diff --git a/examples/Apollo12_soils.py b/examples/Apollo12_soils.py
index ddc0da45e2ffc78b5197c4536d07ed2d6b445fa6..e7c2faa4b321b6298d521b1576452c77dd770262 100644
--- a/examples/Apollo12_soils.py
+++ b/examples/Apollo12_soils.py
@@ -1,6 +1,6 @@
-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]))
diff --git a/examples/example1.ipynb b/examples/example1.ipynb
index d3c69faa90b890b6d56353c01e573754efa92c53..c30e54f3037c45ee7ad73ef29d3a5e0d16ce5084 100644
--- a/examples/example1.ipynb
+++ b/examples/example1.ipynb
@@ -1,111 +1,246 @@
{
"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": [
- "f = moondb.Filter()\n",
- "#f.specimenType = [\"SOIL\"]\n",
- "results = f.get_results()"
+ "# 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": 34,
+ "execution_count": 106,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "MoonDB holds 2991 specimens from Apollo 17.\n"
+ ]
+ }
+ ],
+ "source": [
+ "# 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": 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,
diff --git a/examples/specimen.py b/examples/specimen.py
old mode 100644
new mode 100755
index 9aa96f178909c774e869a0cf297ad437b2b958a6..d295d5f3d65dd1710c408f31b650666c8cef8618
--- a/examples/specimen.py
+++ b/examples/specimen.py
@@ -1,4 +1,22 @@
+#!/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))
+
+
diff --git a/examples/specimens_weight.py b/examples/total_specimens_weight.py
similarity index 55%
rename from examples/specimens_weight.py
rename to examples/total_specimens_weight.py
index 7e446da5f975cf3b402dbaa7856b183353bbdac8..8acd8140eb16acd2fc43bce4f51dc84052f9db0b 100644
--- a/examples/specimens_weight.py
+++ b/examples/total_specimens_weight.py
@@ -1,3 +1,5 @@
+#!/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()
+print("\nMoonDB contains a total of {:.3f} kg of specimen from the Moon!".format(weight_cum/1000.0))
-for r in results:
- for dr in r.dataResults:
- print(dr)
- #print(dr.laboratory,dr.variable,dr.value,dr.unit)
-
diff --git a/moondb/__pycache__/__init__.cpython-37.pyc b/moondb/__pycache__/__init__.cpython-37.pyc
index 4ec4ae538fe0135d4b4557ef750fe953cfffc882..adf878aed3b8987b69e4ea9b800bebce4a87163d 100644
Binary files a/moondb/__pycache__/__init__.cpython-37.pyc and b/moondb/__pycache__/__init__.cpython-37.pyc differ
diff --git a/moondb/__pycache__/core.cpython-37.pyc b/moondb/__pycache__/core.cpython-37.pyc
index 563654845ade61e7230a3d4fbc4a3b2f8ef6331a..96bb62901a8a7c6de0f215953d4f30ea33a80d2e 100644
Binary files a/moondb/__pycache__/core.cpython-37.pyc and b/moondb/__pycache__/core.cpython-37.pyc differ
diff --git a/moondb/__pycache__/helpers.cpython-37.pyc b/moondb/__pycache__/helpers.cpython-37.pyc
index c7e04cde9e47a478e03dff61959bf3d407710eb1..9c6fa48130fde75483ad9a95d797f6f6d62d5f4d 100644
Binary files a/moondb/__pycache__/helpers.cpython-37.pyc and b/moondb/__pycache__/helpers.cpython-37.pyc differ
diff --git a/moondb/core.py b/moondb/core.py
index 8083d633199e598b4911a488202d3fd74f2e06c8..9272b71362ffb5519adf2d60bb9e8e4eb931588f 100644
--- a/moondb/core.py
+++ b/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)