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Diffstat (limited to 'uploader/templates')
109 files changed, 8281 insertions, 0 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html new file mode 100644 index 0000000..3c0d0d4 --- /dev/null +++ b/uploader/templates/base.html @@ -0,0 +1,161 @@ +<!DOCTYPE html> +<html lang="en"> + + <head> + + <meta charset="UTF-8" /> + <meta application-name="GeneNetwork Quality-Control Application" /> + <meta name="viewport" content="width=device-width, initial-scale=1.0" /> + {%block extrameta%}{%endblock%} + + <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title> + + <link rel="stylesheet" type="text/css" + href="{{url_for('base.bootstrap', + filename='css/bootstrap.min.css')}}" /> + <link rel="stylesheet" type="text/css" + href="{{url_for('base.datatables', + filename='css/dataTables.bootstrap5.min.css')}}" /> + <link rel="stylesheet" type="text/css" href="/static/css/styles.css" /> + + {%block css%}{%endblock%} + + </head> + + <body> + <header id="header"> + <span id="header-text">GeneNetwork</span> + <nav id="header-nav"> + <ul class="nav justify-content-end"> + <li> + {%if user_logged_in()%} + <a href="{{url_for('oauth2.logout')}}" + title="Log out of the system"> + <span class="glyphicon glyphicon-user"></span> + {{user_email()}} Sign Out</a> + {%else%} + <a href="{{authserver_authorise_uri()}}" + title="Log in to the system">Sign In</a> + {%endif%} + </li> + </ul> + </nav> + </header> + + <aside id="nav-sidebar"> + <ul class="nav flex-column"> + <li {%if activemenu=="home"%}class="activemenu"{%endif%}> + <a href="/" >Home</a></li> + <li {%if activemenu=="publications"%}class="activemenu"{%endif%}> + <a href="{{url_for('publications.index')}}" + title="View and manage publications.">Publications</a></li> + <li {%if activemenu=="species"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.list_species')}}" + title="View and manage species information.">Species</a></li> + <li {%if activemenu=="platforms"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.platforms.index')}}" + title="View and manage species platforms.">Sequencing Platforms</a></li> + <li {%if activemenu=="populations"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.index')}}" + title="View and manage species populations.">Populations</a></li> + <li {%if activemenu=="samples"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.samples.index')}}" + title="Upload population samples.">Samples</a></li> + <li {%if activemenu=="genotypes"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.genotypes.index')}}" + title="Upload Genotype data.">Genotype Data</a></li> + <!-- + TODO: Maybe include menus here for managing studies and dataset or + maybe have the studies/datasets managed under their respective + sections, e.g. "Publish*" studies/datasets under the "Phenotypes" + section, "ProbeSet*" studies/datasets under the "Expression Data" + sections, etc. + --> + <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.phenotypes.index')}}" + title="Upload phenotype data.">Phenotype Data</a></li> + <!-- + <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.expression-data.index')}}" + title="Upload expression data." + class="not-implemented">Expression Data</a></li> + <li {%if activemenu=="individuals"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="Upload individual data.">Individual Data</a></li> + <li {%if activemenu=="rna-seq"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="Upload RNA-Seq data.">RNA-Seq Data</a></li> + <li {%if activemenu=="async-jobs"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="View and manage the backgroud jobs you have running"> + Background Jobs</a></li> + --> + </ul> + </aside> + + <main id="main" class="main"> + + <div id="pagetitle" class="pagetitle"> + <span class="title">Data Upload and Quality Control: {%block pagetitle%}{%endblock%}</span> + <!-- + <nav> + <ol class="breadcrumb"> + <li {%if activelink is not defined or activelink=="home"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('base.index')}}">Home</a> + </li> + {%block lvl1_breadcrumbs%}{%endblock%} + </ol> + </nav> + --> + </div> + + <div id="all-content"> + <div id="main-content"> + {%block contents%}{%endblock%} + </div> + <div id="sidebar-content"> + {%block sidebarcontents%}{%endblock%} + </div> + </div> + </main> + + + <!-- + Core dependencies + --> + <script src="{{url_for('base.jquery', + filename='jquery.min.js')}}"></script> + <script src="{{url_for('base.bootstrap', + filename='js/bootstrap.min.js')}}"></script> + + <!-- + DataTables dependencies + --> + <script type="text/javascript" + src="{{url_for('base.datatables', + filename='js/dataTables.min.js')}}"></script> + <script type="text/javascript" + src="{{url_for('base.datatables_extensions', + filename='scroller/js/dataTables.scroller.min.js')}}"></script> + <script type="text/javascript" + src="{{url_for('base.datatables_extensions', + filename='buttons/js/dataTables.buttons.min.js')}}"></script> + <script type="text/javascript" + src="{{url_for('base.datatables_extensions', + filename='select/js/dataTables.select.min.js')}}"></script> + + <!-- + local dependencies + --> + <script type="text/javascript" src="/static/js/utils.js"></script> + <script type="text/javascript" src="/static/js/datatables.js"></script> + {%block javascript%}{%endblock%} + </body> +</html> diff --git a/uploader/templates/cli-output.html b/uploader/templates/cli-output.html new file mode 100644 index 0000000..64b1a9a --- /dev/null +++ b/uploader/templates/cli-output.html @@ -0,0 +1,8 @@ +{%macro cli_output(job, stream)%} + +<h4 class="subheading">{{stream | upper}} Output</h4> +<div class="cli-output" style="max-height: 10em; overflow: auto;"> + <pre>{{job.get(stream, "")}}</pre> +</div> + +{%endmacro%} diff --git a/uploader/templates/continue_from_create_dataset.html b/uploader/templates/continue_from_create_dataset.html new file mode 100644 index 0000000..03bb49c --- /dev/null +++ b/uploader/templates/continue_from_create_dataset.html @@ -0,0 +1,52 @@ +{%extends "base.html"%} +{%from "dbupdate_hidden_fields.html" import hidden_fields%} + +{%block title%}Create Study{%endblock%} + +{%block css%} +<link rel="stylesheet" href="/static/css/two-column-with-separator.css" /> +{%endblock%} + +{%block contents%} +<h2 class="heading">{{filename}}: create study</h2> + +{%with messages = get_flashed_messages(with_categories=true)%} +{%if messages:%} +<ul> + {%for category, message in messages:%} + <li class="{{category}}">{{message}}</li> + {%endfor%} +</ul> +{%endif%} +{%endwith%} + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.final_confirmation')}}" + id="select-platform-form" data-genechips="{{genechips_data}}" + class="two-col-sep-col1"> + <legend>continue with new dataset</legend> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid, datasetid=datasetid, totallines=totallines)}} + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> + +<div class="row"> + <p class="two-col-sep-separator">OR</p> +</div> + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.select_dataset')}}" + id="select-platform-form" data-genechips="{{genechips_data}}" + class="two-col-sep-col2"> + <legend>Select from existing dataset</legend> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid, datasetid=datasetid, totallines=totallines)}} + + <button type="submit" class="btn btn-primary">go back</button> + </form> +</div> +{%endblock%} diff --git a/uploader/templates/continue_from_create_study.html b/uploader/templates/continue_from_create_study.html new file mode 100644 index 0000000..34e6e5e --- /dev/null +++ b/uploader/templates/continue_from_create_study.html @@ -0,0 +1,52 @@ +{%extends "base.html"%} +{%from "dbupdate_hidden_fields.html" import hidden_fields%} + +{%block title%}Create Study{%endblock%} + +{%block css%} +<link rel="stylesheet" href="/static/css/two-column-with-separator.css" /> +{%endblock%} + +{%block contents%} +<h2 class="heading">{{filename}}: create study</h2> + +{%with messages = get_flashed_messages(with_categories=true)%} +{%if messages:%} +<ul> + {%for category, message in messages:%} + <li class="{{category}}">{{message}}</li> + {%endfor%} +</ul> +{%endif%} +{%endwith%} + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.select_dataset')}}" + id="select-platform-form" data-genechips="{{genechips_data}}" + class="two-col-sep-col1"> + <legend>continue with new study</legend> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid, totallines=totallines)}} + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> + +<div class="row"> + <p class="two-col-sep-separator">OR</p> +</div> + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.select_study')}}" + id="select-platform-form" data-genechips="{{genechips_data}}" + class="two-col-sep-col2"> + <legend>Select from existing study</legend> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid, totallines=totallines)}} + + <button type="submit" class="btn btn-primary">go back</button> + </form> +</div> +{%endblock%} diff --git a/uploader/templates/dbupdate_error.html b/uploader/templates/dbupdate_error.html new file mode 100644 index 0000000..e1359d2 --- /dev/null +++ b/uploader/templates/dbupdate_error.html @@ -0,0 +1,12 @@ +{%extends "base.html"%} + +{%block title%}DB Update Error{%endblock%} + +{%block contents%} +<h1 class="heading">database update error</h2> + +<p class="alert-danger"> + <strong>Database Update Error</strong>: {{error_message}} +</p> + +{%endblock%} diff --git a/uploader/templates/dbupdate_hidden_fields.html b/uploader/templates/dbupdate_hidden_fields.html new file mode 100644 index 0000000..ccbc299 --- /dev/null +++ b/uploader/templates/dbupdate_hidden_fields.html @@ -0,0 +1,29 @@ +{%macro hidden_fields(filename, filetype):%} + +<!-- {{kwargs}}: mostly for accessing the kwargs in macro --> + +<input type="hidden" name="filename" value="{{filename}}" /> +<input type="hidden" name="filetype" value="{{filetype}}" /> +{%if kwargs.get("totallines")%} +<input type="hidden" name="totallines" value="{{kwargs['totallines']}}" /> +{%endif%} +{%if kwargs.get("species"):%} +<input type="hidden" name="species" value="{{kwargs['species']}}" /> +{%endif%} +{%if kwargs.get("genechipid"):%} +<input type="hidden" name="genechipid" value="{{kwargs['genechipid']}}" /> +{%endif%} +{%if kwargs.get("inbredsetid"):%} +<input type="hidden" name="inbredsetid" value="{{kwargs['inbredsetid']}}" /> +{%endif%} +{%if kwargs.get("tissueid"):%} +<input type="hidden" name="tissueid" value="{{kwargs['tissueid']}}" /> +{%endif%} +{%if kwargs.get("studyid"):%} +<input type="hidden" name="studyid" value="{{kwargs['studyid']}}" /> +{%endif%} +{%if kwargs.get("datasetid"):%} +<input type="hidden" name="datasetid" value="{{kwargs['datasetid']}}" /> +{%endif%} + +{%endmacro%} diff --git a/uploader/templates/errors_display.html b/uploader/templates/errors_display.html new file mode 100644 index 0000000..715cfcf --- /dev/null +++ b/uploader/templates/errors_display.html @@ -0,0 +1,47 @@ +{%macro errors_display(errors, no_error_msg, error_message, complete)%} + +{%if errors | length == 0 %} +<span {%if complete%}class="alert-success"{%endif%}>{{no_error_msg}}</span> +{%else %} +<p class="alert-danger">{{error_message}}</p> + +<table class="table reports-table"> + <thead> + <tr> + <th>line number</th> + <th>column(s)</th> + <th>error</th> + <th>error message</th> + </tr> + </thead> + + <tbody> + {%for error in errors%} + <tr> + <td>{{error["line"]}}</td> + <td> + {%if isinvalidvalue(error):%} + {{error.column}} + {%elif isduplicateheading(error): %} + {{error.columns}} + {%else: %} + - + {%endif %} + </td> + <td> + {%if isinvalidvalue(error):%} + Invalid Value + {%elif isduplicateheading(error): %} + Duplicate Header + {%else%} + Inconsistent Columns + {%endif %} + </td> + <td>{{error["message"]}}</td> + </tr> + {%endfor%} + </tbody> +</table> +{%endif%} + +{%endmacro%} diff --git a/uploader/templates/expression-data/base.html b/uploader/templates/expression-data/base.html new file mode 100644 index 0000000..d63fd7e --- /dev/null +++ b/uploader/templates/expression-data/base.html @@ -0,0 +1,13 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="expression-data"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.expression-data.index')}}"> + Expression Data</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/expression-data/data-review.html b/uploader/templates/expression-data/data-review.html new file mode 100644 index 0000000..c985b03 --- /dev/null +++ b/uploader/templates/expression-data/data-review.html @@ -0,0 +1,85 @@ +{%extends "base.html"%} + +{%block title%}Data Review{%endblock%} + +{%block contents%} +<h1 class="heading">data review</h1> + +<div class="row"> + <h2 id="data-concerns">Data Concerns</h2> + <p>The following are some of the requirements that the data in your file + <strong>MUST</strong> fulfil before it is considered valid for this system: + </p> + + <ol> + <li>File headings + <ul> + <li>The first row in the file should contains the headings. The number of + headings in this first row determines the number of columns expected for + all other lines in the file.</li> + <li>Each heading value in the first row MUST appear in the first row + <strong>ONE AND ONLY ONE</strong> time</li> + <li>The sample/cases (previously 'strains') headers in your first row will be + against those in the <a href="https://genenetwork.org" + title="Link to the GeneNetwork service"> + GeneNetwork</a> database.<br /> + <small class="text-muted"> + If you encounter an error saying your sample(s)/case(s) do not exist + in the GeneNetwork database, then you will have to use the + <a href="{{url_for('species.populations.samples.index')}}" + title="Upload samples/cases feature">Upload Samples/Cases</a> + option on this system to upload them. + </small> + </ul> + </li> + + <li>Data + <ol> + <li><strong>NONE</strong> of the data cells/fields is allowed to be empty. + All fields/cells <strong>MUST</strong> contain a value.</li> + <li>The first column of the data rows will be considered a textual field, + holding the "identifier" for that row<li> + <li>Except for the first column/field for each data row, + <strong>NONE</strong> of the data columns/cells/fields should contain + spurious characters like `eeeee`, `5.555iloveguix`, etc...<br /> + All of them should be decimal values</li> + <li>decimal numbers must conform to the following criteria: + <ul> + <li>when checking an average file decimal numbers must have exactly three + decimal places to the right of the decimal point.</li> + <li>when checking a standard error file decimal numbers must have six or + greater decimal places to the right of the decimal point.</li> + <li>there must be a number to the left side of the decimal place + (e.g. 0.55555 is allowed but .55555 is not).</li> + </ul> + </li> + </ol> + </li> + </ol> +</div> + + +<div class="row"> + <h2 id="file-types">Supported File Types</h2> + We support the following file types: + + <ul> + <li>Tab-Separated value files (.tsv) + <ul> + <li>The <strong>TAB</strong> character is used to separate the fields of each + column</li> + <li>The values of each field <strong>ARE NOT</strong> quoted.</li> + <li>Here is an + <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv" + target="_blank">example file</a> with a single data row.</li> + </ul> + </li> + <li>.txt files: Content has the same format as .tsv file above</li> + <li>.zip files: each zip file should contain + <strong>ONE AND ONLY ONE</strong> file of the .tsv or .txt type above. + <br />Any zip file with more than one file is invalid, and so is an empty + zip file.</li> + </ul> + +</div> +{%endblock%} diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html new file mode 100644 index 0000000..9ba3582 --- /dev/null +++ b/uploader/templates/expression-data/index.html @@ -0,0 +1,33 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Expression Data{%endblock%} + +{%block pagetitle%}Expression Data{%endblock%} + +{%block breadcrumb%} +<li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Home</a> +</li> +<li class="breadcrumb-item active"> + <a href="{{url_for('species.populations.expression-data.index')}}" + title="Upload expression data."> + Expression Data</a> +</li> +{%endblock%} + +{%block contents%} +<div class="row"> + <h2 class="heading">Expression Data</h2> + {{flash_all_messages()}} + + <p>This section allows you to enter the expression data for your experiment. + You will need to select the species that your data concerns below.</p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.populations.expression-data.index"), + species)}} +</div> +{%endblock%} diff --git a/uploader/templates/expression-data/job-progress.html b/uploader/templates/expression-data/job-progress.html new file mode 100644 index 0000000..ef264e1 --- /dev/null +++ b/uploader/templates/expression-data/job-progress.html @@ -0,0 +1,47 @@ +{%extends "base.html"%} +{%from "errors_display.html" import errors_display%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5"> +{%endblock%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">{{job_name}}</h2> + +<div class="row"> + <form action="{{url_for('species.populations.expression-data.abort', + species_id=species.SpeciesId, + population_id=population.Id)}}" method="POST"> + <legend class="heading">Status</legend> + <div class="form-group"> + <label for="job_status" class="form-label">status:</label> + <span class="form-text">{{job_status}}: {{message}}</span><br /> + </div> + + <div class="form-group"> + <label for="job_{{job_id}}" class="form-label">parsing: </label> + <progress id="job_{{job_id}}" + value="{{progress/100}}" + class="form-control"> + {{progress}}</progress> + <span class="form-text text-muted">{{"%.2f" | format(progress)}}%</span> + </div> + + <input type="hidden" name="job_id" value="{{job_id}}" /> + + <button type="submit" class="btn btn-danger">Abort</button> + </form> +</div> + +<div class="row"> + {{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}} +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/expression-data/no-such-job.html b/uploader/templates/expression-data/no-such-job.html new file mode 100644 index 0000000..d22c429 --- /dev/null +++ b/uploader/templates/expression-data/no-such-job.html @@ -0,0 +1,15 @@ +{%extends "base.html"%} + +{%block extrameta%} +<meta http-equiv="refresh" + content="5;url={{url_for('species.populations.expression-data.index.upload_file')}}"> +{%endblock%} + +{%block title%}No Such Job{%endblock%} + +{%block contents%} +<h1 class="heading">No Such Job: {{job_id}}</h2> + +<p>No job, with the id '<em>{{job_id}}</em>' was found!