diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/edit_phenotype.html | 5 |
2 files changed, 22 insertions, 2 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 49205b76..30acf4d4 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -28,6 +28,8 @@ from gn3.authentication import AdminRole from gn3.authentication import get_highest_user_access_role from gn3.csvcmp import create_dirs_if_not_exists from gn3.csvcmp import csv_diff +from gn3.csvcmp import extract_invalid_csv_headers +from gn3.csvcmp import get_allowable_sampledata_headers from gn3.csvcmp import remove_insignificant_edits from gn3.db import diff_from_dict from gn3.db import fetchall @@ -40,10 +42,10 @@ from gn3.db.phenotypes import Probeset from gn3.db.phenotypes import Publication from gn3.db.phenotypes import PublishXRef from gn3.db.phenotypes import probeset_mapping -from gn3.db.sample_data import get_trait_csv_sample_data -from gn3.db.sample_data import update_sample_data from gn3.db.sample_data import delete_sample_data +from gn3.db.sample_data import get_trait_csv_sample_data from gn3.db.sample_data import insert_sample_data +from gn3.db.sample_data import update_sample_data metadata_edit = Blueprint('metadata_edit', __name__) @@ -187,6 +189,7 @@ def display_phenotype_metadata(dataset_id: str, name: str): publication=_d.get("publication"), dataset_id=dataset_id, resource_id=request.args.get("resource-id"), + headers=get_allowable_sampledata_headers(conn), version=os.environ.get("GN_VERSION"), ) @@ -239,6 +242,18 @@ def update_phenotype(dataset_id: str, name: str): delta_csv=(delta_csv := file_.read().decode()), tmp_dir=TMPDIR), epsilon=0.001) + headers = get_allowable_sampledata_headers(conn) + invalid_headers = extract_invalid_csv_headers( + allowed_headers=headers, + csv_text=delta_csv) + if invalid_headers: + flash("You have invalid headers: " + f"""{', '.join(invalid_headers)}. Valid headers """ + f"""are: {', '.join(headers)}""", + "warning") + return redirect( + f"/datasets/{dataset_id}/traits/{name}" + f"?resource-id={request.args.get('resource-id')}") # Edge case where the csv file has not been edited! if not any(diff_data.values()): flash("You have not modified the csv file you downloaded!", diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html index 76d15043..5458247e 100644 --- a/wqflask/wqflask/templates/edit_phenotype.html +++ b/wqflask/wqflask/templates/edit_phenotype.html @@ -224,6 +224,11 @@ <div class="form-group"> <input type = "file" class="col-sm-4 control-label" name = "file" /> </div> + <div class="col-xs-6"> + <p> + Note: Current allowable sample headers are: {{ ', '.join(headers) }} + </p> + </div> <div class="controls center-block" style="width: max-content;"> <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/> <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/> |