diff options
| -rw-r--r-- | wqflask/wqflask/oauth2/data.py | 36 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list.html | 200 |
2 files changed, 149 insertions, 87 deletions
diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py index 8005a2a0..0cd110f6 100644 --- a/wqflask/wqflask/oauth2/data.py +++ b/wqflask/wqflask/oauth2/data.py @@ -23,15 +23,47 @@ def list_data(): **{key:val for key,val in kwargs.items() if key not in ("groups", "data_items", "user_privileges")}) + def __process_menus__(mns): + return { + species_id: { + "display_name": display_name, + "family": family, + "groups": { + group_id: { + "group_name": group_name, + "family": family, + "types": { + type_id: { + "menu_value": type_menu_value, + "menu_heading": type_menu_heading, + "datasets": tuple( + dict(zip(("accession_id", "dataset_id", + "dataset_fullname"), + dataset_row)) + for dataset_row in mns["datasets"][ + species_id][group_id][type_id]) + } + for type_id, type_menu_value, type_menu_heading + in mns["types"][species_id][group_id] + } + } + for group_id, group_name, family in mns["groups"][species_id] + } + } + for species_id, display_name, family in mns["species"]} + groups = oauth2_get("oauth2/group/list").either( lambda err: {"groups_error": process_error(err)}, lambda grp: {"groups": grp}) roles = oauth2_get("oauth2/user/roles").either( lambda err: {"roles_error": process_error(err)}, lambda roles: {"roles": roles}) + menus = oauth2_get("menu/generate/json").either( + lambda err: {"menus_error": process_error(err)}, + lambda mns: {"menus": __process_menus__(mns)}) if request.method == "GET": - return __render__(**{**groups, **roles}) + return __render__(**{**groups, **roles, **menus}) dataset_type = request.form["dataset_type"] offset = int(request.form.get("offset", 0)) + ( @@ -47,7 +79,7 @@ def list_data(): lambda err: {"data_items_error": process_error(err)}, lambda data: {"data_items": data}) return __render__(**{ - **groups, **roles, **data_items, "dataset_type": dataset_type, + **groups, **roles, **menus, **data_items, "dataset_type": dataset_type, "offset": offset }) diff --git a/wqflask/wqflask/templates/oauth2/data-list.html b/wqflask/wqflask/templates/oauth2/data-list.html index 6d0ae427..019e2346 100644 --- a/wqflask/wqflask/templates/oauth2/data-list.html +++ b/wqflask/wqflask/templates/oauth2/data-list.html @@ -12,23 +12,46 @@ <div class="row"> <form method="POST" action="{{url_for('oauth2.data.list_data')}}"> <legend>Dataset Type</legend> + <input type="hidden" name="offset" value="0" /> + <input type="hidden" name="menus" value="{{menus | tojson}}" /> + <div class="form-group"> + <label for="select-menu">Dataset</label> + <select id="select-menu" name="dataset"> + {%for species_id, species_data in menus.items()%} + <optgroup label="{{species_data.display_name}}"> + {%for group_id, group_data in species_data["groups"].items()%} + <optgroup label=" {{group_data.group_name}}"> + {%for type_id, type_data in group_data["types"].items()%} + <optgroup label="{{type_data.menu_heading}}"> + {%for dataset in type_data["datasets"]%} + <option value="{{dataset.dataset_id}}"> + {{dataset.dataset_fullname}} + </option> + {%endfor%} + </optgroup> + {%endfor%} + </optgroup> + {%endfor%} + </optgroup> + {%endfor%} + </select> + </div> <div class="form-group"> - <input type="hidden" name="offset" value="0" /> <label for="dataset_type" class="form-label">Dataset Type</label> <select name="dataset_type" required="required"> <option value="">Select dataset type</option> <option value="mrna" {%if dataset_type=="mrna"%} - selected="selected" + selected="selected" {%endif%}>mRNA Assay Datasets</option> - <option value="genotype" - {%if dataset_type=="genotype"%} - selected="selected" - {%endif%}>Genotype Datasets</option> - <option value="phenotype" - {%if dataset_type=="phenotype"%} - selected="selected" - {%endif%}>Phenotype/Publish Datasets</option> + <option value="genotype" + {%if dataset_type=="genotype"%} + selected="selected" + {%endif%}>Genotype Datasets</option> + <option value="phenotype" + {%if dataset_type=="phenotype"%} + selected="selected" + {%endif%}>Phenotype/Publish Datasets</option> </select> </div> <input type="submit" value="Fetch Unlinked Data" class="btn btn-primary" /> @@ -39,87 +62,94 @@ {%if data_items_error is defined%} {{display_error("Data Error", data_items_error)}} {%else%} - <div class="row"> - <table class="table"> - <caption>Link Data to Group</caption> + <div class="row"> + <form