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Updated submodules
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parent
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commit
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3 changed files with 2 additions and 275 deletions
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Subproject commit d382a9411c539b36139df5d1d25eb09fe6602fdb
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Subproject commit c463b7fb1db83679bb0c95e1c7822ccfaa6c0c82
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Subproject commit b1f6da3c04d68dc8cdbeaaf9392c8f8ef6d80586
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Subproject commit 04568107105e3663b3f79321d95bfd4f3a6de9af
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#!/usr/bin/env python
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"""
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Script to create Hugo markdown
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files from iNaturalist Observations
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"""
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from urllib import request
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from glob import glob
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from http.client import HTTPResponse
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from pathlib import Path
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from typing import Any, Dict, Optional
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import json
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import sys
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import time
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CONTENT_LOCATION = "content/observations"
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USER_ID = "brandonrozek"
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MIN_OBS_ID = -1
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def retrieve_data_from_server():
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server_data = []
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server_ids = retrieve_obs_ids_from_server()
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time.sleep(1) # 60 requests / second cap
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for id_num in server_ids:
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# Grab observation from iNaturalist
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url = f"https://api.inaturalist.org/v1/observations/{id_num}"
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response: Optional[HTTPResponse] = None
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try:
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response = request.urlopen(url)
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except Exception:
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print(f"Unable to grab observation {id_num} from iNaturalist.")
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if response is None:
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continue
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# Parse server response
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server_data_part = None
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try:
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server_data_part = json.loads(response.read())['results'][0]
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# Note: there is only one observation as a result
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except Exception:
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print(f"Malformed JSON response for observation {id_num}.")
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continue
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server_data_part = reformat_obs(id_num, server_data_part)
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server_data.append(server_data_part)
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time.sleep(1) # 60 requests / second cap
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print(f"Successfully obtained {len(server_data)} observations from the server.")
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return server_data
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def retrieve_obs_ids_from_server():
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"""
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Grabs observation ids from iNaturalist server
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"""
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global MIN_OBS_ID
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server_data = []
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finished_retrieving = False
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while not finished_retrieving:
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# Grab observations from iNaturalist
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id_below = "&id_below=" + str(MIN_OBS_ID) \
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if MIN_OBS_ID > 0 else ""
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url = "https://api.inaturalist.org/v1/observations?order=desc&order_by=created_at&only_id=true&user_id=" + USER_ID + id_below
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response: Optional[HTTPResponse] = None
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try:
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response = request.urlopen(url)
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except Exception:
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print("Unable to grab observations from iNaturalist.")
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if response is None:
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sys.exit(-1)
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# Parse server response
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server_data_part: Optional[list] = None
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try:
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server_data_part = json.loads(response.read())['results']
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except Exception:
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print("Malformed JSON response from server.")
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if server_data is None:
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sys.exit(-1)
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if not isinstance(server_data_part, list):
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print("Unexpected JSON response, should be of form list.")
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sys.exit(-1)
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# No more to retrieve
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if len(server_data_part) == 0:
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finished_retrieving = True
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break
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server_data_part = [d['id'] for d in server_data_part]
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# print(f"Retrieved {len(server_data_part)} observations from server")
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server_data.extend(server_data_part)
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MIN_OBS_ID = server_data_part[-1]
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print(f"Parsed a total of {len(server_data)} ids from server")
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return server_data
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def reformat_obs(obsid, obs_json):
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"""
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Takes a obs_json and
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slightly modifies it to match
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some of the fields Hugo expects.
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"""
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obs_data = dict(
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id=str(obsid),
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metadata={},
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content=""
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)
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# Turn URL -> Syndication
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obs_data['metadata']['syndication'] = obs_json['uri']
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# Turn Created At -> Date
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obs_data['metadata']['date'] = obs_json['time_observed_at']
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# Grab some taxonomy information about the organism
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obs_data['metadata']['taxon'] = dict(
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name=obs_json['taxon']['name'],
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common_name=obs_json['taxon']['preferred_common_name']
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)
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# Grab only a few fields
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desired_fields = [
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'quality_grade', 'identifications_most_agree',
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'species_guess', 'identifications_most_disagree',
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'captive', 'project_ids',
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'community_taxon_id', 'geojson',
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'owners_identification_from_vision',
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'identifications_count', 'obscured',
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'num_identification_agreements',
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'num_identification_disagreements',
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'place_guess', "photos"
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]
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for key in desired_fields:
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obs_data['metadata'][key] = obs_json[key]
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return obs_data
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############################################################################
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def findall(p, s):
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"""
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Yields all the positions of
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the pattern p in the string s.
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Source: https://stackoverflow.com/a/34445090
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"""
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i = s.find(p)
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while i != -1:
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yield i
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i = s.find(p, i+1)
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def hugo_markdown_to_json(markdown_contents) -> Optional[Dict[Any, Any]]:
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"""
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Take the contents from a Hugo markdown
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file and read the JSON frontmatter if it
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exists.
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"""
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front_matter_indices = list(findall('---', markdown_contents))
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if len(front_matter_indices) < 2:
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return None
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front_matter = markdown_contents[(front_matter_indices[0] + 3):front_matter_indices[1]]
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json_contents = None
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try:
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json_contents = json.loads(front_matter)
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except Exception:
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pass
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if not isinstance(json_contents, dict):
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json_contents = None
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html_contents = markdown_contents[front_matter_indices[1] + 19:-17]
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return json_contents, html_contents
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def create_markdown_str(frontmatter, content):
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"""
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Takes a JSON frontmatter
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and creates a string representing
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the contents of a Hugo markdown
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file.
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"""
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return "---\n" + \
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f"{json.dumps(frontmatter)}\n" +\
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"---\n" +\
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"{{< unsafe >}}\n" +\
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f"{content}\n" +\
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"{{< /unsafe >}}\n"
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def file_from_id(idnum):
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"""Returns filename from id"""
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return f"{CONTENT_LOCATION}/{idnum}.md"
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def read_hugo_markdown(idnum) -> Optional[Dict[Any, Any]]:
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"""
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Given an id, return the markdown file
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frontmatter and contents stored in Hugo
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if it exists.
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"""
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try:
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with open(file_from_id(idnum), "r", encoding="UTF-8") as hugo_file:
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frontmatter, contents = hugo_markdown_to_json(hugo_file.read())
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return frontmatter, contents
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except Exception:
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return None
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def write_markdown(id_num, frontmatter, contents):
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"""
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Takes a frontmatter json
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and writes it to a hugo
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markdown content file.
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"""
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try:
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with open(file_from_id(id_num), "w", encoding="UTF-8") as hugo_file:
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hugo_file.write(create_markdown_str(frontmatter, contents))
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except Exception as e:
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print("Failed to write", id_num)
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############################################################################
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# Read in saved data
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saved_filenames = glob(CONTENT_LOCATION + "/*.md")
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saved_ids = { Path(fname).stem for fname in saved_filenames }
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server_data = retrieve_data_from_server()
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# Data is structured like [{id: '', metadata: '', contents: ''}]
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# Where metadata is a JSON and contents is HTML
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for data in server_data:
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id_num = data['id']
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# If the observation already exists
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if id_num in saved_ids:
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saved_fm, saved_content = read_hugo_markdown(id_num)
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if saved_fm is None:
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print("Unable to read saved data id", id_num)
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# Only update if observation has changed
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elif saved_fm != data['metadata']:
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print("Updating id", id_num)
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write_markdown(id_num, data['metadata'], data['content'])
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# New observation found
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else:
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print("Creating id", id_num)
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write_markdown(id_num, data['metadata'], data['content'])
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print("Completed")
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