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  • 11-test-fix-tests-to-handle-licensed-data-resources-from-trud-snd-omop
  • 61-feature-add-optional-backwards-mapping-for-consistency-with-older-version
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  • meldb/concepts-processing
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  • 11-test-fix-tests-to-handle-licensed-data-resources-from-trud-snd-omop
  • 61-feature-add-optional-backwards-mapping-for-consistency-with-older-version
  • 61-feature-add-optional-backwards-mapping-for-consistency-with-older-version-2
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with 2876 additions and 2696 deletions
acmc/main.py
View file @ e396067b
......@@ -78,7 +78,13 @@ def _phen_copy(args: argparse.Namespace):
def _phen_diff(args: argparse.Namespace):
"""Handle the `phen diff` command."""
phen.diff(args.phen_dir, args.version, args.old_phen_dir, args.old_version, args.not_check_config)
phen.diff(
args.phen_dir,
args.version,
args.old_phen_dir,
args.old_version,
args.not_check_config,
)
def main():
......@@ -219,13 +225,13 @@ def main():
)
phen_map_parser.add_argument(
"--not-translate",
action='store_true',
action="store_true",
default=False,
help="(Optional) Prevent any phenotype translation using NHS TRUD vocabularies.",
)
phen_map_parser.add_argument(
"--no-metadata",
action='store_true',
action="store_true",
default=False,
help="(Optional) Prevent copying of metadata columns to output.",
)
......@@ -337,7 +343,7 @@ def main():
)
phen_diff_parser.add_argument(
"--not-check-config",
action='store_true',
action="store_true",
default=False,
help="(Optional) Prevent loading and comparing config file, in the case where one does not exist",
)
......
acmc/phen.py
View file @ e396067b
......@@ -143,10 +143,9 @@ CONFIG_SCHEMA = {
"schema": {
"divide_col": {"type": "string"},
"split_col": {"type": "string"},
"codes_col": {"type": "string"}
"codes_col": {"type": "string"},
},
},
},
},
},
......@@ -663,7 +662,10 @@ def _preprocess_source_concepts(
# Translate Df with multiple codes into single code type Series
def translate_codes(
source_df: pd.DataFrame, target_code_type: str, concept_name: str, not_translate:bool
source_df: pd.DataFrame,
target_code_type: str,
concept_name: str,
not_translate: bool,
) -> pd.DataFrame:
"""Translates each source code type the source coding list into a target type and returns all conversions as a concept set"""
......@@ -735,7 +737,8 @@ def _write_code_errors(code_errors: list, code_errors_path: Path):
"SOURCE": err.codes_file,
"CAUSE": err.message,
}
for err in code_errors if err.mask is not None
for err in code_errors
if err.mask is not None
]
)
......@@ -807,7 +810,9 @@ def map(phen_dir: str, target_code_type: str, not_translate:bool, no_metadata:bo
)
if target_code_type is not None:
_map_target_code_type(phen_path, phenotype, target_code_type, not_translate, no_metadata)
_map_target_code_type(
phen_path, phenotype, target_code_type, not_translate, no_metadata
)
else:
for t in phenotype["map"]:
_map_target_code_type(phen_path, phenotype, t, not_translate, no_metadata)
......@@ -815,7 +820,13 @@ def map(phen_dir: str, target_code_type: str, not_translate:bool, no_metadata:bo
_logger.info(f"Phenotype processed successfully")
def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: str, not_translate:bool, no_metadata:bool):
def _map_target_code_type(
phen_path: Path,
phenotype: dict,
target_code_type: str,
not_translate: bool,
no_metadata: bool,
):
_logger.debug(f"Target coding format: {target_code_type}")
concepts_path = phen_path / CONCEPTS_DIR
# Create output dataframe
......@@ -1000,7 +1011,9 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
# Add metadata dict to each row of Df codes
def add_metadata(
codes: pd.DataFrame, metadata: dict, no_metadata:bool,
codes: pd.DataFrame,
metadata: dict,
no_metadata: bool,
) -> pd.DataFrame:
"""Add concept set metadata, stored as a dictionary, to each concept row"""
......@@ -1413,7 +1426,6 @@ def diff_phen(
report += f" - {new_version}\n"
report += f" - {str(new_phen_path.resolve())}\n"
# Convert list of dicts into a dict: {name: file}
report += diff_config(old_config, new_config)
......@@ -1432,7 +1444,13 @@ def diff_phen(
_logger.info(f"Phenotypes diff'd successfully")
