working fasta_api, with proper error handling. #629

fasta_api/fasta_api/http_server.py

@@ -2,157 +2,220 @@
 import aiohttp_cors
 from aiohttp import web
 
+from fastapi import HTTPException, status
+
+
 async def http_index(request):
     return web.Response(text="Index")
 
+
 async def http_help(request):
-    test = request.match_info.get('test')
-    print(test)
     resources = [str(resource) for resource in request.app.router.resources()]
     return web.json_response(resources)
 
+
 async def http_fasta_range(request):
     seqid = request.match_info.get('seqid')
     start = request.match_info.get('start')
     end = request.match_info.get('end')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     range = handler.fasta_range(url, seqid, start, end)
+    if "error" in range:
+        return web.json_response(range, status=range["status"])
     return web.json_response(range)
 
+
 async def http_fasta_references(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     references = handler.fasta_references(url)
+    if "error" in references:
+        return web.json_response(references, status=references["status"])
     return web.json_response(references)
 
+
 async def http_fasta_lengths(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     lengths = handler.fasta_lengths(url)
+    if "error" in lengths:
+        return web.json_response(lengths, status=lengths["status"])
     return web.json_response(lengths)
 
+
 async def http_fasta_nreferences(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     nreferences = handler.fasta_nreferences(url)
+    if "error" in nreferences:
+        return web.json_response(nreferences, status=nreferences["status"])
     return web.json_response(nreferences)
 
+
 async def http_gff_references(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     references = handler.gff_references(url)
+    if "error" in references:
+        return web.json_response(references, status=references["status"])
     return web.json_response(references)
 
+
 async def http_gff_features(request):
     seqid = request.match_info.get('seqid')
     start = request.match_info.get('start')
     end = request.match_info.get('end')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     features = handler.gff_features(url, seqid, start, end)
+    if "error" in features:
+        return web.json_response(features, status=features["status"])
     return web.json_response(features)
 
+
 async def http_bed_features(request):
     seqid = request.match_info.get('seqid')
     start = request.match_info.get('start')
     end = request.match_info.get('end')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     features = handler.bed_features(url, seqid, start, end)
+    if "error" in features:
+        return web.json_response(features, status=features["status"])
     return web.json_response(features)
 
+
 async def http_vcf_contigs(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     contigs = handler.vcf_contigs(url)
+    if "error" in contigs:
+        return web.json_response(contigs, status=contigs["status"])
     return web.json_response(contigs)
 
+
 async def http_vcf_features(request):
     seqid = request.match_info.get('seqid')
     start = request.match_info.get('start')
     end = request.match_info.get('end')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     features = handler.vcf_features(url, seqid, start, end)
+    if "error" in features:
+        return web.json_response(features, status=features["status"])
     return web.json_response(features)
 
+
 async def http_alignment_references(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     references = handler.alignment_references(url)
+    if "error" in references:
+        return web.json_response(references, status=references["status"])
     return web.json_response(references)
 
+
 async def http_alignment_unmapped(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     unmapped = handler.alignment_unmapped(url)
+    if "error" in unmapped:
+        return web.json_response(unmapped, status=unmapped["status"])
     return web.json_response(unmapped)
 
+
 async def http_alignment_nreferences(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     nreferences = handler.alignment_nreferences(url)
+    if "error" in nreferences:
+        return web.json_response(nreferences, status=nreferences["status"])
     return web.json_response(nreferences)
 
+
 async def http_alignment_nocoordinate(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     nocoordinate = handler.alignment_nocoordinate(url)
+    if "error" in nocoordinate:
+        return web.json_response(nocoordinate, status=nocoordinate["status"])
     return web.json_response(nocoordinate)
 
+
 async def http_alignment_mapped(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     mapped = handler.alignment_mapped(url)
+    if "error" in mapped:
+        return web.json_response(mapped, status=mapped["status"])
     return web.json_response(mapped)
 
+
 async def http_alignment_lengths(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     lengths = handler.alignment_lengths(url)
+    if "error" in lengths:
+        return web.json_response(lengths, status=lengths["status"])
     return web.json_response(lengths)
 
+
 async def http_alignment_index_statistics(request):
     url = request.match_info.get('url')
     handler = request.app["handler"]
     statistics = handler.alignment_index_statistics(url)
+    if "error" in statistics:
+        return web.json_response(statistics, status=statistics["status"])
     return web.json_response(statistics)
 
+
 async def http_alignment_count(request):
     contig = request.match_info.get('contig')
     start = request.match_info.get('start')
     stop = request.match_info.get('stop')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     count = handler.alignment_count(url, contig, start, stop)
+    if "error" in count:
+        return web.json_response(count, status=count["status"])
     return web.json_response(count)
 
+
 async def http_alignment_count_coverage(request):
     contig = request.match_info.get('contig')
     start = request.match_info.get('start')
     stop = request.match_info.get('stop')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     coverage = handler.alignment_count_coverage(url, contig, start, stop)
+    if "error" in coverage:
+        return web.json_response(coverage, status=coverage["status"])
     return web.json_response(coverage)
 
+
 async def http_alignment_fetch(request):
     contig = request.match_info.get('contig')
     start = request.match_info.get('start')
     stop = request.match_info.get('stop')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     fetch = handler.alignment_fetch(url, contig, start, stop)
+    if "error" in fetch:
+        return web.json_response(fetch, status=fetch["status"])
     return web.json_response(fetch)
 
+
 async def http_alignment_reference_lengths(request):
     reference = request.match_info.get('reference')
     url = request.match_info.get('url')
     handler = request.app["handler"]
     lengths = handler.alignment_reference_lengths(url, reference)
+    if "error" in lengths:
+        return web.json_response(lengths, status=lengths["status"])
     return web.json_response(lengths)
 
+
 def run_http_server(host, port, handler):
     # make the app
     app = web.Application()
@@ -170,7 +233,7 @@ def run_http_server(host, port, handler):
     )
     route = app.router.add_get("/", http_index)
     cors.add(route)
-    route = app.router.add_get("/help/{test}", http_help)
+    route = app.router.add_get("/help", http_help)
     cors.add(route)
     route = app.router.add_get("/fasta/fetch/{seqid}:{start}-{end}/{url}", http_fasta_range)
     cors.add(route)