</p> + +{%endblock%} diff --git a/uploader/templates/expression-data/parse-failure.html b/uploader/templates/expression-data/parse-failure.html new file mode 100644 index 0000000..31f6be8 --- /dev/null +++ b/uploader/templates/expression-data/parse-failure.html @@ -0,0 +1,26 @@ +{%extends "base.html"%} + +{%block title%}Worker Failure{%endblock%} + +{%block contents%} +<h1 class="heading">Worker Failure</h1> + +<p> + There was an error while parsing your file. +</p> + +<p> + Please notify the developers of this issue when you encounter it, + providing the information below. +</p> + +<h4>Debugging Information</h4> + +<ul> + <li><strong>job id</strong>: {{job["job_id"]}}</li> + <li><strong>filename</strong>: {{job["filename"]}}</li> + <li><strong>line number</strong>: {{job["line_number"]}}</li> + <li><strong>Progress</strong>: {{job["percent"]}} %</li> +</ul> + +{%endblock%} diff --git a/uploader/templates/expression-data/parse-results.html b/uploader/templates/expression-data/parse-results.html new file mode 100644 index 0000000..03a23e2 --- /dev/null +++ b/uploader/templates/expression-data/parse-results.html @@ -0,0 +1,39 @@ +{%extends "base.html"%} +{%from "errors_display.html" import errors_display%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Parse Results{%endblock%} + +{%block contents%} + +<div class="row"> + <h2 class="heading">{{job_name}}: parse results</h2> + + {%if user_aborted%} + <span class="alert-warning">Job aborted by the user</span> + {%endif%} + + {{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} + + {%if errors | length == 0 and not user_aborted %} + <form method="post" action="{{url_for('dbinsert.select_platform')}}"> + <input type="hidden" name="job_id" value="{{job_id}}" /> + <input type="submit" value="update database" class="btn btn-primary" /> + </form> + {%endif%} + + {%if errors | length > 0 or user_aborted %} + <br /> + <a href="{{url_for('species.populations.expression-data.upload_file', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Back to index page." + class="btn btn-primary">Go back</a> + + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/expression-data/select-file.html b/uploader/templates/expression-data/select-file.html new file mode 100644 index 0000000..4ca461e --- /dev/null +++ b/uploader/templates/expression-data/select-file.html @@ -0,0 +1,115 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "upload_progress_indicator.html" import upload_progress_indicator%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Expression Data — Upload Data{%endblock%} + +{%block pagetitle%}Expression Data — Upload Data{%endblock%} + +{%block contents%} +{{upload_progress_indicator()}} + +<div class="row"> + <h2 class="heading">Upload Expression Data</h2> + + <p>This feature enables you to upload expression data. It expects the data to + be in <strong>tab-separated values (TSV)</strong> files. The data should be + a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a + list of the <em>phenotypes</em> and the first row is a list of + <em>samples/cases</em>.</p> + + <p>If you haven't done so please go to this page to learn the requirements for + file formats and helpful suggestions to enter your data in a fast and easy + way.</p> + + <ol> + <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies + with our system requirements. ( + <a href="{{url_for('species.populations.expression-data.data_review')}}#data-concerns" + title="Details for the data expectations.">Help</a> + )</li> + <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept + <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong> + files (<a href="{{url_for('species.populations.expression-data.data_review')}}#file-types" + title="Details for the data expectations.">Help</a>)</li> + </ol> +</div> + +<div class="row"> + <form action="{{url_for( + 'species.populations.expression-data.upload_file', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST" + enctype="multipart/form-data" + id="frm-upload-expression-data"> + {{flash_messages("error-expr-data")}} + + <div class="form-group"> + <legend class="heading">File Type</legend> + + <div class="radio"> + <label for="filetype_average" class="form-check-label"> + <input type="radio" name="filetype" value="average" id="filetype_average" + required="required" class="form-check-input" /> + Average</label> + <p class="form-text text-muted"> + <small>The averages data …</small></p> + </div> + + <div class="radio"> + <label for="filetype_standard_error" class="form-check-label"> + <input type="radio" name="filetype" value="standard-error" + id="filetype_standard_error" required="required" + class="form-check-input" /> + Standard Error + </label> + <p class="form-text text-muted"> + <small>The standard errors computed from the averages …</small></p> + </div> + </div> + + <div class="form-group"> + <span id="no-file-error" class="alert-danger" style="display: none;"> + No file selected + </span> + <label for="file_upload" class="form-label">Select File</label> + <input type="file" name="qc_text_file" id="file_upload" + accept="text/plain, text/tab-separated-values, application/zip" + class="form-control"/> + <p class="form-text text-muted"> + <small>Select the file to upload.</small></p> + </div> + + <button type="submit" + class="btn btn-primary" + data-toggle="modal" + data-target="#upload-progress-indicator">upload file</button> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/upload_progress.js"></script> +<script type="text/javascript"> + function setup_formdata(form) { + var formdata = new FormData(); + formdata.append( + "qc_text_file", + form.querySelector("input[type='file']").files[0]); + formdata.append( + "filetype", + selected_filetype( + Array.from(form.querySelectorAll("input[type='radio']")))); + return formdata; + } + + setup_upload_handlers( + "frm-upload-expression-data", make_data_uploader(setup_formdata)); +</script> +{%endblock%} diff --git a/uploader/templates/expression-data/select-population.html b/uploader/templates/expression-data/select-population.html new file mode 100644 index 0000000..8555e27 --- /dev/null +++ b/uploader/templates/expression-data/select-population.html @@ -0,0 +1,29 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Expression Data{%endblock%} + +{%block pagetitle%}Expression Data{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>You have selected the species. Now you need to select the population that + the expression data belongs to.</p> +</div> + +<div class="row"> + {{select_population_form(url_for( + "species.populations.expression-data.select_population", + species_id=species.SpeciesId), + populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/final_confirmation.html b/uploader/templates/final_confirmation.html new file mode 100644 index 0000000..0727fc8 --- /dev/null +++ b/uploader/templates/final_confirmation.html @@ -0,0 +1,47 @@ +{%extends "base.html"%} +{%from "dbupdate_hidden_fields.html" import hidden_fields%} + +{%block title%}Confirmation{%endblock%} + +{%macro display_item(item_name, item_data):%} +<li> + <strong>{{item_name}}</strong> + {%if item_data%} + <ul> + {%for term,value in item_data.items():%} + <li><strong>{{term}}:</strong> {{value}}</li> + {%endfor%} + </ul> + {%endif%} +</li> +{%endmacro%} + +{%block contents%} +<h2 class="heading">Final Confirmation</h2> + +<div class="two-col-sep-col1"> + <p><strong>Selected Data</strong></p> + <ul> + <li><strong>File</strong> + <ul> + <li><strong>Filename</strong>: {{filename}}</li> + <li><strong>File Type</strong>: {{filetype}}</li> + </ul> + </li> + {{display_item("Species", the_species)}} + {{display_item("Platform", platform)}} + {{display_item("Study", study)}} + {{display_item("Dataset", dataset)}} + </ul> +</div> + +<form method="POST" action="{{url_for('dbinsert.insert_data')}}"> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid,datasetid=datasetid, totallines=totallines)}} + <fieldset> + <input type="submit" class="btn btn-primary" value="confirm" /> + </fieldset> +</form> +</div> +{%endblock%} diff --git a/uploader/templates/flash_messages.html b/uploader/templates/flash_messages.html new file mode 100644 index 0000000..b7af178 --- /dev/null +++ b/uploader/templates/flash_messages.html @@ -0,0 +1,25 @@ +{%macro flash_all_messages()%} +{%with messages = get_flashed_messages(with_categories=true)%} +{%if messages:%} +<ul> + {%for category, message in messages:%} + <li class="{{category}}">{{message}}</li> + {%endfor%} +</ul> +{%endif%} +{%endwith%} +{%endmacro%} + +{%macro flash_messages(filter_class)%} +{%with messages = get_flashed_messages(with_categories=true)%} +{%if messages:%} +<ul> + {%for category, message in messages:%} + {%if filter_class in category%} + <li class="{{category}}">{{message}}</li> + {%endif%} + {%endfor%} +</ul> +{%endif%} +{%endwith%} +{%endmacro%} diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html new file mode 100644 index 0000000..7d61312 --- /dev/null +++ b/uploader/templates/genotypes/base.html @@ -0,0 +1,23 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="genotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + {%if dataset is defined and dataset is mapping%} + {{dataset.Name}} + {%else%} + Genotypes + {%endif%}</a> + {%else%} + <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a> + {%endif%} +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html new file mode 100644 index 0000000..10331c1 --- /dev/null +++ b/uploader/templates/genotypes/create-dataset.html @@ -0,0 +1,82 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes — Create Dataset{%endblock%} + +{%block pagetitle%}Genotypes — Create Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-geno-create-dataset" + method="POST" + action="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + <legend>Create a new Genotype Dataset</legend> + + <div class="form-group"> + <label for="txt-geno-dataset-name" class="form-label">Name</label> + <input type="text" + id="txt-geno-dataset-name" + name="geno-dataset-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a short representative, but constrained name for the genotype + dataset.<br /> + The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens + and underscores. Any other character will cause the name to be + rejected.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-fullname" class="form-label">Full Name</label> + <input type="text" + id="txt-geno-dataset-fullname" + name="geno-dataset-fullname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a longer, more descriptive name for your dataset.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-shortname" + class="form-label">Short Name</label> + <input type="text" + id="txt-geno-dataset-shortname" + name="geno-dataset-shortname" + class="form-control" /> + <small class="form-text text-muted"> + <p>A short name for your dataset. If you leave this field blank, the + short name will be set to the same value as the + "<strong>Name</strong>" field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create dataset" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html new file mode 100644 index 0000000..b50ebc5 --- /dev/null +++ b/uploader/templates/genotypes/index.html @@ -0,0 +1,32 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p> + This section allows you to upload genotype information for your experiments, + in the case that you have not previously done so. + </p> + <p> + We'll need to link the genotypes to the species and population, so do please + go ahead and select those in the next two steps. + </p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.populations.genotypes.index"), + species)}} +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html new file mode 100644 index 0000000..0f074fd --- /dev/null +++ b/uploader/templates/genotypes/list-genotypes.html @@ -0,0 +1,149 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-genotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}">List genotypes</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genetic Markers</h2> + <p>There are a total of {{total_markers}} currently registered genetic markers + for the "{{species.FullName}}" species. You can click + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View genetic markers for species '{{species.FullName}}"> + this link to view the genetic markers + </a>. + </p> +</div> + +<div class="row"> + <h2>Genotype Encoding</h2> + <p> + The genotype encoding used for the "{{population.FullName}}" population from + the "{{species.FullName}}" species is as shown in the table below. + </p> + <table class="table"> + + <thead> + <tr> + <th>Allele Type</th> + <th>Allele Symbol</th> + <th>Allele Value</th> + </tr> + </thead> + + <tbody> + {%for row in genocode%} + <tr> + <td>{{row.AlleleType}}</td> + <td>{{row.AlleleSymbol}}</td> + <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td> + </tr> + {%else%} + <tr> + <td colspan="7" class="text-info"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no explicit genotype encoding defined for this population. + </td> + </tr> + {%endfor%} + </tbody> + </table> + + {%if genocode | length < 1%} + <a href="#add-genotype-encoding" + title="Add a genotype encoding system for this population" + class="btn btn-primary not-implemented"> + add genotype encoding + </a> + {%endif%} +</div> + +<div class="row text-danger"> + <h3>Some Important Concepts to Consider/Remember</h3> + <ul> + <li>Reference vs. Non-reference alleles</li> + <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> + </ul> + <h3>Possible references</h3> + <ul> + <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> + <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> + </ul> +</div> + +<div class="row"> + <h2>Genotype Datasets</h2> + + <p>The genotype data is organised under various genotype datasets. You can + click on the link for the relevant dataset to view a little more information + about it.</p> + + {%if dataset is not none%} + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td><a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="View details regarding and manage dataset '{{dataset.FullName}}'"> + {{dataset.FullName}}</a></td> + </tr> + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no genotype dataset defined for this population. + </p> + <p> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." + class="btn btn-primary"> + create new genotype dataset</a></p> + {%endif%} +</div> +<div class="row text-warning"> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a + single genotype dataset. If there is more than one, the system apparently + fails in unpredictable ways. + </p> + <p>Fix this to allow multiple datasets, each with a different assembly from + all the rest.</p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html new file mode 100644 index 0000000..a705ae3 --- /dev/null +++ b/uploader/templates/genotypes/list-markers.html @@ -0,0 +1,105 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Genotypes: List Markers{%endblock%} + +{%block pagetitle%}Genotypes: List Markers{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-markers"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id)}}">List markers</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +{%if markers | length > 0%} +<div class="row"> + <p> + There are a total of {{total_markers}} genotype markers for this species. + </p> + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id, + start_from=start_from-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying markers {{start_from+1}} to {{start_from+count if start_from+count < total_markers else total_markers}} of + {{total_markers}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_markers%} + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id, + start_from=start_from+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + <table class="table"> + <thead> + <tr> + <th title="">#</th> + <th title="">Marker Name</th> + <th title="Chromosome">Chr</th> + <th title="Physical location of the marker in megabasepairs"> + Location (Mb)</th> + <th title="">Source</th> + <th title="">Source2</th> + </thead> + + <tbody> + {%for marker in markers%} + <tr> + <td>{{marker.sequence_number}}</td> + <td>{{marker.Marker_Name}}</td> + <td>{{marker.Chr}}</td> + <td>{{marker.Mb}}</td> + <td>{{marker.Source}}</td> + <td>{{marker.Source2}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%else%} +<div class="row"> + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + This species does not currently have any genetic markers uploaded, therefore, + there is nothing to display here. + </p> + <p> + <a href="#add-genetic-markers-for-species-{{species.SpeciesId}}" + title="Add genetic markers for this species" + class="btn btn-primary"> + add genetic markers + </a> + </p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html new file mode 100644 index 0000000..acdd063 --- /dev/null +++ b/uploader/templates/genotypes/select-population.html @@ -0,0 +1,25 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%endblock%} diff --git a/uploader/templates/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html new file mode 100644 index 0000000..e7ceb36 --- /dev/null +++ b/uploader/templates/genotypes/view-dataset.html @@ -0,0 +1,61 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes: View Dataset{%endblock%} + +{%block pagetitle%}Genotypes: View Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">view dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genotype Dataset Details</h2> + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row text-warning"> + <h2>Assembly Details</h2> + + <p>Maybe include the assembly details here if found to be necessary.</p> +</div> + +<div class="row"> + <h2>Genotype Data</h2> + + <p class="text-danger"> + Provide link to enable uploading of genotype data here.</p> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/http-error.html b/uploader/templates/http-error.html new file mode 100644 index 0000000..374fb86 --- /dev/null +++ b/uploader/templates/http-error.html @@ -0,0 +1,18 @@ +{%extends "base.html"%} + +{%block title%}HTTP Error: {{exc.code}}{%endblock%} + +{%block contents%} +<h1>{{exc.code}}: {{exc.description}}</h1> + +<div class="row"> + <p> + You attempted to access {{request_url}} which failed with the following + error: + </p> +</div> + +<div class="row"> + <pre>{{"\n".join(trace)}}</pre> +</div> +{%endblock%} diff --git a/uploader/templates/index.html b/uploader/templates/index.html new file mode 100644 index 0000000..aa1414e --- /dev/null +++ b/uploader/templates/index.html @@ -0,0 +1,107 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Home{%endblock%} + +{%block pagetitle%}Home{%endblock%} + +{%block contents%} + +<div class="row"> + {{flash_all_messages()}} + <div class="explainer"> + <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control + System</strong>.</p> + <p>This tool helps you prepare and upload research data to GeneNetwork for + analysis.</p> + + <h2 class="heading">Getting Started</h2> + <p>The sections below explain the features of the system. Review this guide + to learn how to use the system.