def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str, not_check_config:bool):
def diff(
phen_dir: str,
version: str,
old_phen_dir: str,
old_version: str,
not_check_config: bool,
):
# make tmp directory .acmc
timestamp = time.strftime("%Y%m%d_%H%M%S")
temp_dir = Path(f".acmc/diff_{timestamp}")
......@@ -1449,9 +1467,9 @@ def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str, not_c
f"Old phenotype directory does not exist: {str(old_phen_path.resolve())}"
)
t_path = old_phen_path / "config.yml"
with t_path.open("r") as file:
c = yaml.safe_load(file)
# t_path = old_phen_path / "config.yml"
# with t_path.open("r") as file:
# c = yaml.safe_load(file)
try:
# Create the directory
......@@ -1493,10 +1511,11 @@ def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str, not_c
report_filename = f"{version}_{old_version}_diff.md"
report_path = changed_phen_path / report_filename
# diff old with new
diff_phen(changed_path, version, old_path, old_version, report_path, not_check_config)
diff_phen(
changed_path, version, old_path, old_version, report_path, not_check_config
)
finally:
# clean up tmp directory
if temp_dir.exists():
shutil.rmtree(temp_dir)
print(f"Temporary directory removed: {temp_dir}")
docs/api/acmc.html
View file @ e396067b
......@@ -3,14 +3,14 @@
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<title>acmc API documentation</title>
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......@@ -384,7 +384,7 @@
</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a>
</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read3</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">&quot;Read3&quot;</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">&quot;read3.parquet&quot;</span><span class="p">)</span>
</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">&quot;read3&quot;</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">&quot;read3.parquet&quot;</span><span class="p">)</span>
</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a>
</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="p">(</span>
......@@ -423,7 +423,7 @@
</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="sa">f</span><span class="s2">&quot;QA Alphanumeric Dot&quot;</span><span class="p">,</span>
</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;^[a-zA-Z0-9.]+$&quot;</span><span class="p">),</span>
</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a> <span class="p">)</span>
</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a> <span class="p">)</span>
......@@ -438,7 +438,7 @@
</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a> <span class="sa">f</span><span class="s2">&quot;QA In Database&quot;</span><span class="p">,</span>
</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a> <span class="p">)</span>
</span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a> <span class="p">)</span>
......@@ -760,7 +760,7 @@
<section id="SUPPORTED_CODE_TYPES">
<div class="attr variable">
<span class="name">SUPPORTED_CODE_TYPES</span> =
<span class="default_value">{&#39;atc&#39;, &#39;read2&#39;, &#39;read3&#39;, &#39;opcs4&#39;, &#39;snomed&#39;, &#39;icd10&#39;}</span>
<span class="default_value">{&#39;read3&#39;, &#39;read2&#39;, &#39;snomed&#39;, &#39;opcs4&#39;, &#39;icd10&#39;, &#39;atc&#39;}</span>
</div>
......@@ -1268,7 +1268,7 @@
<a class="headerlink" href="#Read3"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Read3-194"><a href="#Read3-194"><span class="linenos">194</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read3</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Read3-195"><a href="#Read3-195"><span class="linenos">195</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Read3-196"><a href="#Read3-196"><span class="linenos">196</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">&quot;Read3&quot;</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">&quot;read3.parquet&quot;</span><span class="p">)</span>
</span><span id="Read3-196"><a href="#Read3-196"><span class="linenos">196</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">&quot;read3&quot;</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">&quot;read3.parquet&quot;</span><span class="p">)</span>
</span><span id="Read3-197"><a href="#Read3-197"><span class="linenos">197</span></a>
