diff --git a/firebase_to_xml/.python-version b/firebase_to_xml/.python-version new file mode 100644 index 00000000..e4fba218 --- /dev/null +++ b/firebase_to_xml/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/firebase_to_xml/firebase_to_xml/__main__.py b/firebase_to_xml/firebase_to_xml/__main__.py index aae5768e..d81a77c3 100644 --- a/firebase_to_xml/firebase_to_xml/__main__.py +++ b/firebase_to_xml/firebase_to_xml/__main__.py @@ -3,29 +3,23 @@ """ Command line interface to part of firebase_to_xml """ + import argparse +import os import traceback from pathlib import Path import yaml from dotenv import load_dotenv +from get_records_from_firebase import get_records_from_firebase +from loguru import logger from metadata_xml.template_functions import metadata_to_xml - -from firebase_to_xml.get_records_from_firebase import get_records_from_firebase -from firebase_to_xml.record_json_to_yaml import record_json_to_yaml - - -def parse_status(status: str): - """Return a list version fo their status selection""" - - if "," in status: - return status.split(",") - - return [status] +from record_json_to_yaml import record_json_to_yaml +from tqdm import tqdm def get_filename(record): - """Creates a filename by combinig the title and UUID """ + """Creates a filename by combinig the title and UUID""" name = record["title"][record["language"]][0:30] + "_" + record["identifier"][0:5] char_list = [ character if character.isalnum() else "_" for character in name.strip().lower() @@ -48,9 +42,7 @@ def main(): parser.add_argument( "--yaml", action="store_true", help="Whether to output yaml file as well as xml" ) - parser.add_argument( - "--region", required=True, help="Eg pacific/stlaurent/atlantic" - ) + parser.add_argument("--region", required=True, help="Eg pacific/stlaurent/atlantic") parser.add_argument( "--status", default="published", @@ -63,7 +55,18 @@ def main(): ], ) parser.add_argument("--record_url", required=False) - + parser.add_argument( + "--database_url", + default=os.getenv("DATABASE_URL"), + required=False, + help="Firebase database URL (default: %(default)s)", + ) + parser.add_argument( + "--encoding", + default="utf-8", + required=False, + help="Encoding of the output files", + ) args = vars(parser.parse_args()) region = args["region"] @@ -73,10 +76,15 @@ def main(): firebase_auth_key_file = args["key"] also_save_yaml = args["yaml"] + encoding = args["encoding"] # get list of records from Firebase record_list = get_records_from_firebase( - region, firebase_auth_key_file, record_url, record_status + region=args["region"], + firebase_auth_key_file=args["key"], + record_url=record_url, + record_status=args["status"].split(","), + database_url=args["database_url"], ) # translate each record to YAML and then to XML @@ -107,9 +115,11 @@ def main(): # output yaml if also_save_yaml: - filename = f"{xml_directory}/{name}.yaml" - file = open(filename, "w") - file.write(yaml.dump(record_yaml, allow_unicode=True, sort_keys=False)) + yaml_file = output_directory / f"{filename}.yaml" + yaml_file.write_text( + yaml.dump(record_yaml, allow_unicode=True, sort_keys=False), + encoding=encoding, + ) # render xml template and write to file xml = metadata_to_xml(record_yaml) @@ -121,6 +131,9 @@ def main(): file.write(xml) print("Wrote " + file.name) + xml_file = output_directory / f"{filename}.xml" + xml_file.write_text(xml, encoding=encoding) + except Exception: print(traceback.format_exc()) diff --git a/firebase_to_xml/firebase_to_xml/get_records_from_firebase.py b/firebase_to_xml/firebase_to_xml/get_records_from_firebase.py index a11ee807..3e4c20b2 100644 --- a/firebase_to_xml/firebase_to_xml/get_records_from_firebase.py +++ b/firebase_to_xml/firebase_to_xml/get_records_from_firebase.py @@ -10,10 +10,16 @@ from google.auth.transport.requests import AuthorizedSession from google.oauth2 import service_account +from loguru import logger def get_records_from_firebase( - region, firebase_auth_key_file, record_url, record_status, firebase_auth_key_json=None + region: str, + firebase_auth_key_file: str, + record_url: str, + record_status: list, + database_url: str, + firebase_auth_key_json: str = None, ): """ Returns list of records from firebase for this region, @@ -43,23 +49,18 @@ def get_records_from_firebase( records = [] if record_url: - response = authed_session.get( - f"https://cioos-metadata-form.firebaseio.com/{record_url}.json" - ) + response = authed_session.get(f"{database_url}{record_url}.json") body = json.loads(response.text) records.append(body) return records else: - response = authed_session.get( - f"https://cioos-metadata-form.firebaseio.com/{region}/users.json" - ) + response = authed_session.get(f"{database_url}{region}/users.json") body = json.loads(response.text) # Parse response - if not body or type(body) != dict : - print("Region",region,"not found?") - # print(response.content) + if not body or not isinstance(body, dict): + logger.warning("Region", region, "not found?") sys.exit() for users_tree in body.values(): diff --git a/firebase_to_xml/firebase_to_xml/record_json_to_yaml.py b/firebase_to_xml/firebase_to_xml/record_json_to_yaml.py index 89529ce8..75754441 100644 --- a/firebase_to_xml/firebase_to_xml/record_json_to_yaml.py +++ b/firebase_to_xml/firebase_to_xml/record_json_to_yaml.py @@ -6,45 +6,52 @@ """ import json -from firebase_to_xml.scrubbers import scrub_dict, scrub_keys, remove_nones import os + +from firebase_to_xml.scrubbers import remove_nones, scrub_dict, scrub_keys + dir = os.path.dirname(os.path.realpath(__file__)) + def get_licenses(): - with open(dir + '/resources/licenses.json') as f: + with open(dir + "/resources/licenses.json") as f: return json.load(f) + def get_eov_translations(): - with open(dir + '/resources/eov.json') as f: - eovs= json.load(f) - translation={} + with open(dir + "/resources/eov.json") as f: + eovs = json.load(f) + translation = {} for eov in eovs: - translation[eov['value']]=eov['label FR'] + translation[eov["value"]] = eov["label FR"] return translation def get_epsg(): - with open(dir + '/resources/epsg.json') as f: + with open(dir + "/resources/epsg.json") as f: epsgDict = {} epsgJson = json.load(f) if epsgJson: - epsgDict = {str(x['Code']): x for x in epsgJson} + epsgDict = {str(x["Code"]): x for x in epsgJson} return epsgDict -licenses=get_licenses() -eov_translations=get_eov_translations() + +licenses = get_licenses() +eov_translations = get_eov_translations() epsg = get_epsg() def eovs_to_fr(eovs_en): - """ Translate a list of EOVs in english to a list in french""" - return [eov_translations.get(eov,"") for eov in eovs_en if eov] + """Translate a list of EOVs in english to a list in french""" + return [eov_translations.get(eov, "") for eov in eovs_en if eov] + def verify_translation(verified, message): if not verified: return message return "" + def strip_keywords(keywords): """Strips whitespace from each keyword in either language""" stripped = { @@ -61,33 +68,40 @@ def date_from_datetime_str(datetime_str): return None return (datetime_str or "")[:10] + def fix_lat_long_polygon(polygon): """Change lat,long to long, lat, which is what is expected in the XML""" if not polygon: return "" fixed = [] - cleanPolygon = polygon.replace(", ",",") + cleanPolygon = polygon.replace(", ", ",") coords = cleanPolygon.split(" ") for coord in coords: [lat, long] = coord.split(",") fixed.append(",".join([long, lat])) return " ".join(fixed) + def format_taxa(taxa): taxaKeywords = [] if isinstance(taxa, str): taxa = [taxa] for t in taxa: - taxaKeywords = taxaKeywords + ",".join(filter(None, ( - t.get("kingdom"), - t.get("phylum"), - t.get("class"), - t.get("order"), - t.get("family"), - t.get("genus"), - t.get("species") - ))).split(",") - + taxaKeywords = taxaKeywords + ",".join( + filter( + None, + ( + t.get("kingdom"), + t.get("phylum"), + t.get("class"), + t.get("order"), + t.get("family"), + t.get("genus"), + t.get("species"), + ), + ) + ).split(",") + return taxaKeywords @@ -102,7 +116,6 @@ def record_json_to_yaml(record): base_url = "https://cioos-siooc.github.io/metadata-entry-form#" full_url = f"{base_url}/{language}/{region}/{user_id}/{record_id}" - polygon = record.get("map", {}).get("polygon", "") record_yaml = { @@ -110,8 +123,7 @@ def record_json_to_yaml(record): "naming_authority": "ca.cioos", "identifier": record.get("identifier"), "language": record.get("language"), - "maintenance_note": "Generated from " - + full_url, + "maintenance_note": "Generated from " + full_url, "use_constraints": { "limitations": record.get("limitations", "None"), "licence": licenses.get( @@ -139,13 +151,19 @@ def record_json_to_yaml(record): else "", "polygon": fix_lat_long_polygon(polygon), "vertical": [ - 0 if record.get("noVerticalExtent") else float( - record.get("verticalExtentMin")), - 0 if record.get("noVerticalExtent") else float( - record.get("verticalExtentMax")), + 0 + if record.get("noVerticalExtent") + else float(record.get("verticalExtentMin")), + 0 + if record.get("noVerticalExtent") + else float(record.get("verticalExtentMax")), ], - "vertical_positive": "heightPositive" if record.get("noVerticalExtent") else record.get("verticalExtentDirection"), - "vertical_epsg": epsg.get("5829") if record.get("noVerticalExtent") else epsg.get(record.get("verticalExtentEPSG")), + "vertical_positive": "heightPositive" + if record.get("noVerticalExtent") + else record.get("verticalExtentDirection"), + "vertical_epsg": epsg.get("5829") + if record.get("noVerticalExtent") + else epsg.get(record.get("verticalExtentEPSG")), "description": record["map"].get("description"), "descriptionIdentifier": record["map"].get("descriptionIdentifier"), }, @@ -161,8 +179,14 @@ def record_json_to_yaml(record): }, "keywords": { "default": strip_keywords(record.get("keywords", {"en": [], "fr": []})), - "eov": {"en": record.get("eov",[]), "fr": eovs_to_fr(record.get("eov",[]))}, - "taxa": {"en": format_taxa(record.get("taxa",[])), "fr": format_taxa(record.get("taxa",[]))} + "eov": { + "en": record.get("eov", []), + "fr": eovs_to_fr(record.get("eov", [])), + }, + "taxa": { + "en": format_taxa(record.get("taxa", [])), + "fr": format_taxa(record.get("taxa", [])), + }, }, "temporal_begin": record.get("dateStart"), "temporal_end": record.get("dateEnd"), @@ -184,7 +208,14 @@ def record_json_to_yaml(record): "ror": contact.get("orgRor"), }, "individual": { - "name": ", ".join(remove_nones([contact.get("lastName") or None, contact.get("givenNames") or None])), + "name": ", ".join( + remove_nones( + [ + contact.get("lastName") or None, + contact.get("givenNames") or None, + ] + ) + ), "position": contact.get("indPosition"), "email": contact.get("indEmail"), "orcid": contact.get("indOrcid"), @@ -203,14 +234,14 @@ def record_json_to_yaml(record): ], } - if record.get("noTaxa") and record_yaml.get("identification",{}).get("keywords"): + if record.get("noTaxa") and record_yaml.get("identification", {}).get("keywords"): record_yaml["identification"]["keywords"].pop("taxa", None) - + if record.get("noPlatform"): record_yaml["instruments"] = record.get("instruments") else: - instrumentsList = record.get("instruments",[]) - platformList = record.get("platforms",[]) + instrumentsList = record.get("instruments", []) + platformList = record.get("platforms", []) # If platforms has only one element, add it to the platform dict and add all instruments as a key if len(platformList) == 1: record["platforms"][0]["instruments"] = instrumentsList diff --git a/firebase_to_xml/firebase_to_xml/scrubbers.py b/firebase_to_xml/firebase_to_xml/scrubbers.py index b79121c2..a4524570 100644 --- a/firebase_to_xml/firebase_to_xml/scrubbers.py +++ b/firebase_to_xml/firebase_to_xml/scrubbers.py @@ -18,7 +18,7 @@ def scrub_dict(d_in): val = scrub_dict(val) if isinstance(val, list): val = scrub_list(val) - if val not in (u"", None, {}): + if val not in ("", None, {}): new_dict[key] = val return new_dict @@ -41,5 +41,6 @@ def scrub_keys(d_in): scrubbed[k] = d_in[k] return scrubbed -def remove_nones(l): - return list(filter(lambda item: item is not None, l)) + +def remove_nones(items): + return list(filter(lambda item: item is not None, items)) diff --git a/firebase_to_xml/pyproject.toml b/firebase_to_xml/pyproject.toml new file mode 100644 index 00000000..39873c0b --- /dev/null +++ b/firebase_to_xml/pyproject.toml @@ -0,0 +1,24 @@ +[project] +name = "firebase-to-xml" +version = "0.1.0" +description = "Python module translates metadata records from Firebase into XML" +readme = "README.md" +requires-python = ">=3.12" +dependencies = [ + "firebase-to-xml", + "google-auth>=2.35.0", + "google-oauth>=1.0.1", + "loguru>=0.7.2", + "metadata-xml", + "python-dotenv>=1.0.1", + "tqdm>=4.66.5", +] + +[tool.uv] +dev-dependencies = [ + "ruff>=0.7.0", +] + +[tool.uv.sources] +metadata-xml = { git = "https://github.com/cioos-siooc/metadata-xml.git" } +firebase-to-xml 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