method="POST" action="{{url_for('oauth2.data.link_data')}}"> + <legend>Link Data to Group</legend> + <input type="hidden" name="offset" value="{{offset or 0}}" /> + <input type="hidden" name="dataset_type" value="{{dataset_type}}" /> - <thead> - <tr> - {%if dataset_type == "phenotype"%} - <th>Trait ID</th> - <th>Data Group</th> - {%endif%} - <th>Dataset Name</th> - <th>Dataset Full Name</th> - <th>Group</th> - <th>Link</th> - </tr> - </thead> + <div class="form-group"> + <label for="select-group-id">Group</label> + <select name="group_id" required="required"> + <option value="">Select group</option> + {%for group in groups%} + <option value="{{group.group_id}}">{{group.group_name}}</option> + {%endfor%} + </select> + </div> - <tbody> - {%for data_item in data_items%} - <tr> - <form method="POST" action="{{url_for('oauth2.data.link_data')}}"> - <input type="hidden" name="offset" value="{{offset or 0}}" /> - <input type="hidden" name="dataset_id" value="{{data_item.Id}}" /> - <input type="hidden" name="dataset_type" value="{{dataset_type}}" /> - {%if dataset_type == "phenotype"%} - <td> - <a href="/show_trait?trait_id={{data_item.Id}}&dataset={{data_item.dataset_name}}" - title="Trait Page"> - {{data_item.Id}} - </a> - </td> - <td>{{data_item.InbredSetName}}</td> - {%endif%} - <td> - <a href="https://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{data_item.accession_id}}&InfoPageName={{data_item.dataset_name}}" - title="Link to information on dataset '{{data_item.dataset_fullname}}'" - target="_blank"> - {{data_item.dataset_name}} - </a> - </td> - <td>{{data_item.dataset_fullname}}</td> - <td> - <select name="group_id" required="required"> - <option value="">Select group</option> - {%for group in groups%} - <option value="{{group.group_id}}">{{group.group_name}}</option> - {%endfor%} - </select> - </td> - <td> - <input type="submit" value="Link" class="btn btn-info" /> - </td> - </form> - </tr> - {%else%} - <tr> - <td colspan="4"> - <span class="glyphicon glyphicon-info-sign text-danger"> - </span> - - <strong class="text-info">No available data to link</strong> - </td> - </tr> - {%endfor%} - </tbody> - </table> + <table class="table"> + <caption>Link Data to Group</caption> - <form method="POST" action="{{url_for('oauth2.data.list_data')}}"> - <input type="hidden" name="dataset_type" value="{{dataset_type}}" /> - <input type="hidden" name="offset" value="{{offset or 0}}" /> - <div class="form-group" style="margin: auto;width: 50%;"> - {%if offset != 0%} - <input type="submit" name="offset_submit" value="Previous" class="btn btn-warning" /> + <thead> + <tr> + <th>Select</th> + {%if dataset_type == "phenotype"%} + <th>Trait ID</th> + <th>Data Group</th> {%endif%} - {%if data_items | length == 100:%} - <input type="submit" name="offset_submit" value="Next" class="btn btn-warning" /> + <th>Dataset Name</th> + <th>Dataset Full Name</th> + <th>Link</th> + </tr> + </thead> + + <tbody> + {%for data_item in data_items%} + <tr> + <td> + <input type="checkbox" value="{{data_item.Id}}" + name="dataset_ids" /> + </td> + {%if dataset_type == "phenotype"%} + <td> + <a href="/show_trait?trait_id={{data_item.Id}}&dataset={{data_item.dataset_name}}" + title="Trait Page"> + {{data_item.Id}} + </a> + </td> + <td>{{data_item.InbredSetName}}</td> {%endif%} - </div> - </form> + <td> + <a href="https://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{data_item.accession_id}}&InfoPageName={{data_item.dataset_name}}" + title="Link to information on dataset '{{data_item.dataset_fullname}}'" + target="_blank"> + {{data_item.dataset_name}} + </a> + </td> + <td>{{data_item.dataset_fullname}}</td> + <td> + <input type="submit" value="Link" class="btn btn-info" /> + </td> + </tr> + {%else%} + <tr> + <td colspan="4"> + <span class="glyphicon glyphicon-info-sign text-danger"> + </span> + + <strong class="text-info">No available data to link</strong> + </td> + </tr> + {%endfor%} + </tbody> + </table> + </form> + + <form method="POST" action="{{url_for('oauth2.data.list_data')}}"> + <input type="hidden" name="dataset_type" value="{{dataset_type}}" /> + <input type="hidden" name="offset" value="{{offset or 0}}" /> + <div class="form-group" style="margin: auto;width: 50%;"> + {%if offset != 0%} + <input type="submit" name="offset_submit" value="Previous" class="btn btn-warning" /> + {%endif%} + {%if data_items | length == 100:%} + <input type="submit" name="offset_submit" value="Next" class="btn btn-warning" /> + {%endif%} </div> - {%endif%} + </form> + </div> + {%endif%} {%endif%} </div> |