Merge pull request #216 from pepkit/dev

Release `v0.9.7`

docs/changelog.md

@@ -2,6 +2,13 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.9.7] - 07-24-2023
+
+### Fixed
+
+- sample table would exhibit odd, erratic behavior if column names were left blank
+- alnding page styling was not otpimal
+
 ## [0.9.6] - 07-20-2023
 
 ### Fixed

pephub/_version.py

@@ -1 +1 @@
-__version__ = "0.9.6"
+__version__ = "0.9.7"

pephub/routers/api/v1/namespace.py

@@ -38,6 +38,12 @@ async def get_namespace(
 ):
     """
     Fetch namespace. Returns a JSON representation of the namespace.
+
+    Don't have a namespace?
+
+    Use the following:
+
+        namespace: databio
     """
     nspace = nspace.dict()
     nspace["projects_endpoint"] = f"{str(request.url)[:-1]}/projects"
@@ -60,6 +66,12 @@ async def get_namespace_projects(
 ):
     """
     Fetch the projects for a particular namespace
+
+    Don't have a namespace?
+
+    Use the following:
+
+        namespace: databio
     """
 
     # TODO, this API will change. Searching
@@ -118,6 +130,12 @@ async def create_pep(
     ),
     agent: PEPDatabaseAgent = Depends(get_db),
 ):
+    """
+    Create a PEP for a particular namespace you have write access to.
+
+    Don't know your namespace? Log in to see.
+
+    """
     if files is not None:
         init_file = parse_user_file_upload(files)
         init_file, other_files = split_upload_files_on_init_file(files, init_file)
@@ -226,6 +244,12 @@ async def upload_raw_pep(
     project_from_json: ProjectJsonRequest,
     agent: PEPDatabaseAgent = Depends(get_db),
 ):
+    """
+    Upload a raw project for a particular namespace you have write access to.
+
+    Don't know your namespace? Log in to see.
+
+    """
     try:
         is_private = project_from_json.is_private
         tag = project_from_json.tag

pephub/routers/api/v1/project.py

@@ -38,6 +38,14 @@ async def get_a_pep(
 ):
     """
     Fetch a PEP from a certain namespace
+
+    Don't have a namespace or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
+
     """
     if not isinstance(proj, peppy.Project):
         try:
@@ -93,6 +101,13 @@ async def update_a_pep(
 ):
     """
     Update a PEP from a certain namespace
+
+    Don't have a namespace or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
     """
     # if not logged in, they cant update
     if namespace not in (list_of_admins or []):
@@ -255,6 +270,16 @@ async def get_pep_samples(
     format: Optional[str] = None,
     raw: Optional[bool] = False,
 ):
+    """
+    Get samples from a certain project and namespace
+
+    Don't have a namespace or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
+    """
     if format is not None:
         conversion_func: Callable = SAMPLE_CONVERSION_FUNCTIONS.get(format, None)
         if conversion_func is not None:
@@ -288,6 +313,16 @@ async def get_pep_samples(
     format: Optional[Literal["JSON", "String"]] = "JSON",
     raw: Optional[bool] = False,
 ):
+    """
+    Get project configuration file from a certain project and namespace
+
+    Don't have a namespace or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
+    """
     if raw:
         proj_config = proj[CONFIG_KEY]
     else:
@@ -303,6 +338,17 @@ async def get_pep_samples(
 
 @project.get("/samples/{sample_name}")
 async def get_sample(sample_name: str, proj: peppy.Project = Depends(get_project)):
+    """
+    Get a particular sample from a certain project and namespace
+
+    Don't have a sample name, namespace, or project?
+
+    Use the following:
+
+        sample_name: 4-1_11102016
+        project: example
+        namespace: databio
+    """
     if sample_name not in get_project_sample_names(proj):
         raise HTTPException(status_code=404, detail=f"sample '{sample_name}' not found")
     sample = proj.get_sample(sample_name)
@@ -314,6 +360,16 @@ async def get_subsamples(
     proj: peppy.Project = Depends(get_project),
     download: bool = False,
 ):
+    """
+    Get subsamples from a certain project and namespace
+
+    Don't have a namespace, or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
+    """
     subsamples = proj[SUBSAMPLE_RAW_LIST_KEY]
     if subsamples is not None:
         try:
@@ -353,6 +409,14 @@ async def convert_pep(
 
