def samples():
email = session.get('email', None)
api_key = session.get('api_key', None)
api = MetpetAPI(email, api_key).api
filters = ast.literal_eval(json.dumps(request.args))
offset = request.args.get('offset', 0)
filters['offset'] = offset
data = api.sample.get(params=filters)
next, previous, last, total_count = paginate_model('samples', data, filters)
samples = data.data['objects']
for sample in samples:
if 'minerals' in samples:
mineral_names = [mineral['name'] for mineral in sample['minerals']]
sample['mineral_list'] = (', ').join(mineral_names)
first_page_filters = filters
del first_page_filters['offset']
if filters:
first_page_url = url_for('samples') + '?' + urlencode(first_page_filters)
else:
first_page_url = url_for('samples') + urlencode(first_page_filters)
return render_template('samples.html',
samples=samples,
next_url=next,
prev_url=previous,
total=total_count,
first_page=first_page_url,
last_page=last)
def chemical_analyses():
email = session.get('email', None)
api_key = session.get('api_key', None)
api = MetpetAPI(email, api_key).api
filters = ast.literal_eval(json.dumps(request.args))
offset = request.args.get('offset', 0)
filters['offset'] = offset
data = api.chemical_analysis.get(params=filters)
next, previous, last, total_count = paginate_model('chemical_analyses',
data, filters)
chemical_analyses = data.data['objects']
first_page_filters = filters
del first_page_filters['offset']
if filters:
first_page_url = url_for('chemical_analyses') + '?' + urlencode(first_page_filters)
else:
first_page_url = url_for('chemical_analyses') + urlencode(first_page_filters)
return render_template('chemical_analyses.html',
chemical_analyses=chemical_analyses,
next_url=next,
prev_url=previous,
total=total_count,
first_page=first_page_url,
last_page=last)
def chemical_analyses():
api = drest.API(baseurl=env('API_DRF_HOST'))
next = previous = last = total_count = None
filters = literal_eval(json.dumps(request.args))
filters['format'] = 'json'
chemicals = api.make_request('GET', '/chemical_analyses/',
params=filters).data
chem_results = chemicals['results']
next, previous, last, total_count = paginate_model('chemical-analyses',
chemicals, filters)
for c in chem_results:
c['sample'] = api.make_request('GET',
'/samples/' + c['subsample']['sample'],
params={
'fields': 'number',
'format': 'json'
}).data
if c['analysis_date']:
c['analysis_date'] = c['analysis_date'][:-10]
return render_template('chemical_analyses.html',
chemical_analyses=chem_results,
next_url=next,
prev_url=previous,
total=total_count,
first_page=url_for('chemical-analyses') + '?' +
urlencode(filters),
last_page=last)
def samples():
api = drest.API(baseurl=env('API_DRF_HOST'))
next = previous = last = total_count = None
filters = literal_eval(json.dumps(request.args))
filters['format'] = 'json'
samples = api.make_request('GET', '/samples/', params=filters).data
sample_results = samples['results']
next, previous, last, total_count = paginate_model('samples', samples,
filters)
for s in sample_results:
pos = s['location_coords'].split(" ")
s['location_coords'] = [
round(float(pos[2].replace(")", "")), 5),
round(float(pos[1].replace("(", "")), 5)
]
s['minerals'] = (', ').join([m['name'] for m in s['minerals']])
if s['collection_date']:
s['collection_date'] = s['collection_date'][:-10]
return render_template('samples.html',
samples=sample_results,
showmap='showmap' in filters,
next_url=next,
prev_url=previous,
total=total_count,
first_page=url_for('samples') + '?' +
urlencode(filters),
last_page=last)
def chemical_analyses():
#similar to samples
filters = dict(request.args)
for key in filters.keys():
f = ""
for i in range(len(filters[key])):
if filters[key][i]:
f += str(filters[key][i])+','
if f:
filters[key] = f[:-1]
else:
del filters[key]
filters["format"] = "json"
if "minerals_and" in filters:
del filters["minerals_and"]
headers = None
if session.get("auth_token", None):
headers = {"Authorization": "Token "+session.get("auth_token")}
else:
filters["public_data"] = True
##MAKES Chemicals private visible to uploaders
chemicals = get(env("API_HOST")+"chemical_analyses/", params = filters,headers=headers).json()
