updated examples

examples/Apollo12_soils.py

-import moondb,sys
-
+#!/usr/bin/env python3
 
+import moondb,sys
 
 # Let's setup the data filter
 f = moondb.AnalysisFilter()
@@ -11,8 +11,10 @@ f.specimenType = ["SOIL"]
 results = f.get_results()
 
 for r in results:
+   print('\nDataset: ',r.dataset) 
+   print('Lab,Specie,value')
    for dr in r.dataResults:
-      print(dr.laboratory,dr.variable,dr.value,dr.unit)
+      print(",".join([dr.laboratory,dr.variable,dr.value+dr.unit]))
       
 
 

examples/example1.ipynb

 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 9,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "import moondb"
+    "## MoonDB Jupyter notebook workbook\n",
+    "#### Alessandro Frigeri, IAPS/INAF, Rome Italy\n",
+    "\n",
+    "\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 104,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'name': 'Apollo 11'}\n",
-      "{'name': 'Apollo 12'}\n",
-      "{'name': 'Apollo 14'}\n",
-      "{'name': 'Apollo 15'}\n",
-      "{'name': 'Apollo 16'}\n",
-      "{'name': 'Apollo 17'}\n",
-      "{'name': 'Luna 16'}\n",
-      "{'name': 'Luna 20'}\n",
-      "{'name': 'Luna 24'}\n"
+      "The autoreload extension is already loaded. To reload it, use:\n",
+      "  %reload_ext autoreload\n",
+      "/home/alf/gitwrk/pymoondb/moondb/__init__.py\n"
      ]
     }
    ],
    "source": [
-    "m = moondb.get_missions()"
+    "# First we import the moondb module\n",
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "\n",
+    "%aimport moondb\n",
+    "\n",
+    "print(moondb.__file__)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 105,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['Apollo 11',\n",
+       " 'Apollo 12',\n",
+       " 'Apollo 14',\n",
+       " 'Apollo 15',\n",
+       " 'Apollo 16',\n",
+       " 'Apollo 17',\n",
+       " 'Luna 16',\n",
+       " 'Luna 20',\n",
+       " 'Luna 24']"
+      ]
+     },
+     "execution_count": 105,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Let's get a list of the missions in MoonDB\n",
+    "\n",
+    "mlist = moondb.get_missions()\n",
+    "\n",
+    "[m.name for m in mlist]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 106,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "MoonDB holds 2991 specimens from  Apollo 17.\n"
+     ]
+    }
+   ],
    "source": [
-    "f = moondb.Filter()\n",
-    "#f.specimenType = [\"SOIL\"]\n",
-    "results = f.get_results()"
+    "# Now, we want to know how many specimens are available from the Apollo 17 missions\n",
+    "\n",
+    "f = moondb.SpecimenFilter()\n",
+    "mission = 'Apollo 17'\n",
+    "f.missionName = [ mission ]\n",
+    "results = f.get_results()\n",
+    "specimen_list = [r for r in results]\n",
+    "\n",
+    "print(\"MoonDB holds {} specimens from  Apollo 17.\".format(len(specimen_list)))"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 79,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "37034"
+       "['COMPOSITE',\n",
+       " 'ROCK',\n",
+       " 'ROCK/Basalt/Ilmenite Basalt',\n",
+       " 'ROCK/Basalt/Unclassified Basalt',\n",
+       " 'ROCK/Breccia/Fragmental Breccia',\n",
+       " 'ROCK/Breccia/Impact Melt Breccia',\n",
+       " 'ROCK/Breccia/Regolith Breccia',\n",
+       " 'ROCK/Breccia/Unclassified Breccia',\n",
+       " 'ROCK/Crustal/Crustal:Cataclasite',\n",
+       " 'ROCK/Crustal/Crustal:Norite',\n",
+       " 'ROCK/Crustal/Crustal:Troctolite',\n",
+       " 'SOIL/Soil:1-2mm',\n",
+       " 'SOIL/Soil:2-4mm',\n",
+       " 'SOIL/Soil:4-10mm',\n",