</p> + + {%block extrapageinfo%}{%endblock%} + + <h3 class="subheading">Species</h3> + + <p>GeneNetwork supports genetic studies across multiple species (e.g. mice + [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . + Here you can:</p> + <ul> + <li>View all species that are currently supported</li> + <li>Add new species not yet in the system</li> + </ul> + + <h3 class="subheading">Populations</h3> + + <p>A "population" refers to a specific subgroup within a species that you’re + studying (e.g., BXD mice). Here you can:</p> + <ul> + <li>View the populations that exist for a selected species</li> + <li>Add new populations of study for a selected species</li> + </ul> + + <h3 class="subheading">Samples</h3> + + <p>Manage individual specimens or cases used in your experiments. These + include:</p> + + <ul> + <li>Experimental subjects</li> + <li>Data sources (e.g., tissue samples, clinical cases)</li> + <li>Strain means (instead of entering multiple BXD1 individuals, for + example, the mean would be entered for a single BXD1 strain)</li> + </ul> + + + <h3 class="subheading">Genotype Data</h3> + + <p>Upload and review genetic markers and allele encodings for your + population. Key details:</p> + + <ul> + <li>Markers are species-level (e.g., mouse SNP databases).</li> + <li>Allele data is population-specific (tied to your experimental + samples).</li> + </ul> + + <p><strong>Requirement</strong>: Samples must already have been registered + in the system before uploading genotype data.</p> + + <h3 class="subheading">Phenotype Data</h3> + + <p>Phenotypes are the visible traits or features of a living thing. For + example, phenotypes include:</p> + + <ul> + <li>Weight</li> + <li>Height</li> + <li>Color (such as the color of fur or eyes)</li> + </ul> + + <p>This part of the system will allow you to upload and manage the values + for different phenotypes from various samples in your studies.</p> + + <!-- + + <h3 class="subheading">Expression Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h3 class="subheading">Individual Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h3 class="subheading">RNA-Seq Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + </div> + --> +</div> + +{%endblock%} diff --git a/uploader/templates/insert_error.html b/uploader/templates/insert_error.html new file mode 100644 index 0000000..5301288 --- /dev/null +++ b/uploader/templates/insert_error.html @@ -0,0 +1,32 @@ +{%extends "base.html"%} + +{%block title%}Data Insertion Failure{%endblock%} + +{%block contents%} +<h1 class="heading">Insertion Failure</h1> + +<div class="row"> + <p> + There was an error inserting data into the database + </p> + + <p> + Please notify the developers of this issue when you encounter it, + providing the information below. + </p> + + <h4>Debugging Information</h4> + + <ul> + <li><strong>job id</strong>: {{job["jobid"]}}</li> + </ul> +</div> + +<div class="row"> + <h4>STDERR Output</h4> + <pre class="cli-output"> + {{job["stderr"]}} + </pre> +</div> + +{%endblock%} diff --git a/uploader/templates/insert_progress.html b/uploader/templates/insert_progress.html new file mode 100644 index 0000000..52177d6 --- /dev/null +++ b/uploader/templates/insert_progress.html @@ -0,0 +1,46 @@ +{%extends "base.html"%} +{%from "stdout_output.html" import stdout_output%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5"> +{%endblock%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">{{job_name}}</h1> + +<div class="row"> + <form> + <div class="form-group"> + <label for="job_status" class="form-label">status:</label> + <span class="form-text">{{job_status}}: {{message}}</span> + </div> + +{%if job.get("stdout", "").split("\n\n") | length < 3 %} +{%set lines = 0%} +{%else%} +{%set lines = (job.get("stdout", "").split("\n\n") | length / 3) %} +{%endif%} +{%set totallines = job.get("totallines", lines+3) | int %} +{%if totallines > 1000 %} +{%set fraction = ((lines*1000)/totallines) %} +{%else%} +{%set fraction = (lines/totallines)%} +{%endif%} + + <div class="form-group"> + <label for="job_{{job_id}}" class="form-label">inserting: </label> + <progress id="jobs_{{job_id}}" + value="{{(fraction)}}" + class="form-control">{{fraction*100}}</progress> + <span class="form-text text-muted"> + {{"%.2f" | format(fraction * 100 | float)}}%</span> + </div> + </form> +</div> + + +{{stdout_output(job)}} + +{%endblock%} diff --git a/uploader/templates/insert_success.html b/uploader/templates/insert_success.html new file mode 100644 index 0000000..7e1fa8d --- /dev/null +++ b/uploader/templates/insert_success.html @@ -0,0 +1,19 @@ +{%extends "base.html"%} +{%from "stdout_output.html" import stdout_output%} + +{%block title%}Insertion Success{%endblock%} + +{%block contents%} +<h1 class="heading">Insertion Success</h1> + +<div class="row"> +<p>Data inserted successfully!</p> + +<p>The following queries were run:</p> +</div> + +<div class="row"> + {{stdout_output(job)}} +</div> + +{%endblock%} diff --git a/uploader/templates/jobs/job-error.html b/uploader/templates/jobs/job-error.html new file mode 100644 index 0000000..b3015fc --- /dev/null +++ b/uploader/templates/jobs/job-error.html @@ -0,0 +1,17 @@ +{%extends "base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs: Error{%endblock%} + +{%block pagetitle%}Background Jobs: Error{%endblock%} + +{%block contents%} + +<h1>Background Jobs: Error</h1> +<p>Job <strong>{{job["job_id"]}}</strong> failed!</p> +<p>The error details are in the "STDERR" section below.</p> + +<h2>STDERR</h2> +<pre>{{job["stderr"]}}</pre> +{%endblock%} diff --git a/uploader/templates/jobs/job-not-found.html b/uploader/templates/jobs/job-not-found.html new file mode 100644 index 0000000..a71e66f --- /dev/null +++ b/uploader/templates/jobs/job-not-found.html @@ -0,0 +1,11 @@ +{%extends "base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} +<p>Could not find job with ID: {{job_id}}</p> +{%endblock%} diff --git a/uploader/templates/jobs/job-status.html b/uploader/templates/jobs/job-status.html new file mode 100644 index 0000000..83c02fd --- /dev/null +++ b/uploader/templates/jobs/job-status.html @@ -0,0 +1,24 @@ +{%extends "base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5" /> +{%endblock%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} + +<p>Status: {{job["metadata"]["status"]}}</p> +<p>Job Type: {{job["metadata"]["job-type"]}}</p> + +<h2>STDOUT</h2> +<pre>{{job["stdout"]}}</pre> + +<h2>STDERR</h2> +<pre>{{job["stderr"]}}</pre> + +{%endblock%} diff --git a/uploader/templates/login.html b/uploader/templates/login.html new file mode 100644 index 0000000..e76c644 --- /dev/null +++ b/uploader/templates/login.html @@ -0,0 +1,12 @@ +{%extends "index.html"%} + +{%block title%}Data Upload{%endblock%} + +{%block pagetitle%}log in{%endblock%} + +{%block extrapageinfo%} +<p class="text-dark"> + You <strong>need to + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system">sign in</a></strong> to use this system.</p> +{%endblock%} diff --git a/uploader/templates/macro-step-indicator.html b/uploader/templates/macro-step-indicator.html new file mode 100644 index 0000000..ac0be77 --- /dev/null +++ b/uploader/templates/macro-step-indicator.html @@ -0,0 +1,15 @@ +{%macro step_indicator(step, width=100)%} +<svg width="{{width}}" height="{{width}}" xmlns="http://www.w3.org/2000/svg"> + <circle cx="{{0.5*width}}" + cy="{{0.5*width}}" + r="{{0.5*width}}" + fill="#E5E5FF" /> + <text x="{{0.5*width}}" + y="{{0.6*width}}" + font-size="{{0.2*width}}" + text-anchor="middle" + fill="#555555"> + Step {{step}} + </text> +</svg> +{%endmacro%} diff --git a/uploader/templates/macro-table-pagination.html b/uploader/templates/macro-table-pagination.html new file mode 100644 index 0000000..292c531 --- /dev/null +++ b/uploader/templates/macro-table-pagination.html @@ -0,0 +1,26 @@ +{%macro table_pagination(start_at, page_count, total_count, base_uri, name)%} +{%set ns = namespace(forward_uri=base_uri, back_uri=base_uri)%} +{%set ns.forward_uri="brr"%} + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_at > 0%} + <a href="{{base_uri + + '?start_at='+((start_at-page_count)|string) + + '&count='+(page_count|string)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying {{name}} {{start_at+1}} to {{start_at+page_count if start_at+page_count < total_count else total_count}} of {{total_count}}</div> + <div class="col-md-2" style="text-align: end;"> + {%if start_at + page_count < total_count%} + <a href="{{base_uri + + '?start_at='+((start_at+page_count)|string) + + '&count='+(page_count|string)}}"> + Next<span class="glyphicon glyphicon-forward"></span></a> + {%endif%} + </div> + </div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html new file mode 100644 index 0000000..9909c20 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -0,0 +1,166 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-add-phenotypes" + method="POST" + enctype="multipart/form-data" + action="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + use_bundle=use_bundle)}}" + data-resumable-target="{{url_for('files.resumable_upload_post')}}"> + <legend>Add New Phenotypes</legend> + + <div class="form-text help-block"> + {%block frm_add_phenotypes_documentation%}{%endblock%} + <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p> + </div> + + {%block frm_add_phenotypes_elements%}{%endblock%} + + <fieldset id="fldset-publication-info"> + <legend>Publication Information</legend> + <input type="hidden" name="publication-id" id="txt-publication-id" /> + <span class="form-text text-muted"> + Select a publication for your data. <br /> + Can't find a publication you can use? Go ahead and + <a href="{{url_for( + 'publications.create_publication', + return_to='species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">create a new publication</a>.</span> + <table id="tbl-select-publication" class="table compact stripe"> + <thead> + <tr> + <th>#</th> + <th>PubMed ID</th> + <th>Title</th> + <th>Authors</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </fieldset> + + <div class="form-group"> + <input type="submit" + value="upload phenotypes" + class="btn btn-primary" /> + </div> + </form> +</div> + +<div class="row"> + {%block page_documentation%}{%endblock%} +</div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var publicationsDataTable = buildDataTable( + "#tbl-select-publication", + [], + [ + {data: "index"}, + { + searchable: true, + data: (pub) => { + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; + } + }, + { + searchable: true, + data: (pub) => { + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + return `<a href="/publications/view/${pub.Id}" ` + + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; + } + }, + { + searchable: true, + data: (pub) => { + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; + } + } + ], + { + serverSide: true, + ajax: { + url: "/publications/list", + dataSrc: "publications" + }, + select: "single", + paging: true, + scrollY: 700, + deferRender: true, + scroller: true, + scrollCollapse: true, + layout: { + topStart: "info", + topEnd: "search" + } + }); + publicationsDataTable.on("select", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + console.debug(datatable.row(element).data()); + $("#frm-add-phenotypes #txt-publication-id").val( + datatable.row(element).data().Id); + }); + }); + publicationsDataTable.on("deselect", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + $("#frm-add-phenotypes #txt-publication-id").val(null); + }); + }); + }); +</script> + +{%block more_javascript%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html new file mode 100644 index 0000000..67b56e3 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -0,0 +1,847 @@ +{%extends "phenotypes/add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} +{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} +{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block frm_add_phenotypes_documentation%} +<p>This page will allow you to upload all the separate files that make up your + phenotypes. Here, you will have to upload each separate file individually. If + you want instead to upload all your files as a single ZIP file, + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + use_bundle=true)}}" + title="">click here</a>.</p> +{%endblock%} + +{%block frm_add_phenotypes_elements%} +<fieldset id="fldset-file-metadata"> + <legend>File(s) Metadata</legend> + <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-Character</label> + <div class="input-group"> + <input id="txt-file-comment-character" + name="file-comment-character" + type="text" + value="#" + class="form-control" + maxlength="1" /> + <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 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> +</fieldset> + +<fieldset id="fldset-files"> + <legend>Data File(s)</legend> + + <fieldset id="fldset-descriptions-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-descriptions-transposed" + name="phenotype-descriptions-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-descriptions-transposed" + class="form-check-label"> + Description file transposed?</label> + </div> + + <div class="non-resumable-elements"> + <label for="finput-phenotype-descriptions" class="form-label"> + Phenotype Descriptions</label> + <input id="finput-phenotype-descriptions" + name="phenotype-descriptions" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-desc" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the phenotype descriptions, + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + the documentation for the expected format of the file</a>.</span> + </div> + {{display_resumable_elements( + "resumable-phenotype-descriptions", + "phenotype descriptions", + '<p>Drag and drop the CSV file that contains the descriptions of your + phenotypes here.</p> + + <p>The CSV file should be a matrix of + <strong>phenotypes × descriptions</strong> i.e. The first column + contains the phenotype names/identifiers whereas the first row is a list + of metadata fields like, "description", "units", etc.</p> + + <p>If the format is transposed (i.e. + <strong>descriptions × phenotypes</strong>) select the checkbox above. + </p> + + <p>Please see the + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + "Phenotypes Descriptions" documentation</a> section below for more + information on the expected format of the file provided here.</p>')}} + {{display_preview_table( + "tbl-preview-pheno-desc", "phenotype descriptions")}} + </div> + </fieldset> + + + <fieldset id="fldset-data-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-data-transposed" + name="phenotype-data-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-data-transposed" class="form-check-label"> + Data file transposed?</label> + </div> + + <div class="non-resumable-elements"> + <label for="finput-phenotype-data" class="form-label">Phenotype Data</label> + <input id="finput-phenotype-data" + name="phenotype-data" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-data" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the phenotype data. See + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + the documentation for the expected format of the file</a>.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-data", + "phenotype data", + '<p>Drag and drop a CSV file that contains the phenotypes numerical data + here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + <p>Please see the + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format for the file provided here.</p>')}} + {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}} + </div> + </fieldset> + + + {%if population.Family in families_with_se_and_n%} + <fieldset id="fldset-se-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-se-transposed" + name="phenotype-se-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-se-transposed" class="form-check-label"> + Standard-Errors file transposed?</label> + </div> + <div class="group non-resumable-elements"> + <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label> + <input id="finput-phenotype-se" + name="phenotype-se" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-se" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the standard errors for the phenotypes, + computed from the data above.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-se", + "standard errors", + '<p>Drag and drop a CSV file that contains the phenotypes standard-errors + data here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + + <p>Please see the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format of the file provided here.</p>')}} + + {{display_preview_table("tbl-preview-pheno-se", "standard errors")}} + </div> + </fieldset> + + + <fieldset id="fldset-n-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-n-transposed" + name="phenotype-n-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-n-transposed" class="form-check-label"> + Counts file transposed?</label> + </div> + <div class="non-resumable-elements"> + <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label> + <input id="finput-phenotype-n" + name="phenotype-n" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-n" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the number of samples/individuals used in + the computation of the standard errors above.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-n", + "number of samples/individuals", + '<p>Drag and drop a CSV file that contains the samples\' phenotypes counts + data here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + + <p>Please see the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format of the file provided here.</p>')}} + + {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}} + </div> + </fieldset> +</fieldset> +{%endif%} +{%endblock%} + + +{%block page_documentation%} +<div class="row"> + <h2 class="heading" id="docs-help">Help</h2> + <h3 class="subheading">Common Features</h3> + <p>The following are the common expectations for <strong>ALL</strong> the + files provided in the form above: + <ul> + <li>The file <strong>MUST</strong> be character-separated values (CSV) + text file</li> + <li>The first row in the file <strong>MUST</strong> be a heading row, and + will be composed of the list identifiers for all of + samples/individuals/cases involved in your study.</li> + <li>The first column of data in the file <strong>MUST</strong> be the + identifiers for all of the phenotypes you wish to upload.</li> + </ul> + </p> + + <p>If you do not specify the separator character, then we will assume a + <strong>TAB</strong> character was used as your separator.</p> + + <p>We also assume you might include comments lines in your files. In that + case, if you do not specify what character denotes that a line in your files + is a comment line, we will assume the <strong>#</strong> character.<br /> + A comment <strong>MUST ALWAYS</strong> begin at the start of the line marked + with the comment character specified.</p> + + <h3 class="subheading" id="docs-file-metadata">File Metadata</h3> + <p>We request some details about your files to help us parse and process the + files correctly. The details we collect are:</p> + <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 character</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.</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> + + <h3 class="subheading" id="docs-file-phenotype-description"> + file: Phenotypes Descriptions</h3> + <p>The data in this file is a matrix of <em>phenotypes × metadata-fields</em>. + Please note we use the term "metadata-fields" above loosely, due to lack of + a good word for this.</p> + <p>The file <strong>MUST</strong> have columns in this order: + <dl> + <dt>Phenotype Identifiers</dt> + <dd>These are the names/identifiers for your phenotypes. These + names/identifiers are the same ones you will have in all the other files you are + uploading.