     See, http://eido.databio.org/en/latest/filters/#convert-a-pep-into-an-alternative-format-with-a-filter
     for more information.
+
+    Don't have a namespace, or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
+
     """
     # default to basic
     if filter is None:
@@ -381,7 +445,17 @@ async def convert_pep(
 
 @project.get("/zip")
 async def zip_pep_for_download(proj: peppy.Project = Depends(get_project)):
-    """Zip a pep"""
+    """
+    Zip a pep
+
+    Don't have a namespace, or project?
+
+    Use the following:
+
+        project: example
+        namespace: databio
+
+    """
     return zip_pep(proj)
 
 
@@ -396,6 +470,12 @@ async def fork_pep_to_namespace(
     proj_annotation: AnnotationModel = Depends(get_project_annotation),
     agent: PEPDatabaseAgent = Depends(get_db),
 ):
+    """
+    Fork a project for a particular namespace you have write access to.
+
+    Don't know your namespace and/project? Log in to see.
+
+    """
     fork_to = fork_request.fork_to
     fork_name = fork_request.fork_name
     fork_tag = fork_request.fork_tag

pephub/routers/eido/eido.py

@@ -9,6 +9,7 @@
 from starlette.requests import Request
 from starlette.responses import JSONResponse
 from typing import List, Tuple
+from pepdbagent.utils import registry_path_converter
 
 from ...helpers import parse_user_file_upload, split_upload_files_on_init_file
 from ...dependencies import *
@@ -79,9 +80,8 @@ async def validate(
         )
 
     if pep_registry is not None:
-        # split into namespace, name, tag
-        namespace, name_tag = pep_registry.split("/")
-        name, tag = name_tag.split(":")
+        namespace, name, tag = registry_path_converter(pep_registry)
+        tag = tag or DEFAULT_TAG
         p = agent.project.get(namespace, name, tag)
     else:
         init_file = parse_user_file_upload(pep_files)

web/src/components/layout/landing-paths.tsx

@@ -81,8 +81,7 @@ export const LandingPaths: FC = () => {
       >
         <a href={'/databio/example'}>
           <motion.div
-            className="bottom-right-landing-icon fw-bold text-primary bg-gradient rounded shadow border bg-white border-primary cursor-pointer d-flex flex-row align-items-center justify-content-center"
-            // "sink in" on hover
+            className="bottom-right-landing-icon landing-icon-border fw-bold text-primary bg-gradient rounded shadow bg-white cursor-pointer d-flex flex-row align-items-center justify-content-center"
             whileHover={{ scale: 1.05 }}
           >
             <i className="bi bi-eye-fill me-1"></i>
@@ -91,18 +90,16 @@ export const LandingPaths: FC = () => {
         </a>
         <a href="databio/example?fork=true">
           <motion.div
-            className="top-right-landing-icon fw-bold text-primary bg-gradient rounded shadow border bg-white border-primary cursor-pointer d-flex flex-row align-items-center justify-content-center"
-            // "sink in" on hover
+            className="top-right-landing-icon landing-icon-border fw-bold text-primary bg-gradient rounded shadow bg-white cursor-pointer d-flex flex-row align-items-center justify-content-center"
             whileHover={{ scale: 1.05 }}
           >
             <img src="/github-branch-primary.svg" height="20px" className="me-1" />
             Fork PEP
           </motion.div>
         </a>
-        <a href={'/validate?pepRegistryPath=databio/example'}>
+        <a href={'/validate?pepRegistryPath=databio/example:default'}>
           <motion.div
-            className="bottom-left-landing-icon fw-bold text-primary bg-gradient rounded shadow border bg-white border-primary cursor-pointer d-flex flex-row align-items-center justify-content-center"
-            // "sink in" on hover
+            className="bottom-left-landing-icon landing-icon-border fw-bold text-primary bg-gradient rounded shadow bg-white cursor-pointer d-flex flex-row align-items-center justify-content-center"
             whileHover={{ scale: 1.05 }}
             style={{}}
           >
@@ -112,8 +109,7 @@ export const LandingPaths: FC = () => {
         </a>
         <a href={`${API_HOST}/api/v1/projects/databio/example`}>
           <motion.div
-            className="top-left-landing-icon fw-bold text-primary bg-gradient rounded shadow border bg-white border-primary cursor-pointer d-flex flex-row align-items-center justify-content-center"
-            // "sink in" on hover
+            className="top-left-landing-icon landing-icon-border fw-bold text-primary bg-gradient rounded shadow bg-white cursor-pointer d-flex flex-row align-items-center justify-content-center"
             whileHover={{ scale: 1.05 }}
           >
             <i className="bi bi-download me-1"></i>

