Updated the classes with dataclass

moondb/core.py

@@ -5,46 +5,53 @@
 # MoonDB Python module
 # https://realpython.com/api-integration-in-python/
 
-import requests
+import sys
 import json 
 import urllib.parse
 import urllib3,socket
 import logging
-
+from dataclasses import dataclass
 from collections import namedtuple
 
+import requests
+#import attr
+
 class Mission:
    def __init__(self,name):
       self.name = name
    def __str__(self):
       return self.name
 
+@dataclass
 class Landmark:
-   def __init__(self,name):
-      self.name = name
+   """The Landmark class"""
+   name: str
+   GPNFID: int
+   GPNFURL: str
+   latitude: float
+   longitude: float
 
+   def asWkt(self):
+      point = "POINT ({} {})"
+      return point.format(self.longitude,self.latitude)
+
+@dataclass
 class Specimen:
-   def __init__(self):
-       self.specimenCode = ""
-       self.specimenName = ""
-       self.parentSpecimen = ""
-       self.childSpecimens = ""
-       self.specimenType = ""
-       self.samplingTechnique = ""
-       self.mission = ""
-       self.landmark = ""
-       self.lunarStation = ""
-       self.returnContainer = ""
-       self.weight = ""
-       self.pristinity = ""
-       self.pristinityDate = ""
-       self.description = ""
-   def say_hello(self):
-      print('Hello Moon!')
-   def __str__(self):
-      return self.specimenName
-   def __repr__(self):
-      return self.specimenName
+   specimenCode: str
+   specimenName: str
+   parentSpecimen: str
+   childSpecimens: list
+   specimenType: str
+   samplingTechnique: str
+   mission: str
+   landmark: str
+   lunarStation: str
+   returnContainer: str
+   weight: str
+   pristinity: str
+   pristinityDate: str
+   description: str
+
 
 class SpecimenType:
    def __init__(self,name):
@@ -92,9 +99,14 @@ class AnalyisMethod:
    def __init__(self,name):
       self.name = name
 
+class Analysis:
+   __slots__ = ('analysisCode','analyzedMaterial','comment','dataset','citation','dataResults')
+
+class DataResult:
+   __slots__ = ('unit', 'laboratory', 'variable', 'methodName', 'methodComment', 'value', 'methodCode')
 
 def _url(path):
-   print(urllib.parse.quote(path))
+   #print(urllib.parse.quote(path))
    return "http://api.moondb.org" + urllib.parse.quote(path)
 
 def _check_resp(resp):
@@ -115,12 +127,15 @@ def _get_resp(path):
       sys.exit(0)
    _check_resp(resp)
    r = resp.json()
+   #print(r)
    # To be checked with Peng
-   count = r['count']
-   if 'results' in r:
-      return count,r['results']
-   if 'result' in r:
-      return count,r['result']
+   if 'result' and 'count' in r:
+      return r['count'],r['result']
+   if 'results' and 'count' in r:
+      return r['count'],r['results']
+   else:
+      return r
+
 
 
 def _json_object_hook(d): 
@@ -130,9 +145,158 @@ def json2obj(data):
    return json.loads(data, object_hook=_json_object_hook)
 
 
+def get_specimens(sc=None,mn=None,ln=None,sty=None,ste=None):
+   '''
+   Returns the specimen by specifying:
+   
+   Parameters
+   ----------
+   sc: list 
+       list of specimen codes
+   mn: list
+       list of mission names
+   ln: list
+       list of landmark names
+   sty: list
+       list of specimen types
+   ste: list
+       list of sampling techniques
+   '''
+   sp_list = []
+   if sc:
+      for s in sc: 
+         spec = _get_resp('/specimen/'+s) 
+         sp_list.append(spec)
+   if mn:
+      for n in mn:
+         spec = _get_resp('/specimenlist/mission/'+n) 
+         sp_list.append(spec)
+
+   if ln:
+      for n in ln:
+         spec = _get_resp('/specimenlist/mission/'+n) 
+         sp_list.append(spec)
+
+   if sty:
+      for st in sty:
+         spec = _get_resp('/specimenlist/mission/'+st) 
+         sp_list.append(spec)
+
+   if ste:
+      for st in ste:
+         spec = _get_resp('/specimenlist/mission/'+st) 
+         sp_list.append(spec)
+
+   sp_obj_list = []
+
+   for s in sp_list:
+      # dict unpack
+      s_o = Specimen(**s)
+      sp_obj_list.append(s_o)
+
+   return sp_obj_list
+
+
+def get_missions():
+   missions = []
+   resp = requests.get(_url('/authorities/missions/'))
+   _check_resp(resp)
+   for m_item in resp.json()['results']:
+      missions.append( Mission(m_item['name'] ))
+   return missions
+
+## Controlled Vocabularies
+
+def get_specimentypes():
+   st_list = []
+   count,st = _get_resp('/cv/specimentypes') 
+   for s in st:
+      stobj = SpecimenType(s['name'])
+      st_list.append(stobj)
+   return st_list
+
+def get_samplingtechniques():
+   st_list = []
+   count,st = _get_resp('/cv/samplingtechniques') 
+   for s in st:
+      stobj = SamplingTechnique(s['name'])
+      st_list.append(stobj)
+   return st_list
+
+def get_analyzedmaterials():
+   st_list = []
+   count,st = _get_resp('/cv/analyzedmaterials') 
+   for s in st:
+      stobj = AnalyzedMaterial(s['name'])
+      st_list.append(stobj)
+   return st_list
+
+def get_analytes():
+   analytes = []
+   count,an = _get_resp('/cv/analyzedmaterials') 
+   for a in an:
+      analytes.append( Analyte(m_item['name'] ))
+   return analytes
+
+def get_analysismethods():
+   am_list = []
+   count,am = _get_resp('/cv/analysismethods') 
+   for a in am:
+      aobj = AnalysisMethod(s['name'])
+      am_list.append(aobj)
+   return am_list
+
+def get_landmarks():
+   lm_list = []
+   count,lmlist = _get_resp('/authorities/landmarks') 
+   for l in lmlist:
+      lobj = Landmark(**l)
+      lm_list.append(lobj)
+   return lm_list
+
+def get_landmark( landmark_name ):
+   lms = get_landmarks()
+   for l in lms:
+      if l.name == landmark_name:
+         return l
+   return None
+
+def get_samplingtechnique():
+   pass
+
+
+
+class AnalysisFilter:
+   def __init__(self):
+      self.mission = []
+      self.landmark = []
+      self.specimenType = []
+      self.samplingTechnique = []
+      self.analyzedMaterial = []
+      self.analyte = []
+      self.analysisMethod = []
+   def _toJSON(self):
+      return json.dumps(self, default=lambda o: o.__dict__,sort_keys=True,separators=(",", ":"))
+
+   def get_results(self):
+      resp = requests.get(_url('/data/'+self._toJSON() ))
+      res_list = []
+      
+      for r in resp.json()['results']:
+         rd = dict(r)
+         analysis = namedtuple("Analysis", rd.keys())(*rd.values())
+         data_res_list = []
+         for r in analysis.dataResults:
+            data_res = namedtuple("dataResult", r.keys())(*r.values())
+            data_res_list.append(data_res)
+         analysis = analysis._replace(dataResults = data_res_list )
+         res_list.append(analysis) 
+      return res_list
+
+
 if __name__ == "__main__":
    m = get_missions()
-   f = Filter()
+   f = AnalysisFilter()
    f.specimenType = ["SOIL"]
    f.analyte = ["H2O","Ti"]
    f.mission = ["Apollo 11"]

moondb/helpers.py

@@ -4,125 +4,9 @@
 # 
 # MoonDB Python module
 
-def get_specimen(sc=None,mn=None,ln=None,sty=None,ste=None):
-   '''
-   Get specimen by:
-   - specimen code - sc
-   - mission name - mn
-   - landmark name - ln
-   - speciment type - sty
-   - sampling technique - ste
-   '''
-   sp_list = []
-   if sc:
-      for s in sc: 
-         count,spec = _get_resp('/specimen/'+s) 
-         sp_list.extend(spec)
-   if mn:
-      for n in mn:
-         count,spec = _get_resp('/specimenlist/mission/'+n) 
-         sp_list.extend(spec)
-
-   if ln:
-      for n in ln:
-         count,spec = _get_resp('/specimenlist/mission/'+n) 
-         sp_list.extend(spec)
-
-   if sty:
-      for st in sty:
-         count,spec = _get_resp('/specimenlist/mission/'+st) 
-         sp_list.extend(spec)
-
-   if ste:
-      for st in ste:
-         count,spec = _get_resp('/specimenlist/mission/'+st) 
-         sp_list.extend(spec)
+from .core import *
 
 from collections import namedtuple
+import requests
 
-   sp_obj_list = []
-
-   for s in sp_list:
-      s_obj = namedtuple("Specimen", s.keys())(*s.values())
-      sp_obj_list.append(s_obj)
-
-   return sp_obj_list
-
-
-def get_missions():
-   missions = []
-   resp = requests.get(_url('/authorities/missions/'))
-   _check_resp(resp)
-   for m_item in resp.json()['results']:
-      missions.append( Mission(m_item['name'] ))
-   return missions
-
-## Controlled Vocabularies
-
-def get_specimentypes():
-   st_list = []
-   count,st = _get_resp('/cv/specimentypes') 
-   for s in st:
-      stobj = SpecimenType(s['name'])
-      st_list.append(stobj)
-   return st_list
-
-def get_samplingtechniques():
-   st_list = []
-   count,st = _get_resp('/cv/samplingtechniques') 
-   for s in st:
-      stobj = SamplingTechnique(s['name'])
-      st_list.append(stobj)
-   return st_list
-
-def get_analyzedmaterials():
-   st_list = []
-   count,st = _get_resp('/cv/analyzedmaterials') 
-   for s in st:
-      stobj = AnalyzedMaterial(s['name'])
-      st_list.append(stobj)
-   return st_list
-
-def get_analytes():
-   analytes = []
-   count,an = _get_resp('/cv/analyzedmaterials') 
-   for a in an:
-      analytes.append( Analyte(m_item['name'] ))
-   return analytes
-
-def get_analysismethods():
-   am_list = []
-   count,am = _get_resp('/cv/analysismethods') 
-   for a in am:
-      aobj = AnalysisMethod(s['name'])
-      am_list.append(aobj)
-   return am_list
-
-def get_landmark():
-   pass
-
-def get_samplingtechnique():
-   pass
-
-
-
-class Filter:
-   def __init__(self):
-      self.mission = []
-      self.landmark = []
-      self.specimenType = []
-      self.samplingTechnique = []
-      self.analyzedMaterial = []
-      self.analyte = []
-      self.analysisMethod = []
-   def _toJSON(self):
-      return json.dumps(self, default=lambda o: o.__dict__,sort_keys=True,separators=(",", ":"))
-
-   def get_results(self):
-      resp = requests.get(_url('/data/'+self._toJSON() ))
-      res_list = []
 
-      for r in resp.json()['results']:
-         rd = dict(r)
-         res_list.append(rd) 
-      return res_list