</dd> + + <dt>Descriptions</dt> + <dd>Each phenotype will need a description. Good description are necessary + to inform other people of what the data is about. Good description are + hard to construct, so we provide + <a href="https://info.genenetwork.org/faq.php#q-22" + title="How to write phenotype descriptions"> + advice on describing your phenotypes.</a></dd> + + <dt>Units</dt> + <dd>Each phenotype will need units for the measurements taken. If there are + none, then indicate the field is a no-value field.</dd> + </dl></p> + <p>You can add more columns after those three if you want to, but these 3 + <strong>MUST</strong> be present.</p> + <p>The file would, for example, look like the following:</p> + <code>id,description,units,…<br /> + pheno10001|Central nervous system, behavior, cognition; …|mg|…<br /> + pheno10002|Aging, metabolism, central nervous system: …|mg|…<br /> + â‹®<br /></code> + + <p><strong>Note 01</strong>: The first usable row is the heading row.</p> + <p><strong>Note 02: </strong>This example demonstrates a subtle issue that + could make your CSV file invalid — the choice of your field separator + character.<br > + In the example above, we use the pipe character (<code>|</code>) as our + field separator. This is because, if we follow the advice on how to write + good descriptions, then we cannot use the comma as our separator – if + we did, then our CSV file would be invalid because the system would have no + way to tell the difference between the comma as a field separator, and the + comma as a way to separate the "general category and ontology terms".</p> + + <h3 class="subheading">file: Phenotype Data, Standard Errors and/or Sample Counts</h3> + <span id="docs-file-phenotype-data"></span> + <span id="docs-file-phenotype-se"></span> + <span id="docs-file-phenotype-n"></span> + <p>The data is a matrix of <em>samples(or individuals) × phenotypes</em>, e.g.</p> + <code> + # num-cases: 2549 + # num-phenos: 13 + id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…<br /> + IND001,61.400002,49,62.5,55.099998,…<br /> + IND002,54.099998,50.099998,53.299999,55.099998,…<br /> + IND003,483,403,501,403,…<br /> + IND004,49.799999,45.5,62.900002,NA,…<br /> + â‹®<br /></code> + + <p>where <code>IND001,IND002,IND003,IND004,…</code> are the + samples/individuals/cases in your study, and + <code>pheno10001,pheno10002,pheno10004,pheno10004,…</code> are the + identifiers for your phenotypes.</p> + <p>The lines beginning with the "<em>#</em>" symbol (i.e. + <code># num-cases: 2549</code> and <code># num-phenos: 13</code> are comment + lines and will be ignored</p> + <p>In this example, the comma (,) is used as the file separator.</p> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block more_javascript%} +<script src="{{url_for('base.node_modules', + filename='resumablejs/resumable.js')}}"></script> +<script type="text/javascript" src="/static/js/files.js"></script> + +<script type="text/javascript"> + $("#btn-reset-file-separator").on("click", (event) => { + event.preventDefault(); + $("#txt-file-separator").val("\t"); + $("#txt-file-separator").trigger("change"); + }); + $("#btn-reset-file-comment-character").on("click", (event) => { + event.preventDefault(); + $("#txt-file-comment-character").val("#"); + $("#txt-file-comment-character").trigger("change"); + }); + $("#btn-reset-file-na").on("click", (event) => { + event.preventDefault(); + $("#txt-file-na").val("- NA N/A"); + $("#txt-file-na").trigger("change"); + }); + + var update_preview = (table, filedata, formdata, numrows) => { + table.find("thead tr").remove() + table.find(".data-row").remove(); + var linenum = 0; + var tableheader = table.find("thead"); + var tablebody = table.find("tbody"); + var numheadings = 0; + var navalues = formdata + .na_strings + .split(" ") + .map((v) => {return v.trim();}) + .filter((v) => {return Boolean(v);}); + filedata.forEach((line) => { + if(line.startsWith(formdata.comment_char) || linenum >= numrows) { + return false; + } + var row = $("<tr></tr>"); + line.split(formdata.separator) + .map((field) => { + var value = field.trim(); + if(navalues.includes(value)) { + return "⋘NULâ‹™"; + } + return value; + }) + .filter((field) => { + return (field !== "" && field != undefined && field != null); + }) + .forEach((field) => { + if(linenum == 0) { + numheadings += 1; + var tablefield = $("<th></th>"); + tablefield.text(field); + row.append(tablefield); + } else { + add_class(row, "data-row"); + var tablefield = $("<td></td>"); + tablefield.text(field); + row.append(tablefield); + } + }); + + if(linenum == 0) { + tableheader.append(row); + } else { + tablebody.append(row); + } + linenum += 1; + }); + + if(table.find("tbody tr.data-row").length > 0) { + add_class(table.find(".data-row-template"), "visually-hidden"); + } else { + remove_class(table.find(".data-row-template"), "visually-hidden"); + } + }; + + var makePreviewUpdater = (preview_table) => { + return (data) => { + update_preview( + preview_table, + data, + filesMetadata(), + PREVIEW_ROWS); + }; + }; + + var preview_tables_to_elements_map = { + "#tbl-preview-pheno-desc": "#finput-phenotype-descriptions", + "#tbl-preview-pheno-data": "#finput-phenotype-data", + "#tbl-preview-pheno-se": "#finput-phenotype-se", + "#tbl-preview-pheno-n": "#finput-phenotype-n" + }; + + var filesMetadata = () => { + return { + "separator": $("#txt-file-separator").val(), + "comment_char": $( + "#txt-file-comment-character").val(), + "na_strings": $("#txt-file-na").val() + } + }; + + var PREVIEW_ROWS = 5; + + var handler_update_previews = (event) => { + Object.entries(preview_tables_to_elements_map).forEach((mapentry) => { + var preview_table = $(mapentry[0]); + var file_input = $(mapentry[1]); + if(file_input[0].files.length > 0) { + readFirstNLines( + file_input[0].files[0], + 10, + [makePreviewUpdater(preview_table)]); + } + }); + + if(typeof(resumables) !== "undefined") { + resumables.forEach((resumable) => { + if(resumable.files.length > 0) { + readFirstNLines( + resumable.files[0].file, + 10, + [makePreviewUpdater(resumable.preview_table)]); + } + }); + } + }; + + [ + "#txt-file-separator", + "#txt-file-comment-character", + "#txt-file-na" + ].forEach((elementid) => { + $(elementid).on("change", handler_update_previews); + }); + + [ + "#finput-phenotype-descriptions", + "#finput-phenotype-data", + "#finput-phenotype-se", + "#finput-phenotype-n" + ].forEach((elementid) => { + $(elementid).on("change", (event) => { + readFirstNLines( + event.target.files[0], + 10, + [makePreviewUpdater( + $("#" + event.target.getAttribute("data-preview-table")))]); + }); + }); + + + var resumableDisplayFiles = (display_area, files) => { + files.forEach((file) => { + display_area.find(".file-display").remove(); + var display_element = display_area + .find(".file-display-template") + .clone(); + remove_class(display_element, "visually-hidden"); + remove_class(display_element, "file-display-template"); + add_class(display_element, "file-display"); + display_element.find(".filename").text(file.name + || file.fileName + || file.relativePath + || file.webkitRelativePath); + display_element.find(".filesize").text( + (file.size / (1024*1024)).toFixed(2) + "MB"); + display_element.find(".fileuniqueid").text(file.uniqueIdentifier); + display_element.find(".filemimetype").text(file.file.type); + display_area.append(display_element); + }); + }; + + + var indicateProgress = (resumable, progress_bar) => { + return () => {/*Has no event!*/ + var progress = (resumable.progress() * 100).toFixed(2); + var pbar = progress_bar.find(".progress-bar"); + remove_class(progress_bar, "visually-hidden"); + pbar.css("width", progress+"%"); + pbar.attr("aria-valuenow", progress); + pbar.text("Uploading: " + progress + "%"); + }; + }; + + var retryUpload = (retry_button, cancel_button) => { + retry_button.on("click", (event) => { + resumable.files.forEach((file) => {file.retry();}); + add_class(retry_button, "visually-hidden"); + remove_class(cancel_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); + }); + }; + + var cancelUpload = (cancel_button, retry_button) => { + cancel_button.on("click", (event) => { + resumable.files.forEach((file) => { + if(file.isUploading()) { + file.abort(); + } + }); + add_class(cancel_button, "visually-hidden"); + remove_class(retry_button, "visually-hidden"); + remove_class(browse_button, "visually-hidden"); + }); + }; + + + var startUpload = (browse_button, retry_button, cancel_button) => { + return (event) => { + remove_class(cancel_button, "visually-hidden"); + add_class(retry_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); + }; + }; + + var processForm = (form) => { + var formdata = new FormData(form); + uploaded_files.forEach((msg) => { + formdata.delete(msg["file-input-name"]); + formdata.append(msg["file-input-name"], JSON.stringify({ + "uploaded-file": msg["uploaded-file"], + "original-name": msg["original-name"] + })); + }); + formdata.append("resumable-upload", "true"); + formdata.append("publication-id", $("#txt-publication-id").val()); + return formdata; + } + + var uploaded_files = new Set(); + var submitForm = (new_file) => { + uploaded_files.add(new_file); + if(uploaded_files.size === resumables.length) { + var form = $("#frm-add-phenotypes"); + if(form.length !== 1) { + // TODO: Handle error somehow? + alert("Could not find form!!!"); + return false; + } + + $.ajax({ + "url": form.attr("action"), + "type": "POST", + "data": processForm(form[0]), + "processData": false, + "contentType": false, + "success": (data, textstatus, jqxhr) => { + // TODO: Redirect to endpoint that should come as part of the + // success/error message. + console.log("SUCCESS DATA: ", data); + console.log("SUCCESS STATUS: ", textstatus); + console.log("SUCCESS jqXHR: ", jqxhr); + window.location.assign(window.location.origin + data["redirect-to"]); + }, + }); + return false; + } + return false; + }; + + var uploadSuccess = (file_input_name) => { + return (file, message) => { + submitForm({...JSON.parse(message), "file-input-name": file_input_name}); + }; + }; + + + var uploadError = () => { + return (message, file) => { + $("#frm-add-phenotypes input[type=submit]").removeAttr("disabled"); + console.log("THE FILE:", file); + console.log("THE ERROR MESSAGE:", message); + }; + }; + + + + var makeResumableObject = (form_id, file_input_id, resumable_element_id, preview_table_id) => { + var the_form = $("#" + form_id); + var file_input = $("#" + file_input_id); + var submit_button = the_form.find("input[type=submit]"); + if(file_input.length != 1) { + return false; + } + var r = errorHandler( + fileSuccessHandler( + uploadStartHandler( + filesAddedHandler( + markResumableDragAndDropElement( + makeResumableElement( + the_form.attr("data-resumable-target"), + file_input.parent(), + $("#" + resumable_element_id), + submit_button, + ["csv", "tsv", "txt"]), + file_input.parent(), + $("#" + resumable_element_id), + $("#" + resumable_element_id + "-browse-button")), + (files) => { + // TODO: Also trigger preview! + resumableDisplayFiles( + $("#" + resumable_element_id + "-selected-files"), files); + files.forEach((file) => { + readFirstNLines( + file.file, + 10, + [makePreviewUpdater( + $("#" + preview_table_id))]) + }); + }), + startUpload($("#" + resumable_element_id + "-browse-button"), + $("#" + resumable_element_id + "-retry-button"), + $("#" + resumable_element_id + "-cancel-button"))), + uploadSuccess(file_input.attr("name"))), + uploadError()); + + /** Setup progress indicator **/ + progressHandler( + r, + indicateProgress(r, $("#" + resumable_element_id + "-progress-bar"))); + + return r; + }; + + var resumables = [ + ["frm-add-phenotypes", "finput-phenotype-descriptions", "resumable-phenotype-descriptions", "tbl-preview-pheno-desc"], + ["frm-add-phenotypes", "finput-phenotype-data", "resumable-phenotype-data", "tbl-preview-pheno-data"], + ["frm-add-phenotypes", "finput-phenotype-se", "resumable-phenotype-se", "tbl-preview-pheno-se"], + ["frm-add-phenotypes", "finput-phenotype-n", "resumable-phenotype-n", "tbl-preview-pheno-n"], + ].map((row) => { + r = makeResumableObject(row[0], row[1], row[2], row[3]); + r.preview_table = $("#" + row[3]); + return r; + }).filter((val) => { + return Boolean(val); + }); + + $("#frm-add-phenotypes input[type=submit]").on("click", (event) => { + event.preventDefault(); + console.debug(); + if ($("#txt-publication-id").val() == "") { + alert("You MUST provide a publication for the phenotypes."); + return false; + } + // TODO: Check all the relevant files exist + // TODO: Verify that files are not duplicated + var filenames = []; + var nondupfiles = []; + resumables.forEach((r) => { + var fname = r.files[0].file.name; + filenames.push(fname); + if(!nondupfiles.includes(fname)) { + nondupfiles.push(fname); + } + }); + + // Check that all files were provided + if(resumables.length !== filenames.length) { + window.alert("You MUST provide all the files requested."); + event.target.removeAttribute("disabled"); + return false; + } + + // Check that there are no duplicate files + var duplicates = Object.entries(filenames.reduce( + (acc, curr, idx, arr) => { + acc[curr] = (acc[curr] || 0) + 1; + return acc; + }, + {})).filter((entry) => {return entry[1] !== 1;}); + if(duplicates.length > 0) { + var msg = "The file(s):\r\n"; + msg = msg + duplicates.reduce( + (msgstr, afile) => { + return msgstr + " • " + afile[0] + "\r\n"; + }, + ""); + msg = msg + "is(are) duplicated. Please fix and try again."; + window.alert(msg); + event.target.removeAttribute("disabled"); + return false; + } + // TODO: Check all fields + // Start the uploads. + event.target.setAttribute("disabled", "disabled"); + resumables.forEach((r) => {r.upload();}); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html new file mode 100644 index 0000000..898fc0c --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -0,0 +1,207 @@ +{%extends "phenotypes/add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block frm_add_phenotypes_documentation%} +<p>Select the zip file bundle containing information on the phenotypes you + wish to upload, then click the "Upload Phenotypes" button below to + upload the data.</p> +<p>If you wish to upload the files individually instead, + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="">click here</a>.</p> +<p>See the <a href="#section-file-formats">File Formats</a> section below + to get an understanding of what is expected of the bundle files you + upload.</p> +{%endblock%} + +{%block frm_add_phenotypes_elements%} +<div class="form-group"> + <label for="finput-phenotypes-bundle" class="form-label"> + Phenotypes Bundle</label> + <input type="file" + id="finput-phenotypes-bundle" + name="phenotypes-bundle" + accept="application/zip, .zip" + required="required" + class="form-control" /> +</div> +{%endblock%} + +{%block page_documentation%} +<div class="row"> + <h2 class="heading" id="section-file-formats">File Formats</h2> + <p>We accept an extended form of the + <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files" + title="R/qtl2 software input file format documentation"> + input files' format used with the R/qtl2 software</a> as a single ZIP + file</p> + <p>The files that are used for this feature are: + <ul> + <li>the <em>control</em> file</li> + <li><em>pheno</em> file(s)</li> + <li><em>phenocovar</em> file(s)</li> + <li><em>phenose</em> files(s)</li> + </ul> + </p> + <p>Other files within the bundle will be ignored, for this feature.</p> + <p>The following section will detail the expectations for each of the + different file types within the uploaded ZIP file bundle for phenotypes:</p> + + <h3 class="subheading">Control File</h3> + <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts + as the control file. This file can be: + <ul> + <li>a <em>JSON</em> file, or</li> + <li>a <em>YAML</em> file.</li> + </ul> + </p> + + <p>The control file is useful for defining things about the bundle such as:</p> + <ul> + <li>The field separator value (default: <code>sep: ','</code>). There can + only ever be one field separator and it <strong>MUST</strong> be the same + one for <strong>ALL</strong> files in the bundle.</li> + <li>The comment character (default: <code>comment.char: '#'</code>). Any + line that starts with this character will be considered a comment line and + be ignored in its entirety.</li> + <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You + can specify more than one code to indicate missing values, e.g. + <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li> + </ul> + + <h3 class="subheading"><em>pheno</em> File(s)</h3> + <p>These files are the main data files. You must have at least one of these + files in your bundle for it to be valid for this step.</p> + <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as + below:<br /> + <code> + id,10001,10002,10003,10004,…<br /> + BXD1,61.400002,54.099998,483,49.799999,…<br /> + BXD2,49,50.099998,403,45.5,…<br /> + BXD5,62.5,53.299999,501,62.900002,…<br /> + BXD6,53.099998,55.099998,403,NA,…<br /> + â‹®<br /></code> + </p> + <p>If the <code>pheno_transposed</code> value is set to <code>True</code>, + then the data will be a <em>phenotypes × individuals</em> matrix as in the + example below:<br /> + <code> + id,BXD1,BXD2,BXD5,BXD6,…<br /> + 10001,61.400002,49,62.5,53.099998,…<br /> + 10002,54.099998,50.099998,53.299999,55.099998,…<br /> + 10003,483,403,501,403,…<br /> + 10004,49.799999,45.5,62.900002,NA,…<br /> + â‹® + </code> + </p> + + + <h3 class="subheading"><em>phenocovar</em> File(s)</h3> + <p>At least one phenotypes metadata file with the metadata values such as + descriptions, PubMed Identifier, publication titles (if present), etc.</p> + <p>The data in this/these file(s) is a matrix of + <em>phenotypes × phenotypes-covariates</em>. The first column is always the + phenotype names/identifiers — same as in the R/qtl2 format.</p> + <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p> + <p>This file <strong>MUST</strong> be present in the bundle, and have data for + the bundle to be considered valid by our system for this step.<br /> + In addition to that, the following are the fields that <strong>must be + present</strong>, and + have values, in the file before the file is considered valid: + <ul> + <li><em>description</em>: A description for each phenotype. Useful + for users to know what the phenotype is about.</li> + <li><em>units</em>: The units of measurement for the phenotype, + e.g. milligrams for brain weight, centimetres/millimetres for + tail-length, etc.</li> + </ul></p> + + <p>The following <em>optional</em> fields can also be provided: + <ul> + <li><em>pubmedid</em>: A PubMed Identifier for the publication where + the phenotype is published. If this field is not provided, the system will + assume your phenotype is not published.