thompsonmj commited on
Commit
cb3900a
·
verified ·
1 Parent(s): fd1374f

Update metadata.parquet with "gbif_taxon_id" (#3)

Browse files

- Use gbif_taxon_id for GBIF link lookup (e6ca92128986db5f685798081d91fc6d38815a7d)

components/metadata.parquet CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:6af05f1f8f08b0d447b9a4c18680c7de39551a05318f026d30c224a9bbe5283e
3
- size 121162891
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:bc17e3263f1e735162c5f4f3356c297b3723002258698190657d93f759bd669f
3
+ size 131082909
components/query.py CHANGED
@@ -42,7 +42,7 @@ def get_sample(df, pred_taxon, rank):
42
  '''
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  logger.info(f"Getting sample for taxon: {pred_taxon} at rank: {rank}")
44
  try:
45
- filepath, gbif_id, eol_page_id, full_name, is_exact = get_sample_data(df, pred_taxon, rank)
46
  except Exception as e:
47
  logger.error(f"Error retrieving sample data: {e}")
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  return None, f"We encountered the following error trying to retrieve a sample image: {e}."
@@ -58,8 +58,8 @@ def get_sample(df, pred_taxon, rank):
58
  )
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  img_resp = requests.get(img_src)
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  img = Image.open(io.BytesIO(img_resp.content))
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- if gbif_id:
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- gbif_url = GBIF_URL + gbif_id
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  if eol_page_id:
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  eol_url = EOL_URL + eol_page_id
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  if is_exact:
@@ -100,7 +100,7 @@ def get_sample_data(df, pred_taxon, rank):
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  --------
101
  filepath : str
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  Filepath of selected sample image for predicted taxon.
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- gbif_id: str
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  GBIF page ID associated with predicted taxon for more information.
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  eol_page_id : str
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  EOL page ID associated with predicted taxon for more information.
@@ -125,9 +125,9 @@ def get_sample_data(df, pred_taxon, rank):
125
  if exact_df.shape[0] > 0:
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  df_filtered = exact_df.sample()
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  full_name = " ".join(df_filtered.select(RANKS[:rank+1]).row(0))
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- return df_filtered["file_path"][0], df_filtered["gbif_id"].cast(pl.String)[0], df_filtered["eol_page_id"].cast(pl.String)[0], full_name, True
129
 
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  # If no exact matches, return any entry with the specified rank
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  df_filtered = df.sample()
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  full_name = " ".join(df_filtered.select(RANKS[:rank+1]).row(0)) + " " + " ".join(df_filtered.select(RANKS[rank+1:]).row(0))
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- return df_filtered["file_path"][0], df_filtered["gbif_id"].cast(pl.String)[0], df_filtered["eol_page_id"].cast(pl.String)[0], full_name, False
 
42
  '''
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  logger.info(f"Getting sample for taxon: {pred_taxon} at rank: {rank}")
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  try:
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+ filepath, gbif_taxon_id, eol_page_id, full_name, is_exact = get_sample_data(df, pred_taxon, rank)
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  except Exception as e:
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  logger.error(f"Error retrieving sample data: {e}")
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  return None, f"We encountered the following error trying to retrieve a sample image: {e}."
 
58
  )
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  img_resp = requests.get(img_src)
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  img = Image.open(io.BytesIO(img_resp.content))
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+ if gbif_taxon_id:
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+ gbif_url = GBIF_URL + gbif_taxon_id
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  if eol_page_id:
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  eol_url = EOL_URL + eol_page_id
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  if is_exact:
 
100
  --------
101
  filepath : str
102
  Filepath of selected sample image for predicted taxon.
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+ gbif_taxon_id: str
104
  GBIF page ID associated with predicted taxon for more information.
105
  eol_page_id : str
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  EOL page ID associated with predicted taxon for more information.
 
125
  if exact_df.shape[0] > 0:
126
  df_filtered = exact_df.sample()
127
  full_name = " ".join(df_filtered.select(RANKS[:rank+1]).row(0))
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+ return df_filtered["file_path"][0], df_filtered["gbif_taxon_id"].cast(pl.String)[0], df_filtered["eol_page_id"].cast(pl.String)[0], full_name, True
129
 
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  # If no exact matches, return any entry with the specified rank
131
  df_filtered = df.sample()
132
  full_name = " ".join(df_filtered.select(RANKS[:rank+1]).row(0)) + " " + " ".join(df_filtered.select(RANKS[rank+1:]).row(0))
133
+ return df_filtered["file_path"][0], df_filtered["gbif_taxon_id"].cast(pl.String)[0], df_filtered["eol_page_id"].cast(pl.String)[0], full_name, False