def collection_get(cid='', format="json", include_history=False):
logger.info(u"in collection_get".format(cid=cid))
# if not include items, then just return the collection straight from couch
if (request.args.get("include_items") in ["0", "false", "False"]):
coll = collection.get_collection_doc(cid)
if not coll:
abort_custom(404, "collection not found")
# except if format is csv. can't do that.
if format == "csv":
abort_custom(405, "csv method not supported for not include_items")
else:
response_code = 200
resp = make_response(json.dumps(coll, sort_keys=True, indent=4),
response_code)
else:
include_history = (request.args.get("include_history", 0)
in ["1", "true", "True"])
(coll_with_items, something_currently_updating
) = collection.get_collection_with_items_for_client(
cid, myrefsets, myredis, mydao, include_history)
# return success if all reporting is complete for all items
if something_currently_updating:
response_code = 210 # update is not complete yet
else:
response_code = 200
if format == "csv":
# remove scopus before exporting to csv, so don't add magic keep-scopus keys to clean method
clean_items = [
item_module.clean_for_export(item)
for item in coll_with_items["items"]
]
csv = collection.make_csv_stream(clean_items)
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add(
"Content-Disposition",
"attachment; filename=impactstory-{cid}.csv".format(cid=cid))
resp.headers.add("Content-Encoding", "UTF-8")
else:
secret_key = os.getenv("API_ADMIN_KEY")
if request.args.get("api_admin_key"):
supplied_key = request.args.get("api_admin_key", "")
else:
supplied_key = request.args.get("key", "")
clean_if_necessary_items = [
item_module.clean_for_export(item, supplied_key, secret_key)
for item in coll_with_items["items"]
]
coll_with_items["items"] = clean_if_necessary_items
resp = make_response(
json.dumps(coll_with_items, sort_keys=True, indent=4),
response_code)
return resp
def products_get(tiids_string,
format="json",
most_recent_metric_date=None,
most_recent_diff_metric_date=None):
tiids = tiids_string.split(",")
override_export_clean = (format == "csv")
cleaned_items_dict = cleaned_items(tiids, myredis, override_export_clean,
most_recent_metric_date,
most_recent_diff_metric_date)
response_code = 200
if not collection.is_all_done(tiids, myredis):
response_code = 210 # update is not complete yet
if format == "csv":
csv = collection.make_csv_stream(cleaned_items_dict.values())
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add("Content-Encoding", "UTF-8")
else:
resp = make_response(
json.dumps({"products": cleaned_items_dict},
sort_keys=True,
indent=4), response_code)
return resp
def collection_get(cid='', format="json", include_history=False):
logger.info(u"in collection_get".format(cid=cid))
# if not include items, then just return the collection straight from couch
if (request.args.get("include_items") in ["0", "false", "False"]):
coll = collection.get_collection_doc(cid)
if not coll:
abort_custom(404, "collection not found")
# except if format is csv. can't do that.
if format == "csv":
abort_custom(405, "csv method not supported for not include_items")
else:
response_code = 200
resp = make_response(json.dumps(coll, sort_keys=True, indent=4),
response_code)
else:
include_history = (request.args.get("include_history", 0) in ["1", "true", "True"])
(coll_with_items, something_currently_updating) = collection.get_collection_with_items_for_client(cid, myrefsets, myredis, mydao, include_history)
# return success if all reporting is complete for all items
if something_currently_updating:
response_code = 210 # update is not complete yet
else:
response_code = 200
if format == "csv":
# remove scopus before exporting to csv, so don't add magic keep-scopus keys to clean method
clean_items = [item_module.clean_for_export(item) for item in coll_with_items["items"]]
csv = collection.make_csv_stream(clean_items)
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add("Content-Disposition",
"attachment; filename=impactstory-{cid}.csv".format(
cid=cid))
resp.headers.add("Content-Encoding",
"UTF-8")
else:
secret_key = os.getenv("API_ADMIN_KEY")
if request.args.get("api_admin_key"):
supplied_key = request.args.get("api_admin_key", "")
else:
supplied_key = request.args.get("key", "")
clean_if_necessary_items = [item_module.clean_for_export(item, supplied_key, secret_key)
for item in coll_with_items["items"]]
coll_with_items["items"] = clean_if_necessary_items
resp = make_response(json.dumps(coll_with_items, sort_keys=True, indent=4),
response_code)
return resp
def collection_get(cid='', format="json", include_history=False):
coll = mydao.get(cid)
if not coll:
abort(404)
# if not include items, then just return the collection straight from couch
if (request.args.get("include_items") in ["0", "false", "False"]):
