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| -rw-r--r-- | uploader/templates/genotypes/add-genotypes-records-base.html | 39 | ||||
| -rw-r--r-- | uploader/templates/genotypes/add-genotypes-records-csv.html | 146 | ||||
| -rw-r--r-- | uploader/templates/macro-csv-fields.html | 102 |
3 files changed, 287 insertions, 0 deletions
diff --git a/uploader/templates/genotypes/add-genotypes-records-base.html b/uploader/templates/genotypes/add-genotypes-records-base.html new file mode 100644 index 0000000..bf3812f --- /dev/null +++ b/uploader/templates/genotypes/add-genotypes-records-base.html @@ -0,0 +1,39 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + +{%block contents%} + +<div class="row"> + <form id="frm-add-genotypes-records" + method="POST" + enctype="multipart/form-data" + action="{{url_for( + 'species.populations.genotypes.add_genotype_records', + species_id=species.SpeciesId, population_id=population.Id, + dataset_id=dataset.Id)}}" + data-resumable-target="{{url_for('files.resumable_upload_post')}}"> + <legend>Add New Genotype Records</legend> + + {%block frm_add_genotypes_records_elements%}{%endblock%} + + <div class="form-group"> + <input type="submit" + value="upload genotypes" + class="btn btn-primary" /> + </div> + </form> +</div> + +<div class="row"> + <h2 class="heading" id="page-documentation">Help</h2> + {%block page_documentation%}{%endblock%} +</div> +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/genotypes/add-genotypes-records-csv.html b/uploader/templates/genotypes/add-genotypes-records-csv.html new file mode 100644 index 0000000..58dbe81 --- /dev/null +++ b/uploader/templates/genotypes/add-genotypes-records-csv.html @@ -0,0 +1,146 @@ +{%extends "genotypes/add-genotypes-records-base.html"%} +{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} +{%from "macro-csv-fields.html" import display_csv_fields, display_csv_fields_documentation%} +{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} + +{%block frm_add_genotypes_records_elements%} +<div class="form-text help-block"> + <p>You can add new genotype records here.</p> +</div> + +{{display_csv_fields()}} + +<div class="form-group"> + <div class="non-resumable-elements"> + <label for="finput-genotypes-records-file" class="form-label"> + genotypes records</label> + <input id="finput-genotypes-records-file" + name="genotypes-records-file" + class="form-control" + type="file" + data-preview-table="tbl-preview-geno-records" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the genotypes records, + <a href="#docs-file-genotypes-records-csv" + title="Documentation of the genotypes records file format."> + the documentation for the expected format of the file</a>.</span> + </div> + {{display_resumable_elements( + "resumable-genotypes-records-file", + "Genotypes records", + '<p>Drag and drop the CSV file here, that contains the genotype records you + want to add.</p> + + <p>Please see the + <a href="#docs-file-genotypes-records" + title="Documentation of the genotypes records data file format."> + "Genotypes records" documentation</a> section below for more + information on the expected format of the file provided here.</p>')}} + {{display_preview_table("tbl-preview-geno-records", "genotypes records")}} +</div> + +<div class=""> + <h4 class="subheading">Genotype Encoding</h4> + <div class="form-text help-block"> + <p>The symbols in your genotype file need to be mapped to known values to + enable mapping.</p> + </div> + + <div class="form-group"> + <div class="row mb-3"> + <label for="txt-geno-encoding-mat" + class="col-form-label col-sm-2">Maternal</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + maxlength="3" + id="txt-geno-encoding-mat" + name="geno_encoding_mat" + class="form-control" /> + <div class="input-group-append"> + <span class="input-group-text">Value = -1</span> + </div> + </div> + </div> + <span class="form-text text-muted col-sm-12"> + Enter the symbol in your file that represents the allele inherited from + the mother. This allele will be mapped to the value -1.</span> + </div> + </div> + + <div class="form-group"> + <div class="row mb-3"> + <label for="txt-geno-encoding-pat" + class="col-form-label col-sm-2">Paternal</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + maxlength="3" + id="txt-geno-encoding-pat" + name="geno_encoding_pat" + class="form-control" /> + <div class="input-group-append"> + <span class="input-group-text">Value = 1</span> + </div> + </div> + </div> + <span class="form-text text-muted"> + Enter the symbol in your file that represents the allele inherited from + the father. This allele will be mapped to the value 1.</span> + </div> + </div> + + <div class="form-group"> + <div class="row mb-3"> + <label for="txt-geno-encoding-het" + class="col-form-label col-sm-2">Heterozygous (value = 0)</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + maxlength="3" + id="txt-geno-encoding-het" + name="geno_encoding_het" + class="form-control" /> + <div class="input-group-append"> + <span class="input-group-text">Value = 0</span> + </div> + </div> + </div> + <span class="form-text text-muted"> + Enter the symbol in your file that represents the allele inherited from + both parents. This allele will be mapped to the value 0.