</li> + </ul> + </p> + <p>These files will be marked up in the control file with the + <code>phenocovar</code> key, as in the examples below: + <ol> + <li>JSON: single file<br /> + <code>{<br /> + â‹®,<br /> + "phenocovar": "your_covariates_file.csv",<br /> + â‹®<br /> + } + </code> + </li> + <li>JSON: multiple files<br /> + <code>{<br /> + â‹®,<br /> + "phenocovar": [<br /> + "covariates_file_01.csv",<br /> + "covariates_file_01.csv",<br /> + â‹®<br /> + ],<br /> + â‹®<br /> + } + </code> + </li> + <li>YAML: single file or<br /> + <code> + â‹®<br /> + phenocovar: your_covariates_file.csv<br /> + â‹® + </code> + </li> + <li>YAML: multiple files<br /> + <code> + â‹®<br /> + phenocovar:<br /> + - covariates_file_01.csv<br /> + - covariates_file_02.csv<br /> + - covariates_file_03.csv<br /> + …<br /> + â‹® + </code> + </li> + </ol> + </p> + + <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3> + <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are + not supported by the original R/qtl2 file format</p> + <p>We use these files to upload the standard errors (<em>phenose</em>) when + the data file (<em>pheno</em>) is average data. In that case, the + <em>phenonum</em> file(s) contains the number of individuals that were + involved when computing the averages.</p> + <p>Both types of files are matrices of <em>individuals × phenotypes</em> by + default. Like the related <em>pheno</em> files, if + <code>pheno_transposed: True</code>, then the file will be a matrix of + <em>phenotypes × individuals</em>.</p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html new file mode 100644 index 0000000..adbc012 --- /dev/null +++ b/uploader/templates/phenotypes/base.html @@ -0,0 +1,19 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + {%if dataset is mapping%} + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">{{dataset.Name}}</a> + {%else%} + <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a> + {%endif%} +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/bulk-edit-upload.html b/uploader/templates/phenotypes/bulk-edit-upload.html new file mode 100644 index 0000000..d0f38f5 --- /dev/null +++ b/uploader/templates/phenotypes/bulk-edit-upload.html @@ -0,0 +1,62 @@ +{%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" + accept="text/tab-separated-values" + 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/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html new file mode 100644 index 0000000..19a2b34 --- /dev/null +++ b/uploader/templates/phenotypes/create-dataset.html @@ -0,0 +1,108 @@ +{%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=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Create a new phenotype dataset.</p> +</div> + +<div class="row"> + <form id="frm-create-pheno-dataset" + action="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST"> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-name">Name</label> + {%if errors["dataset-name"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-name"]}}</p></small> + {%endif%} + <input type="text" + name="dataset-name" + id="txt-dataset-name" + value="{{original_formdata.get('dataset-name') or (population.Name + 'Publish')}}" + {%if errors["dataset-name"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A short representative name for the dataset.</p> + <p>Recommended: Use the population name and append "Publish" at the end. + <br />This field will only accept names composed of + letters ('A-Za-z'), numbers (0-9), hyphens and underscores.</p> + </small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-fullname">Full Name</label> + {%if errors["dataset-fullname"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-fullname"]}}</p></small> + {%endif%} + <input id="txt-dataset-fullname" + name="dataset-fullname" + type="text" + value="{{original_formdata.get('dataset-fullname', '')}}" + {%if errors["dataset-fullname"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A longer, descriptive name for the dataset. The name is meant for use + by humans, and therefore, it should be clear what the dataset contains + from the name.</p> + </small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-shortname">Short Name</label> + <input id="txt-dataset-shortname" + name="dataset-shortname" + type="text" + class="form-control" + value="{{original_formdata.get('dataset-shortname') or (population.Name + 'Publish')}}" /> + <small class="form-text text-muted"> + <p>An optional, short name for the dataset. <br /> + If this is not provided, it will default to the value provided for the + <strong>Name</strong> field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create phenotype dataset" /> + </div> + + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html new file mode 100644 index 0000000..115d6af --- /dev/null +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -0,0 +1,208 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%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=="edit-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">edit phenotype data</h2> + <p>The forms provided in this page help you update the data for the + phenotypes, and the publication information for the phenotype, + respectively.</p> +</div> + +<div class="row"> + <h3 class="subheading">Basic metadata</h3> + <form name="frm-phenotype-basic-metadata" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <input type="hidden" name="phenotype-id" value="{{phenotype.Id}}" /> + <div class="form-group"> + <label for="txt-pre-publication-description" + class="control-label col-sm-2">Pre-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-description" + name="pre-publication-description" + class="form-control" + value="{{phenotype['Pre_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-pre-publication-abbreviation" + class="control-label col-sm-2">Pre-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-abbreviation" + name="pre-publication-abbreviation" + class="form-control" + value="{{phenotype['Pre_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-description" + class="control-label col-sm-2">Post-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-description" + name="post-publication-description" + class="form-control" + value="{{phenotype['Post_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-abbreviation" + class="control-label col-sm-2">Post-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-abbreviation" + name="post-publication-abbreviation" + class="form-control" + value="{{phenotype['Post_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-original-description" + class="control-label col-sm-2">Original Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-original-description" + name="original-description" + class="form-control" + value="{{phenotype['Original_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-units" + class="control-label col-sm-2">units</label> + <div class="col-sm-10"> + <input type="text" + id="txt-units" + name="units" + class="form-control" + required="required" + value="{{phenotype['Units']}}" /> + </div> + </div> + + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update basic metadata"> + </div> + </div> + </form> +</div> + + +<div class="row"> + <h3 class="subheading">phenotype data</h3> + <form id="frm-edit-phenotype-data" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <div style="max-height: 23.37em;overflow-y: scroll;"> + <table class="table table-striped table-responsive table-form-table"> + <thead style="position: sticky; top: 0;"> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if population.Family in families_with_se_and_n%} + <th>Standard-Error</th> + <th>Number of Samples</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td> + <input type="text" + name="value-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" + class="form-control" /> + <input type="hidden" + name="value-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" /></td> + {%if population.Family in families_with_se_and_n%} + <td> + <input type="text" + name="se-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" + data-original-value="{{item.error or ''}}" + class="form-control" /> + <input type="hidden" + name="se-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" /></td> + <td> + <input type="text" + name="n-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" + data-original-value="{{item.count or "-"}}" + class="form-control" /> + <input type="hidden" + name="n-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" /></td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + </div> + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update data" /> + </div> + </div> + </form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html new file mode 100644 index 0000000..689c28e --- /dev/null +++ b/uploader/templates/phenotypes/index.html @@ -0,0 +1,21 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {{select_species_form(url_for("species.populations.phenotypes.index"), species)}} +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html new file mode 100644 index 0000000..257f726 --- /dev/null +++ b/uploader/templates/phenotypes/job-status.html @@ -0,0 +1,155 @@ +{%extends "phenotypes/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block extrameta%} +{%if job and job.status not in ("success", "completed:success", "error", "completed:error")%} +<meta http-equiv="refresh" content="5" /> +{%endif%} +{%endblock%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} + +{%if job%} +<h4 class="subheading">Progress</h4> +<div class="row" style="overflow:scroll;"> + <p><strong>Process Status:</strong> {{job.status}}</p> + {%if metadata%} + <table class="table table-responsive"> + <thead> + <tr> + <th>File</th> + <th>Status</th> + <th>Lines Processed</th> + <th>Total Errors</th> + </tr> + </thead> + + <tbody> + {%for file,meta in metadata.items()%} + <tr> + <td>{{file}}</td> + <td>{{meta.status}}</td> + <td>{{meta.linecount}}</td> + <td>{{meta["total-errors"]}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} +</div> + +<div class="row"> + {%if job.status in ("completed:success", "success")%} + <p> + {%if errors | length == 0%} + <a href="{{url_for('species.populations.phenotypes.review_job_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" + class="btn btn-primary" + title="Continue to process data">Continue</a> + {%else%} + <span class="text-muted" + disabled="disabled" + style="border: solid 2px;border-radius: 5px;padding: 0.3em;"> + Cannot continue due to errors. Please fix the errors first. + </span> + {%endif%} + </p> + {%endif%} +</div> + +<h4 class="subheading">Errors</h4> +<div class="row" style="max-height: 20em; overflow: scroll;"> + {%if errors | length == 0 %} + <p class="text-info"> + <span class="glyphicon glyphicon-info-sign"></span> + No errors found so far + </p> + {%else%} + <table class="table table-responsive"> + <thead style="position: sticky; top: 0; background: white;"> + <tr> + <th>File</th> + <th>Row</th> + <th>Column</th> + <th>Value</th> + <th>Message</th> + </tr> + </thead> + + <tbody style="font-size: 0.9em;"> + {%for error in errors%} + <tr> + <td>{{error.filename}}</td> + <td>{{error.rowtitle}}</td> + <td>{{error.coltitle}}</td> + <td>{%if error.cellvalue is not none and error.cellvalue | length > 25%} + {{error.cellvalue[0:24]}}… + {%else%} + {{error.cellvalue}} + {%endif%} + </td> + <td> + {%if error.message | length > 250 %} + {{error.message[0:249]}}… + {%else%} + {{error.message}} + {%endif%} + </td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} +</div> + +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +<div class="row"> + {{cli_output(job, "stderr")}} +</div> + +{%else%} +<div class="row"> + <h3 class="text-danger">No Such Job</h3> + <p>Could not find a job with the ID: {{job_id}}</p> + <p> + Please go back to + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="'{{dataset.Name}}' dataset page"> + the '{{dataset.Name}}' dataset page</a> + to upload new phenotypes or edit existing ones.</p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html new file mode 100644 index 0000000..2cf2c7f --- /dev/null +++ b/uploader/templates/phenotypes/list-datasets.html @@ -0,0 +1,68 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%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=="list-datasets"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}">List Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {%if datasets | length > 0%} + <p>The dataset(s) available for this population is/are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + {%for dataset in datasets%} + <tr> + <td><a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">{{dataset.Name}}</a></td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p>Phenotypes need to go into a dataset. We do not currently have a dataset + for species <strong>'{{species["FullName"]}} ({{species["Name"]}})'</strong> + phenotypes.</p> + + <p>Do, please, create a new dataset by clicking on the "Create Dataset" button + below and following the prompts/instructions.</p> + <p><a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + class="btn btn-primary" + title="Create a new phenotype dataset.">create dataset</a></p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/load-phenotypes-success.html b/uploader/templates/phenotypes/load-phenotypes-success.html new file mode 100644 index 0000000..645be16 --- /dev/null +++ b/uploader/templates/phenotypes/load-phenotypes-success.html @@ -0,0 +1,42 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="load-phenotypes-success"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block contents%} +<div class="row"> + <p>You have successfully loaded + <!-- maybe indicate the number of phenotypes here? -->your + new phenotypes into the database.</p> + <!-- TODO: Maybe notify user that they have sole access. --> + <!-- TODO: Maybe provide a link to go to GeneNetwork to view the data. --> + <p>View your data + <a href="{{search_page_uri}}" + target="_blank">on GeneNetwork2</a>. + You might need to login to GeneNetwork2 to view specific traits.</p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block more_javascript%}{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html new file mode 100644 index 0000000..11b108b --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html @@ -0,0 +1,31 @@ +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%macro display_pheno_dataset_card(species, population, dataset)%} +{{display_population_card(species, population)}} + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Phenotypes' Dataset</h5> + <div class="card-text"> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{dataset.Name}}</td> + </tr> + + <tr> + <td>Full Name</td> + <td>{{dataset.FullName}}</td> + </tr> + + <tr> + <td>Short Name</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html new file mode 100644 index 0000000..5a4c422 --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-preview-table.html @@ -0,0 +1,19 @@ +{%macro display_preview_table(tableid, filetype)%} +<div class="card"> + <div class="card-body"> + <h5 class="card-title">{{filetype | title}}: File Preview</h5> + <div class="card-text" style="overflow: scroll;"> + <table id="{{tableid}}" class="table table-condensed table-responsive"> + <thead> + <tr> + </tr> + <tbody> + <tr> + <td class="data-row-template text-info"></td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html new file mode 100644 index 0000000..ed14ea5 --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html @@ -0,0 +1,60 @@ +{%macro display_resumable_elements(id, title, help)%} +<div id="{{id}}" + class="resumable-elements visually-hidden" + style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;"> + <strong style="line-height: 1.2em;">{{title | title}}</strong> + + <span class="form-text text-muted">{{help | safe}}</span> + + <div id="{{id}}-selected-files" + class="resumable-selected-files" + style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"> + <div class="panel panel-info file-display-template visually-hidden"> + <div class="panel-heading filename">The Filename Goes Here!</div> + <div class="panel-body"> + <ul> + <li> + <strong>Name</strong>: + <span class="filename">the file's name</span></li> + + <li><strong>Size</strong>: <span class="filesize">0 MB</span></li> + + <li> + <strong>Unique Identifier</strong>: + <span class="fileuniqueid">brrr</span></li> + + <li> + <strong>Mime</strong>: + <span class="filemimetype">text/csv</span></li> + </ul> + </div> + </div> + </div> + + <a id="{{id}}-browse-button" + class="resumable-browse-button btn btn-info" + href="#{{id}}" + style="margin-left: 80%;">Browse</a> + + <div id="{{id}}-progress-bar" class="progress visually-hidden"> + <div class="progress-bar" + role="progress-bar" + aria-valuenow="60" + aria-valuemin="0" + aria-valuemax="100" + style="width: 0%;"> + Uploading: 60% + </div> + </div> + + <div id="{{id}}-cancel-resume-buttons"> + <a id="{{id}}-resume-button" + class="resumable-resume-button btn btn-info visually-hidden" + href="#">resume upload</a> + + <a id="{{id}}-cancel-button" + class="resumable-cancel-button btn btn-danger visually-hidden" + href="#">cancel upload</a> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html new file mode 100644 index 0000000..859df74 --- /dev/null +++ b/uploader/templates/phenotypes/review-job-data.html @@ -0,0 +1,125 @@ +{%extends "phenotypes/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block extrameta%} +{%if not job%} +<meta http-equiv="refresh" + content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" /> +{%endif%} +{%endblock%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} + +{%if job%} +<div class="row"> + <h3 class="heading">Data Review</h3> + <p class="text-info"><strong> + The data has <em>NOT</em> been added/saved yet. Review the details below + and click "Continue" to save the data.</strong></p> + <p>The “<strong>{{dataset.FullName}}</strong>” dataset from the + “<strong>{{population.FullName}}</strong>” population of the + species “<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>” + will be updated as follows:</p> + + <ul> + {%if publication%} + <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes + are linked to the following publication: + <ul> + <li><strong>Publication Title:</strong> + {{publication.Title or "—"}}</li> + <li><strong>Author(s):</strong> + {{publication.Authors or "—"}}</li> + </ul> + </li> + {%endif%} + {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%} + {%if summary.get(ftype, False)%} + <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed + adding {%if ftype == "phenocovar"%}(possibly){%endif%} + {{summary[ftype]["total-data-rows"]}} new + {%if ftype == "phenocovar"%} + phenotypes + {%else%} + {{summary[ftype]["description"]}} rows + {%endif%} + to the database. + </li> + {%endif%} + {%endfor%} + </ul> + + <form id="frm-review-phenotype-data" + method="POST" + action="{{url_for('species.populations.phenotypes.load_data_to_database', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}"> + <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> + <input type="submit" + value="continue" + class="btn btn-primary" /> + </form> +</div> +{%else%} +<div class="row"> + <h4 class="subheading">Invalid Job</h3> + <p class="text-danger"> + Could not find a job with the ID: <strong>{{job_id}}.