+       " 'SOIL/Soil:<1mm',\n",
+       " 'SOIL/Soil:Unsieved',\n",
+       " 'Unknown']"
       ]
      },
-     "execution_count": 34,
+     "execution_count": 79,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "len(results)"
+    "# Get a list of type of specimen of Apollo 17 available in MoonDB\n",
+    "s_list = [s.specimenType for s in specimen_list]\n",
+    "list(sorted(set(s_list)))"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 108,
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'analysisCode': '15100,3#3#0158', 'analyzedMaterial': 'WHOLE ROCK', 'comment': '0.97 g, 950C', 'dataset': 'IRVING, 1972#TABLE 1', 'citation': 'IRVING, 1972', 'dataResults': [{'unit': 'ppm', 'laboratory': 'UNKNOWN', 'variable': 'H', 'methodName': 'UNKNOWN', 'methodComment': 'COMBUSTION (NEW LINE, YIELDING LOW BLANKS)', 'value': '90.0', 'methodCode': 'UNKNOWN'}, {'unit': 'per mil', 'laboratory': 'UNKNOWN', 'variable': 'DELTA_D', 'methodName': 'UNKNOWN', 'methodComment': 'COMBUSTION (NEW LINE, YIELDING LOW BLANKS)', 'value': '-554.0', 'methodCode': 'UNKNOWN'}, {'unit': 'ppm', 'laboratory': 'UNKNOWN', 'variable': 'C', 'methodName': 'UNKNOWN', 'methodComment': 'COMBUSTION (NEW LINE, YIELDING LOW BLANKS)', 'value': '99.0', 'methodCode': 'UNKNOWN'}, {'unit': 'per mil', 'laboratory': 'UNKNOWN', 'variable': 'DELTA_C13', 'methodName': 'UNKNOWN', 'methodComment': 'COMBUSTION (NEW LINE, YIELDING LOW BLANKS)', 'value': '7.9', 'methodCode': 'UNKNOWN'}]}\n"
+      "2991\n"
      ]
     }
    ],
    "source": [
-    "an = print(results[0])"
+    "#\n",
+    "# Let's see the analyses done on the first specimen\n",
+    "#\n",
+    "\n",
+    "s_list = [s for s in specimen_list]\n",
+    "\n",
+    "print(len(s_list))\n",
+    "\n",
+    "s0 = s_list[0]\n",
+    "\n",
+    "an_list = [a for a in s0.get_analyses()]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 109,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (code MC-ICP-MS), result of CACULATED (code CALC)]\n"
+     ]
+    }
+   ],
+   "source": [
+    "# now we check the results of the first analysis\n",
+    "\n",
+    "#result_of\n",
+    "\n",
+    "print(an_list[0].dataResultsObj)"
+   ]
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
-   "metadata": {},
+   "execution_count": 103,
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "None\n"
+      "Apollo 17 specimen:  76535,16\n",
+      "Result: Os 8.5 ppb (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Ir 55.0 ppb (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Ru 81.0 ppb (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Pt 54.0 ppb (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Pd 89.0 ppb (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Re 9.0 ppb (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Re187_Os188 5.1 Not Applicable (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: Os187_Os188 0.1511 Not Applicable (MULTICOLLECTOR INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY)\n",
+      "Result: G_Os(T) -348.0 Not Applicable (CACULATED)\n"
      ]
     }
    ],
    "source": [
-    "print(anaobj)"
+    "\n",
+    "\n",
+    "\n",
+    "print(mission+\" specimen: \",s0.specimenName)\n",
+    "for r in an_list[0].dataResultsObj:\n",
+    "   print('Result: {} {} {} ({})'.format(r.variable,r.value,r.unit,r.methodName))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -130,7 +265,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

examples/specimen.py

+#!/usr/bin/env python3
+
 import moondb
 
 s_12023 = moondb.get_specimens(sc=['12023'])[0]
 
