ids forwarding service

bin/ids.py

@@ -0,0 +1,70 @@
+#!/usr/local/bin/python3
+
+import cgi, cgitb
+import re, json
+import sys, os
+from urllib.parse import urlparse
+
+# local
+dir_path = os.path.dirname(os.path.abspath(__file__))
+sys.path.append(os.path.join(os.path.abspath(dir_path), '..'))
+from bycon.read_specs import *
+
+"""podmd
+The `ids` service forwards compatible, prefixed ids (see `config/ids.yaml`) to specific
+website endpoints. There is no check if the id exists; this is left to the web
+page handling itself.
+
+Stacking with the "pgx:" prefix is allowed.
+
+* <https://progenetix.org/services/ids/NCIT:C3262>
+podmd"""
+
+################################################################################
+################################################################################
+################################################################################
+
+def main():
+
+    ids("ids")
+
+################################################################################
+
+def ids(service):
+
+    # config = read_bycon_config( os.path.abspath( dir_path ) )
+    these_prefs = read_named_prefs( service, dir_path )
+
+    url_comps = urlparse( environ.get('REQUEST_URI') )
+    p_items = re.split(r'\/|\&', url_comps.path)
+    i = 0
+    id_in = ""
+
+    for p in p_items:
+        i += 1
+        if len(p_items) > i:
+            if p == "ids":
+                id_in = p_items[ i ]
+                break
+
+    for f_p in these_prefs["format_patterns"]:
+        pat = re.compile( f_p["pattern"] )
+        link = f_p["link"]
+        if pat.match(id_in):
+            lid = pat.match(id_in).group(2)
+            print("Status: 302")
+            print("Location: {}{}".format(link, lid))
+            print()
+            exit()
+
+    print('Content-Type: text')
+    print('status:422')
+    print()
+    print("No correct id provided. Please refer to the documentation at http://info.progenetix.org/tags/services/")
+    exit()
+
+################################################################################
+################################################################################
+
+if __name__ == '__main__':
+    main()

bin/services.py

@@ -17,6 +17,7 @@
 from bin.deliveries import deliveries
 from bin.genespans import genespans
 from bin.geolocations import geolocations
+from bin.ids import ids
 from bin.ontologymaps import ontologymaps
 from bin.phenopackets import phenopackets
 from bin.publications import publications
@@ -44,11 +45,12 @@
 def main():
     services = {
         "biosamples": biosamples,
+        "byconplus": byconplus,
         "cytomapper": cytomapper,
         "dbstats": dbstats,
         "deliveries": deliveries,
         "geolocations": geolocations,
-        "byconplus": byconplus,
+        "ids": ids,
         "publications": publications,
         "genespans": genespans,
         "ontologymaps": ontologymaps,
@@ -75,13 +77,7 @@ def main():
                     f = p_items[ i ]
                     # TODO: dynamic loader, then call
                     services[f](f)
-
-    _return_error()
-
-################################################################################
-################################################################################
-
-def _return_error():
+                    exit()
 
     print('Content-Type: text')
     print('status:422')

config/ids.yaml

@@ -0,0 +1,11 @@
+format_patterns:
+  - pattern: '^(pgx\:)?(pgxbs\-[\w\-\.]{4,128})$'
+    link: '/samples/details?datasetIds=progenetix&id='
+  - pattern: '^(pgx\:)?(NCIT(\:C[\d]{4,8})?)$'
+    link: '/subsets/list?datasetIds=progenetix&filters='
+  - pattern: '^(pgx\:)?(icdom(\-[\d]{5})?)$'
+    link: '/subsets/list?datasetIds=progenetix&filters='
+  - pattern: '^(pgx\:)?(icdot(\-C\d\d?\.\d)?)$'
+    link: '/subsets/list?datasetIds=progenetix&filters='
+  - pattern: ^(pgx\:)?(PMID\:\d{5,10})$'
+    link: '/publications/details?id='