</p> + <p>You will be redirected in + <span id="countdown-element" class="text-info">20</span> second(s)</p> + <p class="text-muted"> + <small> + If you are not redirected, please + <a href="{{url_for( + 'species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">click here</a> to continue + </small> + </p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(document).ready(function() { + var countdown = 20; + var countdown_element = $("#countdown-element"); + if(countdown_element.length === 1) { + intv = window.setInterval(function() { + countdown = countdown - 1; + countdown_element.html(countdown); + }, 1000); + } + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/select-population.html b/uploader/templates/phenotypes/select-population.html new file mode 100644 index 0000000..48c19b1 --- /dev/null +++ b/uploader/templates/phenotypes/select-population.html @@ -0,0 +1,26 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + + +<div class="row"> + {{select_population_form(url_for("species.populations.phenotypes.select_population", species_id=species.SpeciesId), species, populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%endblock%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html new file mode 100644 index 0000000..306dcce --- /dev/null +++ b/uploader/templates/phenotypes/view-dataset.html @@ -0,0 +1,150 @@ +{%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%} +{{flash_all_messages()}} + +<div class="row"> + <p>The basic dataset details are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row"> + <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Add a bunch of phenotypes" + class="btn btn-primary">Add phenotypes</a></p> +</div> + +<div class="row"> + <h2>Phenotype Data</h2> + + <p>Click on any of the phenotypes in the table below to view and edit that + phenotype's data.</p> + <p>Use the search to filter through all the phenotypes and find specific + phenotypes of interest.</p> +</div> + + +<div class="row"> + + <table id="tbl-phenotypes-list" class="table compact stripe cell-border"> + <thead> + <tr> + <th></th> + <th>Index</th> + <th>Record</th> + <th>Description</th> + </tr> + </thead> + + <tbody></tbody> + </table> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var species_id = {{species.SpeciesId}}; + var population_id = {{population.Id}}; + var dataset_id = {{dataset.Id}}; + var dataset_name = "{{dataset.Name}}"; + var data = {{phenotypes | tojson}}; + + var dtPhenotypesList = buildDataTable( + "#tbl-phenotypes-list", + data, + [ + { + data: function(pheno) { + return `<input type="checkbox" name="selected-phenotypes" ` + + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" ` + + `value="${pheno.InbredSetCode}_${pheno.xref_id}" ` + + `class="chk-row-select" />` + } + }, + {data: "sequence_number"}, + { + data: function(pheno, type, set, meta) { + var spcs_id = {{species.SpeciesId}}; + var pop_id = {{population.Id}}; + var dtst_id = {{dataset.Id}}; + return `<a href="/species/${spcs_id}` + + `/populations/${pop_id}` + + `/phenotypes/datasets/${dtst_id}` + + `/phenotype/${pheno.xref_id}` + + `" target="_blank">` + + `${pheno.InbredSetCode}_${pheno.xref_id}` + + `</a>`; + } + }, + { + data: function(pheno) { + return (pheno.Post_publication_description || + pheno.Original_description || + pheno.Pre_publication_description); + } + } + ], + { + select: "multi+shift", + layout: { + top1Start: { + pageLength: { + text: "Show _MENU_ of _TOTAL_" + } + }, + topStart: "info", + top1End: null + }, + rowId: function(pheno) { + return `${pheno.InbredSetCode}_${pheno.xref_id}`; + } + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html new file mode 100644 index 0000000..21ac501 --- /dev/null +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -0,0 +1,135 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%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-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_phenotype', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Phenotype</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <div class="panel panel-default"> + <div class="panel-heading"><strong>Basic Phenotype Details</strong></div> + + <table class="table"> + <tbody> + <tr> + <td><strong>Phenotype</strong></td> + <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}} + </tr> + <tr> + <td><strong>Database</strong></td> + <td>{{dataset.FullName}}</td> + </tr> + <tr> + <td><strong>Units</strong></td> + <td>{{phenotype.Units}}</td> + </tr> + {%for key,value in publish_data.items()%} + <tr> + <td><strong>{{key}}</strong></td> + <td>{{value}}</td> + </tr> + {%else%} + <tr> + <td colspan="2" class="text-muted"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + No publication data found. + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> +</div> + +{%if "group:resource:edit-resource" in privileges +or "group:resource:delete-resource" in privileges%} +<div class="row"> + <div class="btn-group btn-group-justified"> + <div class="btn-group"> + {%if "group:resource:edit-resource" in privileges%} + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}" + title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." + class="btn btn-primary">Edit</a> + {%endif%} + </div> + <div class="btn-group"></div> + <div class="btn-group"> + {%if "group:resource:delete-resource" in privileges%} + <a href="#" + title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." + class="btn btn-danger not-implemented" + disabled="disabled">delete</a> + {%endif%} + </div> + </div> +</div> +{%endif%} + +<div class="row"> + <div class="panel panel-default"> + <div class="panel-heading"><strong>Phenotype Data</strong></div> + {%if "group:resource:view-resource" in privileges%} + <table class="table"> + <thead> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if has_se%} + <th>SE</th> + <th>N</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td>{{item.value}}</td> + {%if has_se%} + <td>{{item.error or "-"}}</td> + <td>{{item.count or "-"}}</td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + You do not currently have privileges to view this phenotype in greater + detail. + </p> + {%endif%} + </div> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/platforms/base.html b/uploader/templates/platforms/base.html new file mode 100644 index 0000000..dac965f --- /dev/null +++ b/uploader/templates/platforms/base.html @@ -0,0 +1,13 @@ +{%extends "species/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="platforms"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.platforms.index')}}"> + Sequencing Platforms</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html new file mode 100644 index 0000000..0866d5e --- /dev/null +++ b/uploader/templates/platforms/create-platform.html @@ -0,0 +1,124 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Platforms — Create Platforms{%endblock%} + +{%block pagetitle%}Platforms — Create Platforms{%endblock%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="create-platform"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}">create platform</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Create New Platform</h2> + + <p>You can create a new genetic sequencing platform below.</p> +</div> + +<div class="row"> + <form id="frm-create-platform" + method="POST" + action="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}"> + + <div class="form-group"> + <label for="txt-geo-platform" class="form-label">GEO Platform</label> + <input type="text" + id="txt-geo-platform" + name="geo-platform" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is the platform's + <a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Platforms for '{{species.FullName}}' on NCBI"> + accession value on NCBI</a>. If you do not know the value, click the + link and search on NCBI for species '{{species.FullName}}'.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-name" class="form-label">Platform Name</label> + <input type="text" + id="txt-platform-name" + name="platform-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is name of the genetic sequencing platform.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-shortname" class="form-label"> + Platform Short Name</label> + <input type="text" + id="txt-platform-shortname" + name="platform-shortname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>Use the following conventions for this field: + <ol> + <li>Start with a 4-letter vendor code, e.g. "Affy" for "Affymetrix", "Illu" for "Illumina", etc.</li> + <li>Append an underscore to the 4-letter vendor code</li> + <li>Use the name of the array given by the vendor, e.g. U74AV2, MOE430A, etc.</li> + </ol> + </p> + </small> + </div> + + <div class="form-group"> + <label for="txt-platform-title" class="form-label">Platform Title</label> + <input type="text" + id="txt-platform-title" + name="platform-title" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>The full platform title. Sometimes, this is the same as the Platform + Name above.</p></small> + </div> + + <div class="form-group"> + <label for="txt-go-tree-value" class="form-label">GO Tree Value</label> + <input type="text" + id="txt-go-tree-value" + name="go-tree-value" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a Chip identification value useful for analysis with the + <strong> + <a href="https://www.geneweaver.org/" + title="Go to the GeneWeaver site." + target="_blank">GeneWeaver</a></strong> + and + <strong> + <a href="https://www.webgestalt.org/" + title="Go to the WEB-based GEne SeT AnaLysis Toolkit site." + target="_blank">WebGestalt</a></strong> + tools.<br /> + This can be left blank for custom platforms.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + value="create new platform" + class="btn btn-primary" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/platforms/index.html b/uploader/templates/platforms/index.html new file mode 100644 index 0000000..555b444 --- /dev/null +++ b/uploader/templates/platforms/index.html @@ -0,0 +1,25 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Platforms{%endblock%} + +{%block pagetitle%}Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>In this section, you will be able to view and manage the sequencing + platforms that are currently supported by GeneNetwork.</p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.platforms.index"), species)}} +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html new file mode 100644 index 0000000..a6bcfdc --- /dev/null +++ b/uploader/templates/platforms/list-platforms.html @@ -0,0 +1,93 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Platforms — List Platforms{%endblock%} + +{%block pagetitle%}Platforms — List Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>View the list of the genetic sequencing platforms that are currently + supported by GeneNetwork.</p> + <p>If you cannot find the platform you wish to use, you can add it by clicking + the "New Platform" button below.</p> + <p><a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}" + title="Create a new genetic sequencing platform for species {{species.FullName}}" + class="btn btn-primary">Create Platform</a></p> +</div> + +<div class="row"> + <h2>Supported Platforms</h2> + {%if platforms is defined and platforms | length > 0%} + <p>There are {{total_platforms}} platforms supported by GeneNetwork</p> + + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying platforms {{start_from+1}} to {{start_from+count if start_from+count < total_platforms else total_platforms}} of + {{total_platforms}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_platforms%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + + <table class="table"> + <thead> + <tr> + <th></th> + <th>Platform Name</th> + <th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Gene Expression Omnibus: Platforms section" + target="_blank">GEO Platform</a></th> + <th>Title</th> + </tr> + </thead> + + <tbody> + {%for platform in platforms%} + <tr> + <td>{{platform.sequence_number}}</td> + <td>{{platform.GeneChipName}}</td> + <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{platform.GeoPlatform}}" + title="View platform on the Gene Expression Omnibus" + target="_blank">{{platform.GeoPlatform}}</a></td> + <td>{{platform.Title}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There are no platforms supported at this time!</p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html new file mode 100644 index 0000000..9db8083 --- /dev/null +++ b/uploader/templates/populations/base.html @@ -0,0 +1,18 @@ +{%extends "species/base.html"%} + +{%block lvl2_breadcrumbs%} +<li {%if activelink=="populations"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.view_population', + species_id=species.SpeciesId, + population_id=population.Id)}}">{{population.Name}}</a> + {%else%} + <a href="{{url_for('species.populations.index')}}">Populations</a> + {%endif%} +</li> +{%block lvl3_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html new file mode 100644 index 0000000..007b6bf --- /dev/null +++ b/uploader/templates/populations/create-population.html @@ -0,0 +1,269 @@ +{%extends "populations/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Create Population{%endblock%} + +{%block pagetitle%}Create Population{%endblock%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="create-population"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.create_population', + species_id=species.SpeciesId)}}">create population</a> +</li> +{%endblock%} + + +{%block contents%} +<div class="row"> + <p>The population is the next hierarchical node under Species. Data is grouped under a specific population, under a particular species.</p> + <p> + This page enables you to create a new population, in the case that you + cannot find the population you want in the + <a + href="{{url_for('species.populations.list_species_populations', + species_id=species.SpeciesId)}}" + title="Population for species '{{species.FullName}}'."> + list of species populations + </a> + </p> +</div> + +<div class="row"> + <form method="POST" + action="{{url_for('species.populations.create_population', + species_id=species.SpeciesId, + return_to=return_to)}}"> + + <legend>Create Population</legend> + + {{flash_all_messages()}} + + <input type="hidden" name="return_to" value="{{return_to}}"> + + <div {%if errors.population_fullname%} + class="form-group has-error" + {%else%} + class="form-group" + {%endif%}> + <label for="txt-population-fullname" class="form-label">Full Name</label> + {%if errors.population_fullname%} + <small class="form-text text-danger">{{errors.population_fullname}}</small> + {%endif%} + <input type="text" + id="txt-population-fullname" + name="population_fullname" + required="required" + minLength="3" + maxLength="100" + value="{{error_values.population_fullname or ''}}" + class="form-control" /> + <small class="form-text text-muted"> + <p> + This is a descriptive name for your population — useful for + humans. + </p> + </small> + </div> + + <div {%if errors.population_name%} + class="form-group has-error" + {%else%} + class="form-group" + {%endif%}> + <label for="txt-population-name" class="form-label">Name</label> + {%if errors.population_name%} + <small class="form-text text-danger">{{errors.population_name}}</small> + {%endif%} + <input type="text" + id="txt-population-name" + name="population_name" + required="required" + minLength="3" + maxLength="30" + value="{{error_values.population_name or ''}}" + class="form-control" /> + <small class="form-text text-muted"> + <p> + This is a short representative, but constrained name for your + population. + <br /> + The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens + and underscores. Any other character will cause the name to be + rejected. + </p> + </small> + </div> + + <div class="form-group"> + <label for="txt-population-code" class="form-label">Population Code</label> + <input type="text" + id="txt-population-code" + name="population_code" + maxLength="5" + minLength="3" + value="{{error_values.population_code or ''}}" + class="form-control" /> + <small class="form-text text-muted"> + <p class="form-text text-muted"> + This is a 3-character code for your population, that is prepended to + the phenotype identifiers. e.g. For the "BXD Family" population, the + code is "BXD" and therefore, the phenotype identifiers for the + population look like the following examples: <em>BXD_10148</em>, + <em>BXD_10180</em>, <em>BXD_10197</em>, etc. + </p> + </small> + </div> + + <div {%if errors.population_description%} + class="form-group has-error" + {%else%} + class="form-group" + {%endif%}> + <label for="txt-population-description" class="form-label"> + Description + </label> + {%if errors.population_description%} + <small class="form-text text-danger">{{errors.population_description}}</small> + {%endif%} + <textarea + id="txt-population-description" + name="population_description" + required="required" + class="form-control" + rows="5">{{error_values.population_description or ''}}</textarea> + <small class="form-text text-muted"> + <p> + This is a more detailed description for your population. This is + useful to communicate with other researchers some details regarding + your population, and what its about. + <br /> + Put, here, anything that describes your population but does not go + cleanly under metadata. + </p> + </small> + </div> + + <div {%if errors.population_family%} + class="form-group has-error" + {%else%} + class="form-group" + {%endif%}> + <label for="txt-population-family" class="form-label">Family</label> + <input type="text" + id="txt-population-family" + name="population_family" + class="form-control" + list="families-list" /> + <datalist id="families-list"> + {%for family in families%} + <option value="{{family}}">{{family}}</option> + {%endfor%} + </datalist> + <small class="form-text text-muted"> + <p> + This is <strong>optional</strong> metadata. It is used to group + populations into "families" for presentation in the menus. + {%if families | length > 0%} + Examples of currently existing families are: + <ul> + {%for family in families[0:7]%} + <li>{{family}}</li> + {%endfor%} + <li>etc.</li> + </ul> + {%endif%} + + You can + {%if families|length>0%} select from existing families, or {%endif%} + create a new family by typing in the input box above. You can also + leave the family blank.</p> + </small> + </div> + + <div {%if errors.population_mapping_method_id%} + class="form-group has-error" + {%else%} + class="form-group" + {%endif%}> + <label for="select-population-mapping-methods" + class="form-label">Mapping Methods</label> + + <select id="select-population-mapping-methods" + name="population_mapping_method_id" + class="form-control" + required="required"> + <option value="">Select appropriate mapping methods</option> + {%for mmethod in mapping_methods%} + <option value="{{mmethod.id}}" + {%if error_values.population_mapping_method_id == mmethod.id%} + selected="selected" + {%endif%}>{{mmethod.value}}</option> + {%endfor%} + </select> + + <small class="form-text text-muted"> + <p>Select the mapping methods that your population will support.