+#print(s_12023)
+
+child = moondb.get_specimens(sc=['12023,114'])[0]
+
+#print(' A N A L Y S E S ')
+a = child.get_analyses()
+
+
+print(a[0])
+
+a0_results = a[0].dataResultsObj
+
+
+print('Result: {} {} {}'.format(a0_results[0].variable,a0_results[0].value,a0_results[0].unit,a0_results[0].methodName))
+
+

examples/specimens_weight.py → examples/total_specimens_weight.py

+#!/usr/bin/env python3
+
 import moondb,sys
 
 
@@ -16,22 +18,7 @@ for m in moon_missions:
    weight_cum += weight
    print("MoonDB holds {:.3f} kg of specimens from {}".format(weight/1000.0,m.name))
 
-print("MoonDB contains a total of {:.3f} kg of specimen from the Moon!".format(weight_cum/1000.0))
-
-
-f = moondb.AnalysisFilter()
-f.mission = ["Apollo 11"]
-f.analyte = ["Na2O","CaO"]
-f.specimenType = ["SOIL"]
-
-
-
-results = f.get_results()
-
-for r in results:
-   for dr in r.dataResults:
-      print(dr)
-      #print(dr.laboratory,dr.variable,dr.value,dr.unit)
+print("\nMoonDB contains a total of {:.3f} kg of specimen from the Moon!".format(weight_cum/1000.0))
 
 
 

moondb/core.py

@@ -2,17 +2,19 @@
 # 
 # (c) 2019 Alessandro Frigeri, Istituto Nazionale di Astrofisica
 # 
-# MoonDB Python module
-# https://realpython.com/api-integration-in-python/
+# pymoondb: MoonDB Python module
+
 
 import sys
 import json 
 import urllib.parse
 import urllib3,socket
 import logging
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from collections import namedtuple
 
+#from dataclasses import dataclass, field
+
 import requests
 #import attr
 
@@ -35,6 +37,35 @@ class Landmark:
       point = "POINT ({} {})"
       return point.format(self.longitude,self.latitude)
 
+@dataclass
+class Result:
+   unit: str
+   laboratory: str
+   variable: str
+   methodName: str
+   methodComment:str 
+   value: str 
+   methodCode: str
+
+   def __repr__(self):
+      return "result of "+self.methodName+" (code "+self.methodCode+")"
+
+@dataclass
+class Analysis:
+   analysisCode: str
+   analyzedMaterial: str
+   comment: str
+   dataset: str
+   citation: str
+   dataResults: list = field(default_factory=list)
+   dataResultsObj: list = field(default_factory=list)
+
+   def __repr__(self):
+      return "Analysis:"+self.analysisCode+" on "+self.analyzedMaterial+" material"
+
+   def __str__(self):
+      return self.analysisCode+" on "+self.analyzedMaterial
+
 @dataclass
 class Specimen:
    specimenCode: str
@@ -52,6 +83,28 @@ class Specimen:
    pristinityDate: str
    description: str
 
+   def get_analyses(self):
+      an_obj_list = []
+      n,an_list = _get_resp('/data/specimen/'+self.specimenCode) 
+      for a in an_list:
+         r_o_list = []
+         for r in a['dataResults']:
+            r_o = Result(**r)
+            r_o_list.append(r_o)
+            #print(r_o)
+            a['dataResultsObj'] = r_o_list
+         an_o = Analysis(**a)
+         an_obj_list.append(an_o) 
+      return an_obj_list
+
+
+
+
+
+
+@dataclass
+class People:
+   name: str
 
 class SpecimenType:
    def __init__(self,name):
@@ -99,8 +152,8 @@ class AnalyisMethod:
    def __init__(self,name):
       self.name = name
 
-class Analysis:
-   __slots__ = ('analysisCode','analyzedMaterial','comment','dataset','citation','dataResults')
+#class Analysis:
+#   __slots__ = ('analysisCode','analyzedMaterial','comment','dataset','citation','dataResults')
 
 class DataResult:
    __slots__ = ('unit', 'laboratory', 'variable', 'methodName', 'methodComment', 'value', 'methodCode')
@@ -199,7 +252,6 @@ def get_specimens(sc=None,mn=None,ln=None,sty=None,ste=None):
 
    for s in sp_list:
       # dict unpack
-      # print(s)
       s_o = Specimen(**s)
       sp_obj_list.append(s_o)