</span><span id="Read3-198"><a href="#Read3-198"><span class="linenos">198</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Read3-199"><a href="#Read3-199"><span class="linenos">199</span></a> <span class="p">(</span>
......@@ -1307,7 +1307,7 @@
</span><span id="Read3-232"><a href="#Read3-232"><span class="linenos">232</span></a> <span class="sa">f</span><span class="s2">&quot;QA Alphanumeric Dot&quot;</span><span class="p">,</span>
</span><span id="Read3-233"><a href="#Read3-233"><span class="linenos">233</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read3-234"><a href="#Read3-234"><span class="linenos">234</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read3-235"><a href="#Read3-235"><span class="linenos">235</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;^[a-zA-Z0-9.]+$&quot;</span><span class="p">),</span>
</span><span id="Read3-235"><a href="#Read3-235"><span class="linenos">235</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Read3-236"><a href="#Read3-236"><span class="linenos">236</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read3-237"><a href="#Read3-237"><span class="linenos">237</span></a> <span class="p">)</span>
</span><span id="Read3-238"><a href="#Read3-238"><span class="linenos">238</span></a> <span class="p">)</span>
......@@ -1322,7 +1322,7 @@
</span><span id="Read3-247"><a href="#Read3-247"><span class="linenos">247</span></a> <span class="sa">f</span><span class="s2">&quot;QA In Database&quot;</span><span class="p">,</span>
</span><span id="Read3-248"><a href="#Read3-248"><span class="linenos">248</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read3-249"><a href="#Read3-249"><span class="linenos">249</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read3-250"><a href="#Read3-250"><span class="linenos">250</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Read3-250"><a href="#Read3-250"><span class="linenos">250</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Read3-251"><a href="#Read3-251"><span class="linenos">251</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read3-252"><a href="#Read3-252"><span class="linenos">252</span></a> <span class="p">)</span>
</span><span id="Read3-253"><a href="#Read3-253"><span class="linenos">253</span></a> <span class="p">)</span>
......
docs/api/acmc/phen.html
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docs/api/acmc/trud.html
View file @ e396067b
......@@ -3,14 +3,14 @@
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<title>acmc.trud API documentation</title>
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var(--accent2);}</style>
<style>/*! custom.css */</style></head>
<body>
<nav class="pdoc">
......
docs/api/search.js
View file @ e396067b
Source diff could not be displayed: it is too large. Options to address this: view the blob.
tests/test_acmc.py
View file @ e396067b
......@@ -58,6 +58,7 @@ def test_phen_init_local_specified(tmp_dir, monkeypatch, caplog):
def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
print(f"Temporary directory: {tmp_dir}") # Prints path for debugging
# init phenotype in temp directory
with caplog.at_level(logging.DEBUG):
phen_path = tmp_dir / "phen"
phen_path = phen_path.resolve()
......@@ -69,9 +70,8 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
main.main()
assert "Phenotype initialised successfully" in caplog.text
# validate phenotype and copy examples across
with caplog.at_level(logging.DEBUG):
# validate phenotype
# copy examples across
shutil.rmtree(phen_path / phen.CONCEPTS_DIR)
ex_path = Path("./examples").resolve()
for item in ex_path.iterdir():
......@@ -91,7 +91,7 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
main.main()
assert "Phenotype validated successfully" in caplog.text
# map phenotype
# map phenotypes at read2 and read3
for code_type in ["read2", "read3"]:
with caplog.at_level(logging.DEBUG):
monkeypatch.setattr(
......@@ -130,7 +130,6 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
# diff phenotype
with caplog.at_level(logging.DEBUG):
old_path = tmp_dir / "0.0.1"
monkeypatch.setattr(
sys,
"argv",
......@@ -140,6 +139,8 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
"diff",
"-d",
str(phen_path.resolve()),
"-od",
str(phen_path.resolve()),
"-ov",
"0.0.1",
],
......