From 0a9da36bf4f2d6b2892131e40f1c55a89d003537 Mon Sep 17 00:00:00 2001
From: Alessandro Frigeri <alessandro.frigeri@inaf.it>
Date: Fri, 3 May 2019 14:15:22 +0200
Subject: [PATCH] Updated the classes with dataclass
---
moondb/__pycache__/__init__.cpython-37.pyc | Bin 176 -> 0 bytes
moondb/__pycache__/core.cpython-37.pyc | Bin 6333 -> 0 bytes
moondb/__pycache__/helpers.cpython-37.pyc | Bin 3628 -> 0 bytes
moondb/core.py | 230 ++++++++++++++++++---
moondb/helpers.py | 122 +----------
5 files changed, 200 insertions(+), 152 deletions(-)
delete mode 100644 moondb/__pycache__/__init__.cpython-37.pyc
delete mode 100644 moondb/__pycache__/core.cpython-37.pyc
delete mode 100644 moondb/__pycache__/helpers.cpython-37.pyc
diff --git a/moondb/__pycache__/__init__.cpython-37.pyc b/moondb/__pycache__/__init__.cpython-37.pyc
deleted file mode 100644
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diff --git a/moondb/__pycache__/core.cpython-37.pyc b/moondb/__pycache__/core.cpython-37.pyc
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diff --git a/moondb/core.py b/moondb/core.py
index a5a5a83..edc6285 100644
--- a/moondb/core.py
+++ b/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):
@@ -115,13 +127,16 @@ 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):
return namedtuple('X', d.keys())(*d.values())
@@ -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"]
diff --git a/moondb/helpers.py b/moondb/helpers.py
index ea3a2d8..68efea4 100644
--- a/moondb/helpers.py
+++ b/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)
+from .core import *
- if ln:
- for n in ln:
- count,spec = _get_resp('/specimenlist/mission/'+n)
- sp_list.extend(spec)
+from collections import namedtuple
+import requests
- 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 collections import namedtuple
-
- 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
--
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