Return 204 when responding head request

nodes/VamdcSpeciesDB/README

@@ -2,48 +2,20 @@
 README
 ------
 
-The ExampleNode is intended as a starting point for setting up your own VAMDC node from 
-scratch. The node contains a basic setup and contains some mock data (in example_data) 
-to test the data import and setup tools on.
+The VAMDC Species Database node,
 
-More verbose information can be found in the online documentation.
-You can also build the documentation from the vamdc/doc/ directory.
+Data ingestion cron job script:
+python2 node/cronjob.py
 
 
-Basic steps for testing the examplenode 
-(assuming you have all dependencies): 
----------------------------------------
 
-1) Copy folder ExampleNode to a new name and do everything from that 
+Exporting the data into sqlite database:
+export_sqlite.sh in the VamdcSpeciesDB directory, using the helper scripts and export model in the export/ directory.
 
-2) Setup mysql database (the default used in the example)
+Once the export model is changed, please remove export/migrations contents and run
+    ./manage.py makemigrations export to recreate the exported data model.
 
-3) Configure Django
+The data is exported into speciesdb.sqlite
 
- $ cd <yournode>
- $ python manage.py
 
-Edit the created settings.py file to add all database details
 
-4) Edit mapping_examplenode.py so that all paths given match your actual path
-
-5) Run the database rewrite
-
- $ cd ../importtools
- $ python run_export.py ../node/<YourNode>/mapping_examplenode.py
-
-This will parse the raw data files in example_data and creates new 
-files *.in in node/<YourNode>. 
-
-6) Import preprocessed data into database 
-
- $ cd ../node/<YourNode> 
- $ mysql -d <YourDatabaseName> -u <YourDBusername> -p < load.sql
-
-The preprocessed data should be loaded into the database. 
-
-7) Startup web services
-
-Follow the online manual to start a webserver, then, depending
-on how you set it up, point a webbrowser to something like  
- http://YourURL/node/Yournode/tap/capabilities/ to test if things work.

nodes/VamdcSpeciesDB/django.wsgi

@@ -2,7 +2,7 @@ import os
 import sys
 
 # EDIT THE FOLLOWING TWO LINES
-sys.path.append('/var/cdms/v1_0/NodeSoftware/')
+sys.path.append('/home/doronin/space/doronin/VAMDC/python/NodeSoftware/')
 os.environ['DJANGO_SETTINGS_MODULE'] = 'nodes.VamdcSpeciesDB.settings'
 
 from django.core.wsgi import get_wsgi_application

nodes/VamdcSpeciesDB/manage.py

@@ -117,6 +117,10 @@
         print string
         sys.exit()
     # Run the django setup using our settings file.
-    from django.core.management import execute_manager
+    #from django.core.management import execute_manager
     #from xml.sax import saxutils
-    execute_manager(settings)
+    #execute_manager(settings)
+    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "settings")
+    from django.core.management import execute_from_command_line
+
+    execute_from_command_line(sys.argv)

nodes/VamdcSpeciesDB/node/InchiInfo.py

@@ -0,0 +1,21 @@
+from openbabel import OBConversion,OBMol
+
+
+class InchiInfo:
+
+    def __init__(self,inchi):
+        self.obconversion = OBConversion()
+        self.obconversion.SetInFormat("inchi")
+        self.obmol = OBMol()
+
+        self.obconversion.ReadString(self.obmol, inchi)
+
+        self.totalCharge = self.obmol.GetTotalCharge()
+        self.formula = self.obmol.GetFormula()
+        self.weight = self.obmol.GetMolWt( )
+
+    def getNumAtoms(self):
+        return self.obmol.NumAtoms()
+
+    def getAtoms(self,idx):
+        return self.GetAtom(idx)

nodes/VamdcSpeciesDB/node/admin.py

@@ -3,6 +3,56 @@
 #import your models here like this:
 #from DjNodeExample.node.models import *
 
+from models import *
+
+
 # add your models here to have them in the admin interface
 # for example if you have a model class called "Transition":
-#admin.site.register(Transition)
+
+class VamdcNodesAdmin(admin.ModelAdmin):
+    def make_active(modeladmin, request, queryset):
+      queryset.update(status=RecordStatus.ACTIVE)
+    make_active.short_description = "Activate selected nodes"
+
+
+    def make_disabled(modeladmin, request, queryset):
+      queryset.update(status=RecordStatus.DISABLED)
+    make_disabled.short_description = "Disable selected nodes"
+
+    list_display = ('short_name','status','contact_email','last_update_date')
+
+    actions = [make_active,make_disabled]
+
+
+class VamdcSpeciesAdmin(admin.ModelAdmin):
+  def make_verified(modeladmin, request, queryset):
+    queryset.update(status=RecordStatus.ACTIVE)
+  make_verified.short_description = "Mark as verified"
+
+  def make_disabled(modeladmin, request, queryset):
+    queryset.update(status=RecordStatus.DISABLED)
+  make_disabled.short_description = "Mark as hidden/disabled"
+
+
+  list_display = ('mass_number','stoichiometric_formula', 'structural_formula_all','charge','origin_member_database','status','species_foreign_ids')
+
+  actions = [make_verified,make_disabled]
+
+class VamdcSpeciesNamesAdmin(admin.ModelAdmin):
+  def make_verified(modeladmin, request, queryset):
+    queryset.update(status=RecordStatus.ACTIVE)
+  make_verified.short_description = "Mark as verified"
+
+  def make_disabled(modeladmin, request, queryset):
+    queryset.update(status=RecordStatus.DISABLED)
+  make_disabled.short_description = "Mark as hidden/disabled"
+
+
+  list_display = ('species','name','id', 'species','status')
+
+  actions = [make_verified,make_disabled]
+
+
+admin.site.register(VamdcNodes,VamdcNodesAdmin)
+admin.site.register(VamdcSpecies,VamdcSpeciesAdmin)
+#~ admin.site.register(VamdcSpeciesNames,VamdcSpeciesNamesAdmin)