</span> + </div> + </div> +</div> +{%endblock%} + +{%block page_documentation%} +{{super()}} + +<h3 class="sub-heading">CSV file metadata</h3> +{{display_csv_fields_documentation()}} +{%endblock%} + +{%block javascript%} +{{super()}} +<script src="{{url_for('base.node_modules', + filename='resumablejs/resumable.js')}}"></script> +<script src="/static/js/files.js"></script> + +<script type="text/javascript"> + $(function(evt) { + + var preview_tables_to_elements_map = { + "#tbl-preview-geno-records": "#finput-genotypes-records-file", + }; + + makeResumableObject( + form_id="frm-add-genotypes-records", + file_input_id="finput-genotypes-records-file", + resumable_element_id="resumable-genotypes-records-file", + preview_table_id="tbl-preview-geno-records", + filetypes=["csv", "tsv", "txt", "geno"]); + }); +</script> +{%endblock%} diff --git a/uploader/templates/macro-csv-fields.html b/uploader/templates/macro-csv-fields.html new file mode 100644 index 0000000..d4b0f57 --- /dev/null +++ b/uploader/templates/macro-csv-fields.html @@ -0,0 +1,102 @@ +{%macro display_csv_fields()%} +<div class="form-group"> + <label for="txt-file-separator" class="form-label">File Separator</label> + <div class="input-group"> + <input id="txt-file-separator" + name="file-separator" + type="text" + value="	" + class="form-control" + maxlength="1" /> + <span class="input-group-btn"> + <button id="btn-reset-file-separator" class="btn btn-info">Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + Provide the character that separates the fields in your file(s). It should + be the same character for all files (if more than one is provided).<br /> + A tab character will be assumed if you leave this field blank. See + <a href="#docs-file-separator" + title="Documentation for file-separator characters"> + documentation for more information</a>. + </span> +</div> + +<div class="form-group"> + <label for="txt-file-comment-character" class="form-label">File Comment-Characters</label> + <div class="input-group"> + <input id="txt-file-comment-character" + name="file-comment-character" + type="text" + value="#" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-reset-file-comment-character" class="btn btn-info"> + Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + This specifies that lines that begin with the character(s) provided will be + considered comment lines and ignored in their entirety. See + <a href="#docs-file-comment-character" + title="Documentation for comment characters"> + documentation for more information</a>. + </span> +</div> + +<div class="form-group"> + <label for="txt-file-na" class="form-label">File "No-Value" Indicators</label> + <div class="input-group"> + <input id="txt-file-na" + name="file-na" + type="text" + value="- NA N/A" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + This specifies strings in your file indicate that there is no value for a + particular cell (a cell is where a column and row intersect). Provide a + space-separated list of strings if you have more than one way of + indicating no values. See + <a href="#docs-file-na" title="Documentation for no-value fields"> + documentation for more information</a>.</span> +</div> +{%endmacro%} + + +{%macro display_csv_fields_documentation()%} +<dl> + <dt id="docs-file-separator">File separator</dt> + <dd>The files you provide should be character-separated value (CSV) files. + We need to know what character you used to separate the values in your + file. Some common ones are the Tab character, the comma, etc.<br /> + Providing that information makes it possible for the system to parse and + process your files correctly.<br> + <strong>NOTE:</strong> All the files you upload MUST use the same + separator.</dd> + + <dt id="docs-file-comment-character">Comment characters</dt> + <dd>We support use of comment lines in your files. We only support one type + of comment style, the <em>line comment</em>.<br /> + This mean the comment begins at the start of the line, and the end of that + line indicates the end of that comment. If you have a really long comment, + then you need to break it across multiple lines, marking each line a + comment line.<br /> + The "comment character" is the character at the start of the line that + indicates that the line is a line comment.<br /> + You can provide more than one comment character, separated by spaces.</dd> + + <dt id="docs-file-na">No-Value indicator(s)</dt> + <dd>Data in the real world is messy, and in some cases, entirely absent. You + need to indicate, in your files, that a particular field did not have a + value, and once you do that, you then need to let the system know how you + mark such fields. Common ways of indicating "empty values" are, leaving + the field blank, using a character such as '-', or using strings like + "NA", "N/A", "NULL", etc.<br /> + Providing this information will help with parsing and processing such + no-value fields the correct way.</dd> +</dl> +{%endmacro%} |