web/src/globals.css

@@ -309,6 +309,14 @@
   box-shadow: 0 0 5px #ccc inset;
 }
 
+/*  on mobile, remove all x-margins */
+@media screen and (max-width: 990px) {
+  .landing-table-container {
+    margin-left: 0px !important;
+    margin-right: 0px !important;
+  }
+}
+
 /* subtle glow animation */
 .landing-paths {
   transform: translateY(-40%) translateX(-5%);
@@ -334,6 +342,20 @@
   }
 }
 
+.landing-icon-border {
+  border: 1px solid;
+  animation: border-glow 1s ease-in-out infinite alternate;
+}
+
+@keyframes border-glow {
+  from {
+    border-color: #7ab9fd;
+  }
+  to {
+    border-color: #0d6efd;
+  }
+}
+
 .top-left-landing-icon {
   position: absolute;
   bottom: 332px;

web/src/pages/Home.tsx

@@ -66,7 +66,7 @@ function Home() {
                   </MotionButton>
                 )}
                 <a href="/validate">
-                  <MotionButton className="mt-1 btn btn-outline-dark btn-lg me-3">
+                  <MotionButton className="btn btn-outline-dark btn-lg me-3">
                     <i className="bi bi-check2-circle me-1"></i>Validation
                   </MotionButton>
                 </a>
@@ -98,7 +98,7 @@ function Home() {
               </div>
             </div>
             <div className="col-lg-6 col-sm-12 align-items-center">
-              <div className="mt-5 ms-5">
+              <div className="mt-5 ms-5 landing-table-container">
                 <div className="position-relative">
                   <div className="mobile-gaurd">
                     <LandingPaths />

web/src/utils/sample-table.ts

@@ -71,6 +71,14 @@ export const arraysToSampleList = (arraysList: any[][]) => {
   // first row is the header row
   let headerRow = arraysList[0];
 
+  // look for null values, simply populate with the column name
+  headerRow = headerRow.map((cell, index) => {
+    if (!cell) {
+      return `column_${index + 1}`;
+    }
+    return cell;
+  });
+
   if (headerRow.every((cell) => !cell)) {
     toast.error('Header row cannot be empty! Please add at least one column name.');
     return [];
@@ -80,9 +88,6 @@ export const arraysToSampleList = (arraysList: any[][]) => {
   const theRest = arraysList.slice(1);
   const sampleList: Sample[] = [];
 
-  // restrict header row to only contain non-null values
-  headerRow = headerRow.filter((key) => key !== null && key !== undefined);
-
   // if there's only a header row, return a list with one sample where all the property values are null
   if (arraysAreEmpty(theRest)) {
     const sample: Sample = {};