</p> + </small> + </div> + + <div {%if errors.population_genetic_type%} + class="form-group has-error" + {%else%} + class="form-group" + {%endif%}> + <label for="select-population-genetic-type" + class="form-label">Genetic Type</label> + <select id="select-population-genetic-type" + name="population_genetic_type" + class="form-control"> + <option value="">Select proper genetic type</option> + {%for gtype in genetic_types%} + <option value="{{gtype}}" + {%if error_values.population_genetic_type == gtype%} + selected="selected" + {%endif%}>{{gtype}}</option> + {%endfor%} + </select> + <small class="form-text text-muted text-danger"> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + This might be a poorly named field. + </p> + <p> + It probably has more to do with the mating crosses/crossings used to + produce the individuals in the population. I am no biologist, however, + and I'm leaving this here to remind myself to confirm this. + </p> + <p> + I still don't know what riset is.<br /> + … probably something to do with Recombinant Inbred Strains + </p> + <p> + Possible resources for this: + <ul> + <li>https://www.informatics.jax.org/silver/chapters/3-2.shtml</li> + <li>https://www.informatics.jax.org/silver/chapters/9-2.shtml</li> + </ul> + </p> + </small> + </div> + + <div class="form-group"> + <input type="submit" + value="create population" + class="btn btn-primary" /> + </div> + + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html new file mode 100644 index 0000000..d2bee77 --- /dev/null +++ b/uploader/templates/populations/index.html @@ -0,0 +1,28 @@ +{%extends "populations/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p> + Your experiment data will relate to a particular population from a + particular species. Let us know what species it is you want to work with + below. + </p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.populations.index"), species)}} +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html new file mode 100644 index 0000000..f780e94 --- /dev/null +++ b/uploader/templates/populations/list-populations.html @@ -0,0 +1,93 @@ +{%extends "populations/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="list-populations"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.list_species_populations', + species_id=species.SpeciesId)}}">List populations</a> +</li> +{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} +<div class="row"> + <p> + The following populations/groups exist for the '{{species.FullName}}' + species. + </p> + <p> + Click on the population's name to select and continue using the population. + </p> +</div> + +<div class="row"> + <p> + If the population you need for the species '{{species.FullName}}' does not + exist, click on the "Create Population" button below to create a new one. + </p> + <p> + <a href="{{url_for('species.populations.create_population', + species_id=species.SpeciesId)}}" + title="Create a new population for species '{{species.FullName}}'." + class="btn btn-danger"> + Create Population + </a> + </p> +</div> + +<div class="row"> + <table class="table"> + <caption>Populations for {{species.FullName}}</caption> + <thead> + <tr> + <th></th> + <th>Name</th> + <th>Full Name</th> + <th>Description</th> + </tr> + </thead> + + <tbody> + {%for population in populations%} + <tr> + <td>{{population["sequence_number"]}}</td> + <td> + <a href="{{url_for('species.populations.view_population', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + title="Population '{{population.FullName}}' for species '{{species.FullName}}'."> + {{population.Name}} + </a> + </td> + <td>{{population.FullName}}</td> + <td>{{population.Description}}</td> + </tr> + {%else%} + <tr> + <td colspan="3"> + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-mark"></span> + There were no populations found for {{species.FullName}}! + </p> + </td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html new file mode 100644 index 0000000..16b477f --- /dev/null +++ b/uploader/templates/populations/macro-display-population-card.html @@ -0,0 +1,41 @@ +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%macro display_population_card(species, population)%} +{{display_species_card(species)}} + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Population</h5> + <div class="card-text"> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{population.Name}}</td> + </tr> + + <tr> + <td>Full Name</td> + <td>{{population.FullName}}</td> + </tr> + + <tr> + <td>Code</td> + <td>{{population.InbredSetCode}}</td> + </tr> + + <tr> + <td>Genetic Type</td> + <td>{{population.GeneticType}}</td> + </tr> + + <tr> + <td>Family</td> + <td>{{population.Family}}</td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html new file mode 100644 index 0000000..14b0510 --- /dev/null +++ b/uploader/templates/populations/macro-select-population.html @@ -0,0 +1,52 @@ +{%from "macro-step-indicator.html" import step_indicator%} + +{%macro select_population_form(form_action, species, populations)%} +<form method="GET" action="{{form_action}}" class="form-horizontal"> + + <h2>{{step_indicator("2")}} What population do you want to work with?</h2> + + {%if populations | length != 0%} + + <p class="form-text">Search for, and select the population from the table + below and click "Continue"</p> + + <div class="radio"> + <label class="control-label" for="rdo-cant-find-population"> + <input type="radio" id="rdo-cant-find-population" + name="population_id" value="CREATE-POPULATION" /> + I cannot find the population I want — create it! + </label> + </div> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" value="continue" class="btn btn-primary" /> + </div> + + <div style="margin-top:3em;"> + <table id="tbl-select-population" class="table compact stripe" + data-populations-list='{{populations | tojson}}'> + <thead> + <tr> + <th></th> + <th>Population</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> + + {%else%} + <p class="form-text"> + There are no populations currently defined for {{species['FullName']}} + ({{species['SpeciesName']}}).<br /> + Click "Continue" to create the first!</p> + <input type="hidden" name="population_id" value="CREATE-POPULATION" /> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" value="continue" class="btn btn-primary" /> + </div> + {%endif%} + +</form> +{%endmacro%} diff --git a/uploader/templates/populations/rqtl2/create-tissue-success.html b/uploader/templates/populations/rqtl2/create-tissue-success.html new file mode 100644 index 0000000..d6fe154 --- /dev/null +++ b/uploader/templates/populations/rqtl2/create-tissue-success.html @@ -0,0 +1,106 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Select Tissue</h2> + +<div class="row"> + <p>You have successfully added a new tissue, organ or biological material with + the following details:</p> +</div> + +<div class="row"> + {{flash_all_messages()}} + + <form id="frm-create-tissue-display" + method="POST" + action="#"> + <legend class="heading">Create Tissue</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <div class="form-group"> + <label>Name</label> + <label>{{tissue.TissueName}}</label> + </div> + + <div class="form-group"> + <label>Short Name</label> + <label>{{tissue.Short_Name}}</label> + </div> + + {%if tissue.BIRN_lex_ID%} + <div class="form-group"> + <label>BIRN Lex ID</label> + <label>{{tissue.BIRN_lex_ID}}</label> + </div> + {%endif%} + + {%if tissue.BIRN_lex_Name%} + <div class="form-group"> + <label>BIRN Lex Name</label> + <label>{{tissue.BIRN_lex_Name}}</label> + </div> + {%endif%} + </form> + + <div id="action-buttons" + style="width:65ch;display:inline-grid;column-gap:5px;"> + + <form id="frm-create-tissue-success-continue" + method="POST" + action="{{url_for('expression-data.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + style="display: inline; width: 100%; grid-column: 1 / 2; + padding-top: 0.5em; text-align: center; border: none; + background-color: inherit;"> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> + </div> +</div> + +<div class="row"> + <p style="display:inline;width:100%;grid-column:2/3;text-align:center; + color:#336699;font-weight:bold;"> + OR + </p> +</div> + +<div class="row"> + <form id="frm-create-tissue-success-select-existing" + method="POST" + action="{{url_for('expression-data.rqtl2.select_tissue', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + style="display: inline; width: 100%; grid-column: 3 / 4; + padding-top: 0.5em; text-align: center; border: none; + background-color: inherit;"> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + + <button type="submit" class="btn btn-primary"> + select from existing tissues</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/index.html b/uploader/templates/populations/rqtl2/index.html new file mode 100644 index 0000000..ec6ffb8 --- /dev/null +++ b/uploader/templates/populations/rqtl2/index.html @@ -0,0 +1,54 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Data Upload{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 data upload</h1> + +<h2>R/qtl2 Upload</h2> + +<div class="row"> + <form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}" + id="frm-rqtl2-upload"> + <legend class="heading">upload R/qtl2 bundle</legend> + {{flash_messages("error-rqtl2")}} + + <div class="form-group"> + <label for="select:species" class="form-label">Species</label> + <select id="select:species" + name="species_id" + required="required" + class="form-control"> + <option value="">Select species</option> + {%for spec in species%} + <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + Data that you upload to the system should belong to a know species. + Here you can select the species that you wish to upload data for. + </small> + </div> + + <input type="submit" class="btn btn-primary" value="submit" /> + </form> +</div> + +<div class="row"> + <h2 class="heading">R/qtl2 Bundles</h2> + + <div class="explainer"> + <p>This feature combines and extends the two upload methods below. Instead of + uploading one item at a time, the R/qtl2 bundle you upload can contain both + the genotypes data (samples/individuals/cases and their data) and the + expression data.</p> + <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither + of the methods below can handle.</p> + + <a href="{{url_for('expression-data.rqtl2.select_species')}}" + title="Upload a zip bundle of R/qtl2 files"> + <button class="btn btn-primary">upload R/qtl2 bundle</button></a> + </div> +</div> +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/no-such-job.html b/uploader/templates/populations/rqtl2/no-such-job.html new file mode 100644 index 0000000..b17004f --- /dev/null +++ b/uploader/templates/populations/rqtl2/no-such-job.html @@ -0,0 +1,13 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 job status</h1> + +<h2>R/qtl2 Upload: No Such Job</h2> + +<p class="alert-danger">No job with ID {{jobid}} was found.</p> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-job-error.html new file mode 100644 index 0000000..9817518 --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-job-error.html @@ -0,0 +1,39 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 job status</h1> + +<h2>R/qtl2 Upload: Job Status</h2> + +<div class="explainer"> + <p>The processing of the R/qtl2 bundle you uploaded has failed. We have + provided some information below to help you figure out what the problem + could be.</p> + <p>If you find that you cannot figure out what the problem is on your own, + please contact the team running the system for assistance, providing the + following details: + <ul> + <li>R/qtl2 bundle you uploaded</li> + <li>This URL: <strong>{{request_url()}}</strong></li> + <li>(maybe) a screenshot of this page</li> + </ul> + </p> +</div> + +<h4>stdout</h4> +{{cli_output(job, "stdout")}} + +<h4>stderr</h4> +{{cli_output(job, "stderr")}} + +<h4>Log</h4> +<div class="cli-output"> + {%for msg in messages%} + {{msg}}<br /> + {%endfor%} +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-job-results.html new file mode 100644 index 0000000..4ecd415 --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-job-results.html @@ -0,0 +1,24 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 job status</h1> + +<h2>R/qtl2 Upload: Job Status</h2> + +<div class="explainer"> + <p>The processing of the R/qtl2 bundle you uploaded has completed + successfully.</p> + <p>You should now be able to use GeneNetwork to run analyses on your data.</p> +</div> + +<h4>Log</h4> +<div class="cli-output"> + {%for msg in messages%} + {{msg}}<br /> + {%endfor%} +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-job-status.html new file mode 100644 index 0000000..e896f88 --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-job-status.html @@ -0,0 +1,20 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Job Status{%endblock%} + +{%block extrameta%} +<meta http-equiv="refresh" content="3"> +{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 job status</h1> + +<h2>R/qtl2 Upload: Job Status</h2> + +<h4>Log</h4> +<div class="cli-output"> + <pre>{{"\n".join(messages)}}</pre> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html new file mode 100644 index 0000000..90e8887 --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html @@ -0,0 +1,120 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}R/qtl2 bundle: QC Job Error{%endblock%} + +{%macro errors_table(tableid, errors)%} +<table id="{{tableid}}" class="table error-table"> + <caption>{{caption}}</caption> + <thead> + <tr> + <th>Line</th> + <th>Column</th> + <th>Value</th> + <th>Message</th> + </tr> + </thead> + <tbody> + {%for error in errors%} + <tr> + <td>{{error.line}}</td> + <td>{{error.column}}</td> + <td>{{error.value}}</td> + <td>{{error.message}}</td> + </tr> + {%else%} + <tr> + <td colspan="4">No errors to display here.</td> + </tr> + {%endfor%} + </tbody> +</table> +{%endmacro%} + +{%block contents%} +<h1 class="heading">R/qtl2 bundle: QC job Error</h1> + +<div class="explainer"> + <p>The R/qtl2 bundle has failed some <emph>Quality Control</emph> checks.</p> + <p>We list below some of the errors that need to be fixed before the data can + be uploaded onto GeneNetwork.</p> +</div> + +{%if errorsgeneric | length > 0%} +<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3> +<div class="explainer"> + We found the following generic errors in your R/qtl2 bundle: +</div> + +<h3>Missing Files</h3> +<div class="explainer"> + <p>These files are listed in the bundle's control file, but do not actually + exist in the bundle</p> +</div> +<table id="tbl-errors-missing-files" class="table error-table"> + <thead> + <tr> + <th>Control File Key</th> + <th>Bundle File Name</th> + <th>Message</th> + </tr> + </thead> + <tbody> + {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%} + <tr> + <td>{{error.controlfilekey}}</td> + <td>{{error.filename}}</td> + <td>{{error.message}}</td> + </tr> + {%endfor%} + </tbody> +</table> + +<h3>Other Generic Errors</h3> +{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}} +{%endif%} + +{%if errorsgeno | length > 0%} +<h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3> +<div class="explainer"> + We found the following errors in the 'geno' file in your R/qtl2 bundle: +</div> +{{errors_table("tbl-errors-geno", errorsgeno[0:50])}} +{%endif%} + +{%if errorspheno | length > 0%} +<h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3> +<div class="explainer"> + We found the following errors in the 'pheno' file in your R/qtl2 bundle: +</div> +{{errors_table("tbl-errors-pheno", errorspheno[0:50])}} +{%endif%} + +{%if errorsphenose | length > 0%} +<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3> +<div class="explainer"> + We found the following errors in the 'phenose' file in your R/qtl2 bundle: +</div> +{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}} +{%endif%} + +{%if errorsphenocovar | length > 0%} +<h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3> +<div class="explainer"> + We found the following errors in the 'phenocovar' file in your R/qtl2 bundle: +</div> +{{errorsphenocovar}} +{%endif%} + +<h4>stdout</h4> +{{cli_output(job, "stdout")}} + +<h4>stderr</h4> +{{cli_output(job, "stderr")}} + +<h4>Log</h4> +<div class="cli-output"> + <pre>{{"\n".join(messages)}}</pre> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html new file mode 100644 index 0000000..b3c3a8f --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html @@ -0,0 +1,66 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}R/qtl2 bundle: QC job results{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 bundle: QC job results</h1> + +<div class="row"> + <p>The R/qtl2 bundle you uploaded has passed all automated quality-control + checks successfully.</p> + <p>You may now continue to load the data into GeneNetwork for the bundle, with + the following details:</p> +</div> + +<div class="row"> + <form id="form-qc-job-results" + action="{{url_for('expression-data.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST"> + <div class="form-group"> + <legend>Species</legend> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + + <span class="form-label">Name</span> + <span class="form-text">{{species.Name | capitalize}}</span> + + <span class="form-label">Scientific</span> + <span class="form-text">{{species.FullName | capitalize}}</span> + </div> + + <div class="form-group"> + <legend>population</legend> + <input type="hidden" name="population_id" value="{{population.Id}}" /> + + <span class="form-label">Name</span> + <span class="form-text">{{population.InbredSetName}}</span> + + <span class="form-label">Full Name</span> + <span class="form-text">{{population.FullName}}</span> + + <span class="form-label">Genetic Type</span> + <span class="form-text">{{population.GeneticType}}</span> + + <span class="form-label">Description</span> + <span class="form-text">{{population.Description or "-"}}</span> + </div> + + <div class="form-group"> + <legend>R/qtl2 Bundle File</legend> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" /> + <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" /> + + <span class="form-label">Original Name</span> + <span class="form-text">{{rqtl2bundleorig}}</span> + + <span class="form-label">Internal Name</span> + <span class="form-text">{{rqtl2bundle[0:25]}}…</span> + </div> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html new file mode 100644 index 0000000..f4a6266 --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html @@ -0,0 +1,41 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Job Status{%endblock%} + +{%block extrameta%} +<meta http-equiv="refresh" content="3"> +{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 bundle: QC job status</h1> + +{%if geno_percent%} +<p> + <h2>Checking 'geno' file:</h2> + <progress id="prg-geno-checking" value="{{geno_percent}}" max="100"> + {{geno_percent}}%</progress> + {{geno_percent}}%</p> +{%endif%} + +{%if pheno_percent%} +<p> + <h2>Checking 'pheno' file:</h2> + <progress id="prg-pheno-checking" value="{{pheno_percent}}" max="100"> + {{pheno_percent}}%</progress> + {{pheno_percent}}%</p> +{%endif%} + +{%if phenose_percent%} +<p> + <h2>Checking 'phenose' file:</h2> + <progress id="prg-phenose-checking" value="{{phenose_percent}}" max="100"> + {{phenose_percent}}%</progress> + {{phenose_percent}}%</p> +{%endif%} + +<h4>Log</h4> +<div class="cli-output"> + <pre>{{"\n".join(messages)}}</pre> +</div> +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html new file mode 100644 index 0000000..f126835 --- /dev/null +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html @@ -0,0 +1,37 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%} + +{%block contents%} +<h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2> + +<div class="row"> + <p>The R/qtl2 bundle you uploaded has passed <emph>all</emph> quality control + checks successfully, and is now ready for uploading into the database.