import pandas as pd
from functools import lru_cache
import collections
from ..stores import httpstore
from ..options import OPTIONS
[docs]
class ArgoNVSReferenceTables:
"""Argo Reference Tables
Utility function to retrieve Argo Reference Tables from a NVS server.
By default, this relies on: https://vocab.nerc.ac.uk/collection
Examples
--------
Methods:
>>> R = ArgoNVSReferenceTables()
>>> R.search('sensor')
>>> R.tbl(3)
>>> R.tbl('R09')
Properties:
>>> R.all_tbl_name
>>> R.all_tbl
>>> R.valid_ref
"""
valid_ref = [
"R01",
"R03",
"R04",
"R05",
"R06",
"R07",
"R08",
"R09",
"R10",
"R11",
"R12",
"R13",
"R15",
"R16",
"R18",
"R19",
"R20",
"R21",
"R22",
"R23",
"R24",
"R25",
"R26",
"R27",
"R28",
"R40",
"RD2",
"RMC",
"RP2",
"RR2",
"RTV",
]
"""List of all available Reference Tables"""
[docs]
def __init__(
self,
nvs="https://vocab.nerc.ac.uk/collection",
cache: bool = True,
cachedir: str = "",
):
"""Argo Reference Tables from NVS"""
cachedir = OPTIONS["cachedir"] if cachedir == "" else cachedir
self.fs = httpstore(cache=cache, cachedir=cachedir)
self.nvs = nvs
def _valid_ref(self, rtid):
if rtid not in self.valid_ref:
rtid = "R%0.2d" % rtid
if rtid not in self.valid_ref:
raise ValueError(
"Invalid Argo Reference Table, should be one in: %s"
% ", ".join(self.valid_ref)
)
return rtid
def _jsConcept2df(self, data):
"""Return all skos:Concept as class:`pandas.DataFrame`"""
content = {
"altLabel": [],
"prefLabel": [],
"definition": [],
"deprecated": [],
"id": [],
}
for k in data["@graph"]:
if k["@type"] == "skos:Collection":
Collection_name = k["dc:alternative"]
elif k["@type"] == "skos:Concept":
content["altLabel"].append(k["skos:altLabel"])
content["prefLabel"].append(k["skos:prefLabel"]["@value"])
content["definition"].append(k["skos:definition"]["@value"])
content["deprecated"].append(k["owl:deprecated"])
content["id"].append(k["@id"])
df = pd.DataFrame.from_dict(content)
df.name = Collection_name
return df
def _jsCollection(self, data):
"""Return last skos:Collection information as data"""
for k in data["@graph"]:
if k["@type"] == "skos:Collection":
name = k["dc:alternative"]
desc = k["dc:description"]
rtid = k["@id"]
return (name, desc, rtid)
def get_url(self, rtid, fmt="ld+json"):
"""Return URL toward a given reference table for a given format
Parameters
----------
rtid: {str, int}
Name or number of the reference table to retrieve. Eg: 'R01', 12
fmt: str, default: "ld+json"
Format of the NVS server response. Can be: "ld+json", "rdf+xml" or "text/turtle".
Returns
-------
str
"""
rtid = self._valid_ref(rtid)
if fmt == "ld+json":
fmt_ext = "?_profile=nvs&_mediatype=application/ld+json"
elif fmt == "rdf+xml":
fmt_ext = "?_profile=nvs&_mediatype=application/rdf+xml"
elif fmt == "text/turtle":
fmt_ext = "?_profile=nvs&_mediatype=text/turtle"
else:
raise ValueError(
"Invalid format. Must be in: 'ld+json', 'rdf+xml' or 'text/turtle'."
)
url = "{}/{}/current/{}".format
return url(self.nvs, rtid, fmt_ext)
[docs]
@lru_cache
def tbl(self, rtid):
"""Return an Argo Reference table
Parameters
----------
rtid: {str, int}
Name or number of the reference table to retrieve. Eg: 'R01', 12
Returns
-------
class:`pandas.DataFrame`
"""
rtid = self._valid_ref(rtid)
js = self.fs.open_json(self.get_url(rtid))
df = self._jsConcept2df(js)
return df
[docs]
def tbl_name(self, rtid):
"""Return name of an Argo Reference table
Parameters
----------
rtid: {str, int}
Name or number of the reference table to retrieve. Eg: 'R01', 12
Returns
-------
tuple('short name', 'description', 'NVS id link')
"""
rtid = self._valid_ref(rtid)
js = self.fs.open_json(self.get_url(rtid))
return self._jsCollection(js)
[docs]
def search(self, txt, where="all"):
"""Search for string in tables title and/or description
Parameters
----------
txt: str
where: str, default='all'
Where to search, can be: 'title', 'description', 'all'
Returns
-------
list of table id matching the search
"""
results = []
for tbl_id in self.all_tbl_name:
title = self.tbl_name(tbl_id)[0]
description = self.tbl_name(tbl_id)[1]
if where == "title":
if txt.lower() in title.lower():
results.append(tbl_id)
elif where == "description":
if txt.lower() in description.lower():
results.append(tbl_id)
elif where == "all":
if txt.lower() in description.lower() or txt.lower() in title.lower():
results.append(tbl_id)
return results
@property
def all_tbl(self):
"""Return all Argo Reference tables
Returns
-------
OrderedDict
Dictionary with all table short names as key and table content as class:`pandas.DataFrame`
"""
URLs = [self.get_url(rtid) for rtid in self.valid_ref]
df_list = self.fs.open_mfjson(URLs, preprocess=self._jsConcept2df)
all_tables = {}
[all_tables.update({t.name: t}) for t in df_list]
all_tables = collections.OrderedDict(sorted(all_tables.items()))
return all_tables
@property
def all_tbl_name(self):
"""Return names of all Argo Reference tables
Returns
-------
OrderedDict
Dictionary with all table short names as key and table names as tuple('short name', 'description', 'NVS id link')
"""
URLs = [self.get_url(rtid) for rtid in self.valid_ref]
name_list = self.fs.open_mfjson(URLs, preprocess=self._jsCollection)
all_tables = {}
[
all_tables.update({rtid.split("/")[-3]: (name, desc, rtid)})
for name, desc, rtid in name_list
]
all_tables = collections.OrderedDict(sorted(all_tables.items()))
return all_tables
