_by_offset(
+    dbagent=Depends(get_dbagent), page_size: int = 100, page: int = 0
+):
+    res = dbagent.seqcol.list_by_offset(limit=page_size, offset=page*page_size)
+    res["results"] = [x.digest for x in res["results"]]
+    return JSONResponse(res)
+
+
+# @seqcol_router.get(
+#     "/list-by-cursor",
+#     summary="List sequence collections on the server, paged by cursor",
+#     tags=["Discovering data"],
+# )
+# async def list_collections_by_token(
+#     dbagent=Depends(get_dbagent), page_size: int = 100, cursor: str = None
+# ):
+#     res = dbagent.seqcol.list(page_size=page_size, cursor=cursor)
+#     res["results"] = [x.digest for x in res["results"]]
+#     return JSONResponse(res)
+
+
+
+
+
 @seqcol_router.get(
-    "/list/collections",
-    summary="List sequence collections on the server, paged by offset",
+    "/list/collections/{attribute}/{attribute_digest}",
+    summary="Filtered list of sequence collections that contain a given attribute",
     tags=["Discovering data"],
 )
-async def list_collections_by_offset(
-    dbagent=Depends(get_dbagent), limit: int = 100, offset: int = 0
+async def attribute_search(
+    dbagent=Depends(get_dbagent),
+    attribute: str = "names",
+    attribute_digest: str = example_attribute_digest,
+    page_size: int = 100,
+    page: int = 0,
 ):
-    res = dbagent.seqcol.list_by_offset(limit=limit, offset=offset)
-    res["items"] = [x.digest for x in res["items"]]
+    # attr = dbagent.attribute.get(attribute, digest)
+    res = dbagent.attribute.search(attribute, attribute_digest, limit=page_size, offset=page*page_size)
+    res["results"] = [x.digest for x in res["results"]]
     return JSONResponse(res)
 
 
 @seqcol_router.get(
-    "/list-by-cursor",
-    summary="List sequence collections on the server, paged by cursor",
+    "/list/attributes/{attribute}",
+    summary="List attributes on the server",
     tags=["Discovering data"],
 )
-async def list_collections_by_token(
-    dbagent=Depends(get_dbagent), page_size: int = 100, cursor: str = None
+async def list_attributes(
+    dbagent=Depends(get_dbagent), attribute: str = "names", page_size: int = 100, page: int = 0
 ):
-    res = dbagent.seqcol.list(page_size=page_size, cursor=cursor)
-    res["items"] = [x.digest for x in res["items"]]
+    res = dbagent.attribute.list(attribute, limit=page_size, offset=page*page_size)
+    res["results"] = [x.digest for x in res["results"]]
     return JSONResponse(res)
 
 
@@ -305,8 +316,11 @@ async def list_collections_by_token(
     tags=["Discovering data"],
 )
 async def list_cpangenomes_by_offset(
-    dbagent=Depends(get_dbagent), limit: int = 100, offset: int = 0
+    dbagent=Depends(get_dbagent), page_size: int = 100, page: int = 0
 ):
-    res = dbagent.pangenome.list_by_offset(limit=limit, offset=offset)
-    res["items"] = [x.digest for x in res["items"]]
+    res = dbagent.pangenome.list_by_offset(limit=page_size, offset=page*page_size)
+    res["results"] = [x.digest for x in res["results"]]
     return JSONResponse(res)
+
+
+