diff options
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 4 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 4 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes-raw-files.html | 22 |
3 files changed, 28 insertions, 2 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 699c291..5c89ca0 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -209,12 +209,12 @@ def qc_phenocovar_file( (f"Record {_lc} in file {filepath.name} has a different " "number of columns than the number of headings"))),) _line = dict(zip(_headings, line)) - if not bool(_line["description"]): + if not bool(_line.get("description")): _errs = _errs + ( save_error(InvalidValue(filepath.name, _line[_headings[0]], "description", - _line["description"], + _line.get("description"), "The description is not provided!")),) rconn.hset(file_fqkey(fqkey, "metadata", filepath), diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 6bc7471..f4a302a 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -366,6 +366,7 @@ def process_phenotypes_rqtl2_bundle(error_uri): def process_phenotypes_individual_files(error_uri): """Process the uploaded individual files.""" form = request.form + _transposed = (form.get("file-transposed") or "off") == "on" cdata = { "sep": form["file-separator"], "comment.char": form["file-comment-character"], @@ -400,6 +401,9 @@ def process_phenotypes_individual_files(error_uri): arcname=filepath.name) cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name] + if rqtlkey not in ("phenocovar",): + cdata[f"{rqtlkey}_transposed"] = _transposed + zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2)) return bundlepath diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html index 697c7ad..5c6aaab 100644 --- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -103,6 +103,28 @@ <a href="#docs-file-na" title="Documentation for no-value fields"> documentation for more information</a>.</span> </div> + + <div class="form-check form-group"> + <div class=""> + <input id="chk-file-transposed" + name="file-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-file-transposed" class="form-check-label"> + File transposed</label> + </div> + <span class="form-text text-muted"> + We expect the data in the file as a matrix of + <strong>samples × phenotypes</strong>, but it could be your file is + transposed, (i.e. it is a matrix of + “<em>phenotypes × samples</em>”, rather than the expected + form). + <br /> + If that is the case for your files, mark your files as trasposed by + ensuring that this checkbox is checked. + </span> + </div> </fieldset> <fieldset id="fldset-data-files"> |