diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 115 |
1 files changed, 106 insertions, 9 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index b53b296..d283e47 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -622,6 +622,88 @@ def update_phenotype_metadata(conn, metadata: dict): return cursor.rowcount +def update_phenotype_values(conn, values): + with conn.cursor() as cursor: + cursor.executemany( + "UPDATE PublishData SET value=%(new)s " + "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in values if item["new"] is not None)) + cursor.executemany( + "DELETE FROM PublishData " + "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in values if item["new"] is None)) + return len(values) + return 0 + + +def update_phenotype_se(conn, serrs): + with conn.cursor() as cursor: + cursor.executemany( + "INSERT INTO PublishSE(DataId, StrainId, error) " + "VALUES(%(data_id)s, %(strain_id)s, %(new)s) " + "ON DUPLICATE KEY UPDATE error=VALUES(error)", + tuple(item for item in serrs if item["new"] is not None)) + cursor.executemany( + "DELETE FROM PublishSE " + "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in serrs if item["new"] is None)) + return len(serrs) + return 0 + + +def update_phenotype_n(conn, counts): + with conn.cursor() as cursor: + cursor.executemany( + "INSERT INTO NStrain(DataId, StrainId, count) " + "VALUES(%(data_id)s, %(strain_id)s, %(new)s) " + "ON DUPLICATE KEY UPDATE count=VALUES(count)", + tuple(item for item in counts if item["new"] is not None)) + cursor.executemany( + "DELETE FROM NStrain " + "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in counts if item["new"] is None)) + return len(counts) + + return 0 + + +def update_phenotype_data(conn, data: dict): + """Update the numeric data for a phenotype.""" + def __organise_by_dataid_and_strainid__(acc, current): + _key, dataid, strainid = current[0].split("::") + _keysrc, _keytype = _key.split("-") + newkey = f"{dataid}::{strainid}" + newitem = acc.get(newkey, {}) + newitem[_keysrc] = newitem.get(_keysrc, {}) + newitem[_keysrc][_keytype] = current[1] + return {**acc, newkey: newitem} + + def __separate_items__(acc, row): + key, val = row + return ({**acc[0], key: {**val["value"], "changed?": (not val["value"]["new"] == val["value"]["original"])}}, + {**acc[1], key: {**val["se"] , "changed?": (not val["se"]["new"] == val["se"]["original"])}}, + {**acc[2], key: {**val["n"] , "changed?": (not val["n"]["new"] == val["n"]["original"])}}) + + values, serrs, counts = tuple( + tuple({ + "data_id": row[0].split("::")[0], + "strain_id": row[0].split("::")[1], + "new": row[1]["new"] + } for row in item) + for item in ( + filter(lambda val: val[1]["changed?"], item.items()) + for item in reduce( + __separate_items__, + reduce(__organise_by_dataid_and_strainid__, + data.items(), + {}).items(), + ({}, {}, {})))) + + return (update_phenotype_values(conn, values), + update_phenotype_se(conn, serrs), + update_phenotype_n(conn, counts)) + + @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/phenotype/<int:xref_id>/edit", @@ -706,26 +788,41 @@ def edit_phenotype_data( ).either(__fail__, lambda args: __render__(**args)) ## POST + _change = False match request.form.get("submit", "invalid-action"): case "update basic metadata": - if update_phenotype_metadata(conn, { + _change = update_phenotype_metadata(conn, { + key: value.strip() if bool(value.strip()) else None + for key, value in request.form.items() + if key not in ("submit",) + }) + msg = "Basic metadata was updated successfully." + case "update data": + _update = update_phenotype_data(conn, { key: value.strip() if bool(value.strip()) else None for key, value in request.form.items() if key not in ("submit",) - }): - flash("Basic metadata updated.", "alert-success") - else: - flash("There were no changes to the basic metadata", - "alert-info") - case "update data": - flash("NOT IMPLEMENTED: Would update data", "alert-success") + }) + msg = (f"{_update[0]} value rows, {_update[1]} standard-error " + f"rows and {_update[2]} 'N' rows were updated.") + _change = any(item != 0 for item in _update) case "update publication": flash("NOT IMPLEMENTED: Would update publication data.", "alert-success") case _: flash("Invalid phenotype editing action.", "alert-danger") + if _change: + flash(msg, "alert-success") + return redirect(url_for( + "species.populations.phenotypes.view_phenotype", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"], + xref_id=xref_id)) + + flash("No change was made by the user.", "alert-info") return redirect(url_for( - "species.populations.phenotypes.view_phenotype", + "species.populations.phenotypes.edit_phenotype_data", species_id=species["SpeciesId"], population_id=population["Id"], dataset_id=dataset["Id"], |