Add folder mapping to downloading and data reading task in dodo.py

code/UNFCCC_CRF_reader/UNFCCC_CRF_reader_prod.py

@@ -211,6 +211,7 @@ def read_crf_for_country_datalad(
         country: str,
         submission_year: int,
         submission_date: Optional[str]=None,
+        re_read: Optional[bool]=True
 ) -> None:
     """
     Wrapper around read_crf_for_country which takes care of selecting input
@@ -243,9 +244,12 @@ def read_crf_for_country_datalad(
     print(f"Run the script using datalad run via the python api")
     script = code_path / "UNFCCC_CRF_reader" / "read_UNFCCC_CRF_submission.py"
 
+    cmd = f"./venv/bin/python3 {script.as_posix()} --country={country} "\
+          f"--submission_year={submission_year} --submission_date={submission_date}"
+    if re_read:
+        cmd = cmd + f" --re_read"
     datalad.api.run(
-        cmd=f"./venv/bin/python3 {script.as_posix()} --country={country} "
+        cmd=cmd,
-            f"--submission_year={submission_year} --submission_date={submission_date}",
         dataset=root_path,
         message=f"Read data for {country}, CRF{submission_year}, {submission_date}.",
         inputs=country_info["input"],
@@ -333,7 +337,6 @@ def read_new_crf_for_year_datalad(
         re_read: Optional[bool] = False,
 ) -> None:
     """
-    TODO: this is just a copy of the one country function
     Wrapper around read_crf_for_year_datalad which takes care of selecting input
     and output files and using datalad run to trigger the data reading
 

dodo.py

@@ -33,6 +33,7 @@ def task_map_folders():
         'setup': ['setup_venv'],
     }
 
+
 # Tasks for getting submissions and downloading them
 def task_update_bur():
     """ Update list of BUR submissions """
@@ -54,7 +55,10 @@ def task_download_bur():
         # before download
         'actions': ['datalad run -m "Download BUR submissions" '
                     '-i downloaded_data/UNFCCC/submissions-bur.csv '
-                    './venv/bin/python code/UNFCCC_downloader/download_non-annexI.py --category=BUR.py'],
+                    './venv/bin/python code/UNFCCC_downloader/download_non-annexI.py --category=BUR.py',
+                    f"./venv/bin/python code/UNFCCC_reader/folder_mapping.py "
+                    f"--folder=downloaded_data/UNFCCC"
+                    ],
         'verbosity': 2,
         'setup': ['setup_venv'],
     }
@@ -80,7 +84,10 @@ def task_download_nc():
         # before download
         'actions': ['datalad run -m "Download NC submissions" '
                     '-i downloaded_data/UNFCCC/submissions-nc.csv '
-                    './venv/bin/python code/UNFCCC_downloader/download_non-annexI.py --category=NC'],
+                    './venv/bin/python code/UNFCCC_downloader/download_non-annexI.py --category=NC',
+                    f"./venv/bin/python code/UNFCCC_reader/folder_mapping.py "
+                    f"--folder=downloaded_data/UNFCCC"
+                    ],
         'verbosity': 2,
         'setup': ['setup_venv'],
     }
@@ -118,7 +125,10 @@ def task_download_annexi():
                     f"{update_aI_config['category']}{update_aI_config['year']}' "
                     f"-i downloaded_data/UNFCCC/submissions-annexI_{update_aI_config['year']}.csv "
                     f"./venv/bin/python code/UNFCCC_downloader/download_annexI.py "
-                    f"--category={update_aI_config['category']} --year={update_aI_config['year']}"],
+                    f"--category={update_aI_config['category']} --year={update_aI_config['year']}",
+                    f"./venv/bin/python code/UNFCCC_reader/folder_mapping.py "
+                    f"--folder=downloaded_data/UNFCCC"
+                    ],
         'verbosity': 2,
         'setup': ['setup_venv'],
     }
@@ -128,7 +138,10 @@ def task_download_ndc():
     """ Download NDC submissions """
     return {
         'actions': ['datalad run -m "Download NDC submissions" '
-                    './venv/bin/python code/UNFCCC_downloader/download_ndc.py'],
+                    './venv/bin/python code/UNFCCC_downloader/download_ndc.py',
+                    f"./venv/bin/python code/UNFCCC_reader/folder_mapping.py "
+                    f"--folder=downloaded_data/UNFCCC"
+                    ],
         'verbosity': 2,
         'setup': ['setup_venv'],
     }
@@ -141,6 +154,8 @@ read_config = {
     "submission": get_var('submission', None),
 }
 
+
+# TODO: make individual task for non-UNFCCC submissions
 def task_read_unfccc_submission():
     """ Read submission for a country (if code exists) (not for CRF)"""
     return {
@@ -170,7 +185,10 @@ def task_read_unfccc_crf_submission():
         'actions': [f"./venv/bin/python code/UNFCCC_CRF_reader/read_UNFCCC_CRF_submission_datalad.py "
                     f"--country={read_config_crf['country']} "
                     f"--submission_year={read_config_crf['submission_year']} "
-                    f"--submission_date={read_config_crf['submission_date']} "],
+                    f"--submission_date={read_config_crf['submission_date']} ",
+                    f"./venv/bin/python code/UNFCCC_reader/folder_mapping.py "
+                    f"--folder=extracted_data/UNFCCC"
+                    ],
         'verbosity': 2,
         'setup': ['setup_venv'],
     }
@@ -180,7 +198,10 @@ def task_read_new_unfccc_crf_for_year():
     """ Read CRF submission for all countries for given submission year. by default only reads
     data not present yet. Only reads the latest updated submission for each country."""
     actions = [f"./venv/bin/python code/UNFCCC_CRF_reader/read_new_UNFCCC_CRF_for_year_datalad.py "
-               f"--submission_year={read_config_crf['submission_year']} "]
+               f"--submission_year={read_config_crf['submission_year']} ",
+               f"./venv/bin/python code/UNFCCC_reader/folder_mapping.py "
+               f"--folder=extracted_data/UNFCCC"
+               ]
     if read_config_crf["countries"] is not None:
             actions[0] = actions[0] + f"--countries={read_config_crf['countries']} "
     if read_config_crf["re_read"]: