diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/__init__.py | 6 | ||||
| -rw-r--r-- | uploader/phenotypes/models.py | 7 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 34 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/bulk-edit-upload.html | 61 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 42 |
5 files changed, 137 insertions, 13 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py index cae531b..4f3538c 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -6,6 +6,7 @@ from pathlib import Path from flask import Flask, request from flask_session import Session +from cachelib import FileSystemCache from uploader.oauth2.client import user_logged_in, authserver_authorise_uri @@ -69,6 +70,11 @@ def create_app(): # Silently ignore secrets if the file does not exist. app.config.from_pyfile(secretsfile) + app.config["SESSION_CACHELIB"] = FileSystemCache( + cache_dir=Path(app.config["SESSION_FILESYSTEM_CACHE_PATH"]).absolute(), + threshold=int(app.config["SESSION_FILESYSTEM_CACHE_THRESHOLD"]), + default_timeout=int(app.config["SESSION_FILESYSTEM_CACHE_TIMEOUT"])) + setup_logging(app) # setup jinja2 symbols diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index ce7720c..4a229e6 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -262,8 +262,11 @@ def phenotypes_data_by_ids( ) -> tuple[dict, ...]: """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping.""" _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref)) - _query = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " - "FROM Phenotype AS pheno " + _query = ("SELECT " + "pub.PubMed_ID, pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " + "FROM Publication AS pub " + "RIGHT JOIN PublishXRef AS pxr0 ON pub.Id=pxr0.PublicationId " + "INNER JOIN Phenotype AS pheno ON pxr0.PhenotypeId=pheno.id " "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " "INNER JOIN Strain AS str ON pd.StrainId=str.Id " diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 407493c..a50a8e7 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -866,16 +866,17 @@ def process_phenotype_data_for_download(pheno: dict) -> dict: } } + @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" - "/<int:dataset_id>/download", + "/<int:dataset_id>/edit-download", methods=["POST"]) @require_login @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", redirect_uri="species.populations.phenotypes.list_datasets") -def download_phenotype_data(# pylint: disable=[unused-argument] +def edit_download_phenotype_data(# pylint: disable=[unused-argument] species: dict, population: dict, dataset: dict, @@ -919,7 +920,8 @@ def download_phenotype_data(# pylint: disable=[unused-argument] "Pre_publication_abbreviation", "Pre_publication_description", "Original_description", - "Post_publication_abbreviation" + "Post_publication_abbreviation", + "PubMed_ID" ] + samples_list, dialect="excel-tab") writer.writeheader() @@ -931,3 +933,29 @@ def download_phenotype_data(# pylint: disable=[unused-argument] mimetype="text/csv", as_attachment=True, download_name=secure_filename(f"{dataset['Name']}_data")) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/edit-upload", + methods=["GET", "POST"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def edit_upload_phenotype_data(# pylint: disable=[unused-argument] + species: dict, + population: dict, + dataset: dict, + **kwargs +): + if request.method == "GET": + return render_template( + "phenotypes/bulk-edit-upload.html", + species=species, + population=population, + dataset=dataset, + activelink="edit-phenotype") + + return "NOT Implemented: Would do actual edit." diff --git a/uploader/templates/phenotypes/bulk-edit-upload.html b/uploader/templates/phenotypes/bulk-edit-upload.html new file mode 100644 index 0000000..926bcf5 --- /dev/null +++ b/uploader/templates/phenotypes/bulk-edit-upload.html @@ -0,0 +1,61 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View</a> +</li> +{%endblock%} + +{%block contents%} +<div class="row"> + <p>Upload the edited file you downloaded and edited.</p> +</div> + +<div class="row"> + <form id="frm-bulk-edit-upload" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_upload_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + enctype="multipart/form-data"> + + <div class="form-group row"> + <label for="file-upload-bulk-edit-upload" + class="form-label col-form-label col-sm-2"> + Edited File</label> + <div class="col-sm-10"> + <input id="file-upload-bulk-edit-upload" + name="file_upload_bulk_edit_upload" + class="form-control" + type="file" + required="required" /> + </div> + </div> + + <input type="submit" class="btn btn-primary" + value="upload to edit" /> + + </form> +</div> +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index fa1044b..21563d6 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -147,6 +147,8 @@ }, { text: "Bulk Edit (Download Data)", + className: "btn btn-info btn-bulk-edit", + titleAttr: "Click to download data for editing.", action: (event, dt, node, config) => { var phenoids = []; var selected = dt.rows({selected: true, page: "all"}).data(); @@ -160,10 +162,23 @@ alert("No record selected. Nothing to do!"); return false; } + + $(".btn-bulk-edit").prop("disabled", true); + $(".btn-bulk-edit").addClass("d-none"); + var spinner = $( + "<div id='bulk-edit-spinner' class='spinner-grow text-info'>"); + spinner_content = $( + "<span class='visually-hidden'>"); + spinner_content.html( + "Downloading data …"); + spinner.append(spinner_content) + $(".btn-bulk-edit").parent().append( + spinner); + $.ajax( (`/species/${species_id}/populations/` + `${population_id}/phenotypes/datasets/` + - `${dataset_id}/download`), + `${dataset_id}/edit-download`), { method: "POST", data: JSON.stringify(phenoids), @@ -185,19 +200,30 @@ console.log("Experienced an error: ", textStatus); console.log("The ERROR: ", errorThrown); }, + complete: (jqXHR, textStatus) => { + $("#bulk-edit-spinner").remove(); + $(".btn-bulk-edit").removeClass( + "d-none"); + $(".btn-bulk-edit").prop( + "disabled", false); + }, contentType: "application/json" }); - }, - className: "btn btn-info", - titleAttr: "Click to download data for editing." + } }, { text: "Bulk Edit (Upload Data)", + className: "btn btn-info btn-bulk-edit", + titleAttr: "Click to upload edited data you got by clicking the `Bulk Edit (Download Data)` button.", action: (event, dt, node, config) => { - alert("Not implemented yet!") - }, - className: "btn btn-info", - titleAttr: "Click to upload edited data you got by clicking the `Bulk Edit (Download Data)` button." + window.location.assign( + `${window.location.protocol}//` + + `${window.location.host}` + + `/species/${species_id}` + + `/populations/${population_id}` + + `/phenotypes/datasets/${dataset_id}` + + `/edit-upload`) + } } ] }, |