chem_results = chemicals["results"]
next_url, prev_url, last_page, total = paginate_model("chemical_analyses", chemicals, filters)
#collect sample ids and corresponding names
samples = set()
for c in chem_results:
samples.add(c["subsample"]["sample"])
samples = get(env("API_HOST")+"samples/", params = {"fields": "number,id",
"ids": (",").join(list(samples)), "format": "json"}, headers = headers).json()["results"]
numbers = {}
for s in samples:
numbers[s["id"]] = s
for c in chem_results:
c["sample"] = numbers[c["subsample"]["sample"]]
if c["analysis_date"]:
c["analysis_date"] = c["analysis_date"][:-10]
return render_template("chemical_analyses.html",
chemical_analyses = chem_results,
total = total,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("chemical_analyses")+"?"+urlencode(filters),
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None)
)
def chemical_analyses():
#similar to samples
filters = dict(request.args)
for key in filters.keys():
f = ""
for i in range(len(filters[key])):
if filters[key][i]:
f += str(filters[key][i])+','
if f:
filters[key] = f[:-1]
else:
del filters[key]
filters["format"] = "json"
if "minerals_and" in filters:
del filters["minerals_and"]
headers = None
if session.get("auth_token", None):
headers = {"Authorization": "Token "+session.get("auth_token")}
else:
filters["public_data"] = True
chemicals = get(env("API_HOST")+"chemical_analyses/", params = filters).json()
chem_results = chemicals["results"]
next_url, prev_url, last_page, total = paginate_model("chemical_analyses", chemicals, filters)
#collect sample ids and corresponding names
samples = set()
for c in chem_results:
samples.add(c["subsample"]["sample"])
samples = get(env("API_HOST")+"samples/", params = {"fields": "number,id",
"ids": (",").join(list(samples)), "format": "json"}, headers = headers).json()["results"]
numbers = {}
for s in samples:
numbers[s["id"]] = s
for c in chem_results:
c["sample"] = numbers[c["subsample"]["sample"]]
if c["analysis_date"]:
c["analysis_date"] = c["analysis_date"][:-10]
return render_template("chemical_analyses.html",
chemical_analyses = chem_results,
total = total,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("chemical_analyses")+"?"+urlencode(filters),
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None)
)
def samples():
#filters sent as parameters to API calls
#only return public data samples if not logged in
filters = dict(request.args)
for key in filters.keys():
if key == "polygon_coords" and filters[key][0]:
coords = filters[key][0][1:-1].split("],[")
coords.append(coords[0])
filters[key] = ["[["+("],[").join(coords)+"]]"]
filters["polygon_coord"] = []
filters[key] = (',').join([e for e in filters[key] if e and e[0]])
if not filters[key]:
del filters[key]
filters["format"] = "json"
#get sample data and use meta data to get pagination urls
samples = get(env("API_HOST")+"samples/", params = filters).json()
sample_results = samples["results"]
next_url, prev_url, last_page, total = paginate_model("samples", samples, filters)
#split location into (rounded!) latitude and longitude
#make string of minerals for ... look and clean up date
for s in sample_results:
pos = s["location_coords"].split(" ")
s["location_coords"] = [round(float(pos[2].replace(")","")),5),round(float(pos[1].replace("(","")),5)]
s["minerals"] = (", ").join([m["name"] for m in s["minerals"]])
if s["collection_date"]:
s["collection_date"] = s["collection_date"][:-10]
return render_template("samples.html",
samples = sample_results,
showmap = "showmap" in filters,
extends = "render" in filters,
total = total,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("samples")+"?"+urlencode(filters),
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None)
)
def samples():
#filters sent as parameters to API calls
#only return public data samples if not logged in
filters = dict(request.args)
tmp_var = 0
print("Pre-processing filters")
print(filters)
for key in filters.keys():
# Key is a map polygon
if key == "polygon_coords" and filters[key][0]:
# List of coordinate point strings; remove trailing comma, starting/trailing bracket,
# and split into coordinate points
coords = filters[key][0].strip(',').strip('[').strip(']').split('],[')
# Tack the first coordinate on to the end of the list so that the coordinates
# form a closed loop
coords.append(coords[0])
# Reassemble coordinates to be a list of two-element lists
coords = '[[' + ('],[').join(coords) + ']]'
filters[key] = coords
print(filters[key])
# Unnecessary, empty, or blank key
elif key == "polygon_coord" or not filters[key] or filters[key] == '' or filters[key][0] == '':
del filters[key]
# Any other key
else:
# Turn list into a comma-separated string
filters[key] = (',').join([e for e in filters[key] if e and e[0]])
print("Post-processing filters:")
print(filters)
filters["format"] = "json"
#get sample data and use meta data to get pagination urls
samples = get(env("API_HOST")+"samples/", params = filters).json()
# print samples
try:
sample_results = samples["results"]
except:
try:
error = samples["error"]
print error
samples = {}
except:
samples = {}
next_url, prev_url, last_page, total = paginate_model("samples", samples, filters)
#split location into (rounded!) latitude and longitude
#make string of minerals for ... look and clean up date
for s in sample_results:
pos = s["location_coords"].split(" ")
s["location_coords"] = [round(float(pos[2].replace(")","")),5),round(float(pos[1].replace("(","")),5)]
s["minerals"] = (", ").join([m["name"] for m in s["minerals"]])
if s["collection_date"]:
s["collection_date"] = s["collection_date"][:-10]
return render_template("samples.html",
samples = sample_results,
showmap = "showmap" in filters,
extends = "render" in filters,
total = total,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("samples")+"?"+urlencode(filters),
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None)
)
def chemical_analyses():
#similar to samples
filters = dict(request.args)
for key in filters.keys():
f = ""
for i in range(len(filters[key])):
if filters[key][i]:
f += str(filters[key][i])+','
if f:
filters[key] = f[:-1]
else:
del filters[key]
filters["format"] = "json"
if "minerals_and" in filters:
del filters["minerals_and"]
# handle sorting
sorting_dict = {'Point':'spot_id','Analysis Method':'analysis_method','Analysis Material':'mineral','Subsample Type':'subsample_type', \
'Analysis Location':'where_done','Owner':'owner','Reference':'reference','Analyst':'analyst','Analysis Date':'analysis_date','Total':'total'}
if 'ordering' in filters and filters['ordering'] != ['']:
sorting_name = filters['ordering']
else:
sorting_name = 'Point' # default
if sorting_name in sorting_dict: # all but second page
filters['ordering'] = sorting_dict[sorting_name]
else: # second page
rev_sorting_dict = dict((v, k) for k, v in sorting_dict.iteritems())
sorting_name = rev_sorting_dict[filters['ordering'].strip("'").strip('[').strip(']')]
# dynamic fields
fields_dict = {'Sample Number':'sample','Subsample':'subsample','Point':'spot_id','Analysis Method':'analysis_method','Analysis Material':'mineral', \
'Stage X':'stage_x','Stage Y':'stage_y','Reference':'reference','Reference X':'reference_x','Reference Y':'reference_y','Subsample Type':'subsample_type', \
'Analysis Location':'where_done','Elements':'elements','Oxides':'oxides','Owner':'owner', \
'Analyst':'analyst','Analysis Date':'analysis_date','Total':'total'}
fields_list, fields_dict, field_names = handle_fields(filters,False)
filters['fields'] = fields_list[0]
headers = None
if session.get("auth_token", None):
headers = {"Authorization": "Token "+session.get("auth_token")}
else:
filters["public_data"] = True
# Make chemicals private visible to uploaders
chemicals = get(env("API_HOST")+"chemical_analyses/", params = filters,headers=headers).json()
chem_results = chemicals["results"]
next_url, prev_url, last_page, total, page_num = paginate_model("chemical_analyses", chemicals, filters)
for c in chem_results:
if "analysis_date" in c and c['analysis_date']:
c["analysis_date"] = c["analysis_date"][:-10]
csv_url = env("API_HOST") + "chemical_analyses/?" + urlencode(filters) + "&format=csv"
return render_template("chemical_analyses.html",