# except if format is csv. can't do that.
if format == "csv":
abort(405) # method not supported
else:
response_code = 200
resp = make_response(json.dumps(coll, sort_keys=True, indent=4),
response_code)
resp.mimetype = "application/json"
else:
try:
include_history = (request.args.get("include_history", 0) in ["1", "true", "True"])
(coll_with_items, something_currently_updating) = collection.get_collection_with_items_for_client(cid, myrefsets, myredis, mydao, include_history)
except (LookupError, AttributeError):
logger.error("couldn't get tiids for GET collection '{cid}'".format(cid=cid))
abort(404) # not found
# return success if all reporting is complete for all items
if something_currently_updating:
response_code = 210 # update is not complete yet
else:
response_code = 200
if format == "csv":
# remove scopus before exporting to csv, so don't add magic keep-scopus keys to clean method
clean_items = [item_module.clean_for_export(item) for item in coll_with_items["items"]]
csv = collection.make_csv_stream(clean_items)
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add("Content-Disposition",
"attachment; filename=impactstory-{cid}.csv".format(
cid=cid))
resp.headers.add("Content-Encoding",
"UTF-8")
else:
api_key = request.args.get("key", None)
clean_if_necessary_items = [item_module.clean_for_export(item, api_key, os.getenv("API_KEY"))
for item in coll_with_items["items"]]
coll_with_items["items"] = clean_if_necessary_items
resp = make_response(json.dumps(coll_with_items, sort_keys=True, indent=4),
response_code)
resp.mimetype = "application/json"
return resp
def products_get(tiids_string, format="json"):
tiids = tiids_string.split(",")
cleaned_items_dict = cleaned_items(tiids, myredis)
response_code = 200
if collection.is_something_currently_updating(cleaned_items_dict, myredis):
response_code = 210 # update is not complete yet
if format == "csv":
csv = collection.make_csv_stream(cleaned_items_dict.values())
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add("Content-Encoding", "UTF-8")
else:
resp = make_response(json.dumps({"products": cleaned_items_dict}, sort_keys=True, indent=4),
response_code)
return resp
def products_get(tiids_string, format="json", most_recent_metric_date=None, most_recent_diff_metric_date=None):
tiids = tiids_string.split(",")
override_export_clean = (format=="csv")
cleaned_items_dict = cleaned_items(tiids, myredis, override_export_clean, most_recent_metric_date, most_recent_diff_metric_date)
response_code = 200
if not collection.is_all_done(tiids, myredis):
response_code = 210 # update is not complete yet
if format == "csv":
csv = collection.make_csv_stream(cleaned_items_dict.values())
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add("Content-Encoding", "UTF-8")
else:
resp = make_response(json.dumps({"products": cleaned_items_dict}, sort_keys=True, indent=4),
response_code)
return resp
def products_get(tiids_string, format="json"):
tiids = tiids_string.split(",")
cleaned_items_dict = cleaned_items(tiids, myredis)
response_code = 200
if collection.is_something_currently_updating(cleaned_items_dict, myredis):
response_code = 210 # update is not complete yet
if format == "csv":
csv = collection.make_csv_stream(cleaned_items_dict.values())
resp = make_response(csv, response_code)
resp.mimetype = "text/csv;charset=UTF-8"
resp.headers.add("Content-Encoding", "UTF-8")
else:
resp = make_response(
json.dumps({"products": cleaned_items_dict},
sort_keys=True,
indent=4), response_code)
return resp
def test_make_csv_stream(self):
csv = collection.make_csv_stream(API_ITEMS_JSON)
expected = 'tiid,title,doi,dryad:most_downloaded_file,dryad:package_views,dryad:total_downloads,mendeley:groups,mendeley:readers,plosalm:crossref,plosalm:html_views,plosalm:pdf_views,plosalm:pmc_abstract,plosalm:pmc_figure,plosalm:pmc_full-text,plosalm:pmc_pdf,plosalm:pmc_supp-data,plosalm:pmc_unique-ip,plosalm:pubmed_central,plosalm:scopus,wikipedia:mentions\r\nf2b45fcab1da11e19199c8bcc8937e3f,"Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma",10.1371/journal.pcbi.1000362,,,,1,13,7,2075,484,29,13,232,113,0,251,2,11,\r\nc1eba010b1da11e19199c8bcc8937e3f,"Data from: Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)",10.5061/dryad.1295,70,537,114,,,,,,,,,,,,,,\r\nc202754cb1da11e19199c8bcc8937e3f,Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article,10.1371/journal.pcbi.1000361,,,,4,52,13,11521,1097,70,39,624,149,6,580,12,19,1\r\nf2dc3f36b1da11e19199c8bcc8937e3f,Design Principles for Riboswitch Function,10.1371/journal.pcbi.1000363,,,,4,57,16,3361,1112,37,54,434,285,41,495,9,19,\r\n'
assert_equals(csv, expected)
def test_make_csv_stream(self):
csv = collection.make_csv_stream(API_ITEMS_JSON)
expected = 'tiid,title,doi,dryad:most_downloaded_file,dryad:package_views,dryad:total_downloads,mendeley:groups,mendeley:readers,plosalm:crossref,plosalm:html_views,plosalm:pdf_views,plosalm:pmc_abstract,plosalm:pmc_figure,plosalm:pmc_full-text,plosalm:pmc_pdf,plosalm:pmc_supp-data,plosalm:pmc_unique-ip,plosalm:pubmed_central,plosalm:scopus,wikipedia:mentions\r\nf2b45fcab1da11e19199c8bcc8937e3f,"Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma",10.1371/journal.pcbi.1000362,,,,1,13,7,2075,484,29,13,232,113,0,251,2,11,\r\nc1eba010b1da11e19199c8bcc8937e3f,"Data from: Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)",10.5061/dryad.1295,70,537,114,,,,,,,,,,,,,,\r\nc202754cb1da11e19199c8bcc8937e3f,Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article,10.1371/journal.pcbi.1000361,,,,4,52,13,11521,1097,70,39,624,149,6,580,12,19,1\r\nf2dc3f36b1da11e19199c8bcc8937e3f,Design Principles for Riboswitch Function,10.1371/journal.pcbi.1000363,,,,4,57,16,3361,1112,37,54,434,285,41,495,9,19,\r\n'
assert_equals(csv, expected)