chemical_analyses = chem_results,
field_names = field_names,
fields_dict = fields_dict,
sorting_dict = sorted(sorting_dict),
sorting_name = sorting_name,
total = total,
page_num = page_num,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("chemical_analyses")+"?"+urlencode(filters),
extends = "render" in filters,
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None),
csv_url = csv_url
)
def samples():
#filters sent as parameters to API calls
#only return public data samples if not logged in
# put header data here
headers = None
#this ideally should do nothing if passed to the metpetdb api
filters = dict(request.args)
tmp_var = 0
print("Tokens:")
print(session)
print("Pre-processing filters:")
print(filters)
# Gather polygons to be drawn on map
polygons = []
if "metamorphic_regions" in filters:
names = [] # Keep names of regions because sample only stores name of its metamorphic region, not object
for mr in filters["metamorphic_regions"][0].split(","):
region = get(env("API_HOST")+"metamorphic_regions/" + mr, params={"fields":"shape,name", "format":"json"}).json()
if "shape" in region:
polygons.append({"type": "metamorphic_region", "points": extract_points_from_shape(region["shape"])})
names.append(region["name"])
filters["metamorphic_regions"] = [",".join(names)]
provenance_fields = ["owners", "collectors", "numbers", "references"]
for field in provenance_fields:
# replace comma-space separated elements with just comma (or API will try to match names starting with spaces)
if field in filters:
filters[field][0] = filters[field][0].split(",")
filters[field][0] = ",".join([x.strip(" ") for x in filters[field][0] if x != ""])
if filters[field][0] == "": # delete field if resulting input is an empty string
del filters[field]
# handle sorting
sorting_dict = {'Sample Number':'number','Subsample Count':'subsamples', 'Collection Date':'collection_date','Subsamples':'subsamples', 'Country':'country', \
'Images':'images','Metamorphic Grades':'metamorphic_grades','Owner':'owner__name', 'References':'references__name', 'Rock Type':'rock_type__name', \
'Chemical Analyses':'chemical_analyses'}
if 'ordering' in filters and filters['ordering'] != ['']:
sorting_name = filters['ordering'][0]
else:
sorting_name = 'Sample Number' # default
if sorting_name in sorting_dict: #b all but second page
filters['ordering'] = [sorting_dict[sorting_name]]
else: # second page
rev_sorting_dict = dict((v, k) for k, v in sorting_dict.iteritems())
sorting_name = rev_sorting_dict[filters['ordering'][0]]
# format fields in request and keep list of titles for interface
filters['fields'], fields_dict, field_names = handle_fields(filters, True)
for key in filters.keys():
# Strip unused time values for start & end date queries
if (key == "start_date" or key == "end_date") and filters[key]:
filters[key] = filters[key][0][0:10]
# Unnecessary, empty, or blank key
elif key == "polygon_coord": # or not filters[key] or filters[key] == '' or filters[key][0] == '':
del filters[key]
elif key == "polygon_coords": # pre-process polygon_coords
filters[key] = filters[key][0].rstrip(",") # strip off trailing commas from frontend
# Add first point to the end of list as it is required by the backend to "close" the polygon
# use regex because the input is a string, not a list
first_point = re.search("\[(\-)?[0-9]+(\.[0-9]+)?,(\-)?[0-9]+(\.[0-9]+)?\]", filters[key])
if first_point:
filters[key] += "," + first_point.group(0)
# Finally, enclose the string in brackets since we need to send a list of points
filters[key] = "[" + filters[key] + "]"
# Any other key
else:
# Turn list into a comma-separated string
filters[key] = (',').join([e for e in filters[key] if e and e[0]]).rstrip(",") # strip trailing commas
print("Post-processing filters:")
print(filters)
filters["format"] = "json"
try:
headers = {"Authorization":"Token "+session["auth_token"]}
samples = get(env("API_HOST")+"samples/", params = filters,headers= headers).json()
print "URL: ", get(env("API_HOST")+"samples/", params = filters,headers= headers)
except KeyError:
samples = get(env("API_HOST")+"samples/",params = filters).json()
try:
sample_results = samples["results"]
except:
try:
error = samples["error"]
print error
samples = {}
sample_results = {}
except:
samples = {}
sample_results = {}
# Decode utf8 before encoding as urld
for k, v in filters.iteritems():
if isinstance(v, unicode):
v = v.encode("utf8")
elif isinstance(v, str):
v.decode("utf8")
filters[k] = v
next_url, prev_url, last_page, total, page_num = paginate_model("samples", samples, filters)
# clean up values for samples view
for s in sample_results:
if "metamorphic_grades" in s:
s["metamorphic_grades"] = (", ").join([g for g in sorted(s["metamorphic_grades"])])
if "metamorphic_regions" in s:
s["metamorphic_regions"] = (", ").join([r for r in sorted(s["metamorphic_regions"])])
if "minerals" in s:
s["minerals"] = (", ").join([m for m in sorted(s["minerals"])])
if "references" in s:
s["references"] = (", ").join([r for r in sorted(s["references"])])
if "regions" in s:
s["regions"] = (", ").join([m for m in sorted(s["regions"])])
csv_url = env("API_HOST") + "samples/?" + urlencode(filters) + "&format=csv"
return render_template("samples.html",
samples = sample_results,
field_names = field_names,
fields_dict = fields_dict,
sorting_dict = sorting_dict,
sorting_name = sorting_name,
showmap = "showmap" in filters,
extends = "render" in filters,
polygons = polygons,
total = total,
page_num = page_num,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("samples")+"?"+urlencode(filters),
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None),
csv_url = csv_url
)
def samples():
#filters sent as parameters to API calls
#only return public data samples if not logged in
# put header data here
headers = None
#this ideally should do nothing if passed to the metpetdb api
filters = dict(request.args)
tmp_var = 0
print("tokens")
print(session)
print("Pre-processing filters")
print(filters)
for key in filters.keys():
# Key is a map polygon
if key == "polygon_coords" and filters[key][0]:
# List of coordinate point strings; remove trailing comma, starting/trailing bracket,
# and split into coordinate points
coords = filters[key][0].strip(',').strip('[').strip(']').split('],[')
# Tack the first coordinate on to the end of the list so that the coordinates
# form a closed loop
coords.append(coords[0])
# Reassemble coordinates to be a list of two-element lists
coords = '[[' + ('],[').join(coords) + ']]'
filters[key] = coords
print(filters[key])
# Unnecessary, empty, or blank key
elif key == "polygon_coord" or not filters[key] or filters[key] == '' or filters[key][0] == '':
del filters[key]
# Any other key
else:
# Turn list into a comma-separated string
filters[key] = (',').join([e for e in filters[key] if e and e[0]])
print("Post-processing filters:")
print(filters)
filters["format"] = "json"
samples = {}
try:
headers = {"Authorization":"Token "+session["auth_token"]}
print "HEADER:",headers
samples = get(env("API_HOST")+"samples/", params = filters,headers= headers).json()
print "URL: ",get(env("API_HOST")+"samples/", params = filters,headers= headers)
except KeyError:
samples = get(env("API_HOST")+"samples/",params = filters).json()
# print samples
try:
sample_results = samples["results"]
except:
try:
error = samples["error"]
print error
samples = {}
except:
samples = {}
next_url, prev_url, last_page, total = paginate_model("samples", samples, filters)
#split location into (rounded!) latitude and longitude
#make string of minerals for ... look and clean up date
for s in sample_results:
pos = s["location_coords"].split(" ")
s["location_coords"] = [round(float(pos[2].replace(")","")),5),round(float(pos[1].replace("(","")),5)]
s["minerals"] = (", ").join([m["name"] for m in s["minerals"]])
if s["collection_date"]:
s["collection_date"] = s["collection_date"][:-10]
return render_template("samples.html",
samples = sample_results,
showmap = "showmap" in filters,
extends = "render" in filters,
total = total,
next_url = next_url,
prev_url = prev_url,
first_page = url_for("samples")+"?"+urlencode(filters),
last_page = last_page,
auth_token = session.get("auth_token",None),
email = session.get("email",None),
name = session.get("name",None)
)