</p> + <p>Click "Continue" below to proceed.</p> +</div> + +<!-- + The "action" on this form takes us to the next step, where we can + select all the other data necessary to enter the data into the database. + --> +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('expression-data.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + {{flash_all_messages()}} + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-geno-dataset.html b/uploader/templates/populations/rqtl2/select-geno-dataset.html new file mode 100644 index 0000000..3233abc --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-geno-dataset.html @@ -0,0 +1,69 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Select Genotypes Dataset</h2> + +<div class="row"> + <p>Your R/qtl2 files bundle could contain a "geno" specification. You will + therefore need to select from one of the existing Genotype datasets or + create a new one.</p> + <p>This is the dataset where your data will be organised under.</p> +</div> + +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('expression-data.rqtl2.select_geno_dataset', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">select from existing genotype datasets</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + {{flash_messages("error-rqtl2-select-geno-dataset")}} + + <div class="form-group"> + <legend>Datasets</legend> + <label for="select:geno-datasets" class="form-label">Dataset</label> + <select id="select:geno-datasets" + name="geno-dataset-id" + required="required" + {%if datasets | length == 0%} + disabled="disabled" + {%endif%} + class="form-control" + aria-describedby="help-geno-dataset-select-dataset"> + <option value="">Select dataset</option> + {%for dset in datasets%} + <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> + {%endfor%} + </select> + <span id="help-geno-dataset-select-dataset" class="form-text text-muted"> + Select from the existing genotype datasets for species + {{species.SpeciesName}} ({{species.FullName}}). + </span> + </div> + + <button type="submit" class="btn btn-primary">select dataset</button> + </form> +</div> + +<div class="row"> + <p>If the genotype dataset you need does not currently exist for your dataset, + go the <a href="{{url_for( + 'species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotypes dataset for {{species.FullName}}"> + genotypes page to create the genotype dataset</a></p> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-population.html b/uploader/templates/populations/rqtl2/select-population.html new file mode 100644 index 0000000..ded425f --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-population.html @@ -0,0 +1,57 @@ +{%extends "expression-data/index.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Select Grouping/Population{%endblock%} + +{%block contents%} +<h1 class="heading">Select grouping/population</h1> + +<div class="row"> + <p>The data is organised in a hierarchical form, beginning with + <em>species</em> at the very top. Under <em>species</em> the data is + organised by <em>population</em>, sometimes referred to as <em>grouping</em>. + (In some really old documents/systems, you might see this referred to as + <em>InbredSet</em>.)</p> + <p>In this section, you get to define what population your data is to be + organised by.</p> +</div> + +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.rqtl2.select_population', + species_id=species.SpeciesId)}}"> + <legend class="heading">select grouping/population</legend> + {{flash_messages("error-select-population")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + + <div class="form-group"> + <label for="select:inbredset" class="form-label">population</label> + <select id="select:inbredset" + name="inbredset_id" + required="required" + class="form-control"> + <option value="">Select a grouping/population</option> + {%for pop in populations%} + <option value="{{pop.InbredSetId}}"> + {{pop.InbredSetName}} ({{pop.FullName}})</option> + {%endfor%} + </select> + <span class="form-text text-muted">Select the population for your data from + the list below.</span> + </div> + + <button type="submit" class="btn btn-primary" />select population</button> +</form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html new file mode 100644 index 0000000..74f8f69 --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-probeset-dataset.html @@ -0,0 +1,191 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Phenotype(ProbeSet) Dataset</h2> + +<div class="row"> + <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>" + file(s). This data needs to be organised under a dataset.</p> + <p>This page gives you the ability to do that.</p> +</div> + +{%if datasets | length > 0%} +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.rqtl2.select_probeset_dataset', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-dataset"> + <legend class="heading">Select from existing ProbeSet datasets</legend> + {{flash_messages("error-rqtl2")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select:probe-dataset">Dataset</label> + <select id="select:probe-dataset" + name="probe-dataset-id" + required="required" + {%if datasets | length == 0%}disabled="disabled"{%endif%} + class="form-control" + aria-describedby="help-probe-dataset"> + <option value="">Select a dataset</option> + {%for dataset in datasets%} + <option value={{dataset.Id}}> + {{dataset.Name}} + {%if dataset.FullName%} + -- ({{dataset.FullName}}) + {%endif%} + </option> + {%endfor%} + </select> + + <span id="help-probe-dataset" class="form-text text-muted"> + Select from existing ProbeSet datasets.</span> + </div> + + <button type="submit" class="btn btn-primary" />select dataset</button> +</form> +</div> + +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> +{%endif%} + +<div class="row"> + <p>Create an entirely new ProbeSet dataset for your data.</p> +</div> + +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.rqtl2.create_probeset_dataset', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-dataset"> + <legend class="heading">Create a new ProbeSet dataset</legend> + {{flash_messages("error-rqtl2-create-probeset-dataset")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select:average">averaging method</label> + <select id="select:average" + name="averageid" + required="required" + class="form-control" + aria-describedby="help-average"> + <option value="">Select averaging method</option> + {%for avgmethod in avgmethods%} + <option value="{{avgmethod.Id}}"> + {{avgmethod.Name}} + {%if avgmethod.Normalization%} + ({{avgmethod.Normalization}}) + {%endif%} + </option> + {%endfor%} + </select> + + <span id="help-average" class="form-text text-muted"> + Select the averaging method used for your data. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="txt:datasetname">Name</label> + <input type="text" id="txt:datasetname" name="datasetname" + required="required" + maxlength="40" + title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" + class="form-control" + aria-describedby="help-dataset-name" /> + + <span id="help-dataset-name" class="form-text text-muted"> + Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This + is mandatory <strong>MUST</strong> be provided. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="txt:datasetfullname">Full Name</label> + <input type="text" id="txt:datasetfullname" name="datasetfullname" + required="required" + maxlength="100" + title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" + class="form-control" + aria-describedby="help-dataset-fullname" /> + + <span id="help-dataset-fullname" class="form-text text-muted"> + Provide a longer, more descriptive name for the dataset e.g. + "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and + <strong>MUST</strong> be provided. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="txt:datasetshortname">Short Name</label> + <input type="text" id="txt:datasetshortname" name="datasetshortname" + maxlength="100" + title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" + class="form-control" + aria-describedby="help-dataset-shortname" /> + + <span id="help-dataset-shortname" class="form-text text-muted"> + Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". + This is optional. + </span> + </div> + + <div class="form-check"> + <input type="checkbox" id="chk:public" name="datasetpublic" + checked="checked" + title="Whether or not the dataset is accessible by the general public." + class="form-check-input" + aria-describedby="help-public" /> + <label class="form-check-label" for="chk:datasetpublic">Public?</label> + + <span id="help-public" class="form-text text-muted"> + Check to specify that the dataset will be publicly available. Uncheck to + limit access to the dataset. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="select:datasetdatascale">Data Scale</label> + <select id="select:datasetdatascale" + name="datasetdatascale" + required="required" + class="form-control" + aria-describedby="help-dataset-datascale"> + <option value="log2" selected="selected">log2</option> + <option value="z_score">z_score</option> + <option value="log2_ratio">log2_ratio</option> + <option value="linear">linear</option> + <option value="linear_positive">linear_positive</option> + </select> + + <span id="help-dataset-datascale" class="form-text text-muted"> + Select from a list of scaling methods. + </span> + </div> + + <button type="submit" class="btn btn-primary">create dataset</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html new file mode 100644 index 0000000..e3fd9cc --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-probeset-study-id.html @@ -0,0 +1,143 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages %} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Phenotype(ProbeSet) Study</h2> + +<div class="row"> + <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>" + file(s). This data needs to be organised under a study.</p> + <p>In this page, you can either select from a existing dataset:</p> + + <form method="POST" + action="{{url_for('expression-data.rqtl2.select_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-study"> + <legend class="heading">Select from existing ProbeSet studies</legend> + {{flash_messages("error-rqtl2-select-probeset-study")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <div> + <label for="select:probe-study" class="form-label">Study</label> + <select id="select:probe-study" + name="probe-study-id" + required="required" + aria-describedby="help-select-probeset-study" + {%if studies | length == 0%}disabled="disabled"{%endif%} + class="form-control"> + <option value="">Select a study</option> + {%for study in studies%} + <option value={{study.Id}}> + {{study.Name}} + {%if study.FullName%} + -- ({{study.FullName}}) + {%endif%} + </option> + {%endfor%} + </select> + <small id="help-select-probeset-study" class="form-text text-muted"> + Select from existing ProbeSet studies. + </small> + </div> + + <button type="submit" class="btn btn-primary">select study</button> + </form> +</div> + +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> + +<div class="row"> + + <p>Create a new ProbeSet dataset below:</p> + + <form method="POST" + action="{{url_for('expression-data.rqtl2.create_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-study"> + <legend class="heading">Create new ProbeSet study</legend> + + {{flash_messages("error-rqtl2-create-probeset-study")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <div> + <label for="select:platform" class="form-label">Platform</label> + <select id="select:platform" + name="platformid" + required="required" + aria-describedby="help-select-platform" + {%if platforms | length == 0%}disabled="disabled"{%endif%} + class="form-control"> + <option value="">Select a platform</option> + {%for platform in platforms%} + <option value="{{platform.GeneChipId}}"> + {{platform.GeneChipName}} ({{platform.Name}}) + </option> + {%endfor%} + </select> + <small id="help-select-platform" class="form-text text-muted"> + Select from a list of known genomics platforms. + </small> + </div> + + <div class="form-group"> + <label for="txt:studyname" class="form-label">Study name</label> + <input type="text" id="txt:studyname" name="studyname" + placeholder="Name of the study. (Required)" + required="required" + maxlength="100" + class="form-control" /> + <span class="form-text text-muted" id="help-study-name"> + Provide a name for the study.</span> + </div> + + <div class="form-group"> + <label for="txt:studyfullname" class="form-label">Full Study Name</label> + <input type="text" + id="txt:studyfullname" + name="studyfullname" + placeholder="Longer name of the study. (Optional)" + maxlength="100" + class="form-control" /> + <span class="form-text text-muted" id="help-study-full-name"> + Provide a longer, more descriptive name for the study. This is optional + and you can leave it blank. + </span> + </div> + + <div class="form-group"> + <label for="txt:studyshortname" class="form-label">Short Study Name</label> + <input type="text" + id="txt:studyshortname" + name="studyshortname" + placeholder="Shorter name of the study. (Optional)" + maxlength="100" + class="form-control" /> + <span class="form-text text-muted" id="help-study-short-name"> + Provide a shorter name for the study. This is optional and you can leave + it blank. + </span> + </div> + + <button type="submit" class="btn btn-primary">create study</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html new file mode 100644 index 0000000..fe3080a --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-tissue.html @@ -0,0 +1,115 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Tissue</h2> + +<div class="row"> + <p>The data you are uploading concerns a tissue, cell, organ, or other + biological material used in an experiment.</p> + <p>Select the appropriate biological material below</p> +</div> + +{%if tissues | length > 0%} +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.rqtl2.select_tissue', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-dataset"> + <legend class="heading">Select from existing ProbeSet datasets</legend> + {{flash_messages("error-select-tissue")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select-tissue">Tissue</label> + <select id="select-tissue" + name="tissueid" + required="required" + {%if tissues | length == 0%}disabled="disabled"{%endif%} + class="form-control" + aria-describedby="help-select-tissue"> + <option value="">Select a tissue</option> + {%for tissue in tissues%} + <option value={{tissue.Id}}> + {{tissue.Name}} + {%if tissue.Short_Name%} + -- ({{tissue.Short_Name}}) + {%endif%} + </option> + {%endfor%} + </select> + + <span id="help-select-tissue" class="form-text text-muted"> + Select from existing biological material.</span> + </div> + + <button type="submit" class="btn btn-primary">use selected</button> + </form> +</div> + +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> +{%endif%} + +<div class="row"> + <p>If you cannot find the biological material in the drop-down above, add it + to the system below.</p> + + <form method="POST" + action="{{url_for('expression-data.rqtl2.create_tissue', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-dataset"> + <legend class="heading">Add new tissue, organ or biological material</legend> + {{flash_messages("error-create-tissue")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="tissue-name">name</label> + <input type="text" + id="txt-tissuename" + name="tissuename" + required="required" + title = "A name to identify the tissue, organ or biological material." + class="form-control" + aria-describedby="help-tissue-name" /> + + <span class="form-text text-muted" id="help-tissue-name"> + A name to identify the tissue, organ or biological material. + </span> + </div> + + <div class="form-group"> + <label for="txt-shortname" class="form-label">short name</label> + <input type="text" id="txt-tissueshortname" name="tissueshortname" + required="required" + maxlength="7" + title="A short name (e.g. 'Mam') for the biological material." + class="form-control" + aria-describedby="help-tissue-short-name" /> + + <span class="form-text text-muted" id="help-tissue-short-name"> + Provide a short name for the tissue, organ or biological material used in + the experiment. + </span> + </div> + + <button type="submit" class="btn btn-primary" />add new material</button> +</form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/summary-info.html b/uploader/templates/populations/rqtl2/summary-info.html new file mode 100644 index 0000000..0adba2e --- /dev/null +++ b/uploader/templates/populations/rqtl2/summary-info.html @@ -0,0 +1,65 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Summary</h2> + +<div class="row"> + <p>This is the information you have provided to accompany the R/qtl2 bundle + you have uploaded. Please verify the information is correct before + proceeding.</p> +</div> + +<div class="row"> + <dl> + <dt>Species</dt> + <dd>{{species.SpeciesName}} ({{species.FullName}})</dd> + + <dt>Population</dt> + <dd>{{population.InbredSetName}}</dd> + + {%if geno_dataset%} + <dt>Genotype Dataset</dt> + <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd> + {%endif%} + + {%if tissue%} + <dt>Tissue</dt> + <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd> + {%endif%} + + {%if probe_study%} + <dt>ProbeSet Study</dt> + <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd> + {%endif%} + + {%if probe_dataset%} + <dt>ProbeSet Dataset</dt> + <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd> + {%endif%} + </dl> +</div> + +<div class="row"> + <form id="frm:confirm-rqtl2bundle-details" + action="{{url_for('expression-data.rqtl2.confirm_bundle_details', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">Create ProbeSet dataset</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html new file mode 100644 index 0000000..9d45c5f --- /dev/null +++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html @@ -0,0 +1,276 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "upload_progress_indicator.html" import upload_progress_indicator%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +{%macro rqtl2_file_help()%} +<span class="form-text text-muted"> + <p> + Provide a valid R/qtl2 zip file here. In particular, ensure your zip bundle + contains exactly one control file and the corresponding files mentioned in + the control file. + </p> + <p> + The control file can be either a YAML or JSON file. <em>ALL</em> other data + files in the zip bundle should be CSV files. + </p> + <p>See the + <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html" + target="_blank"> + R/qtl2 file format specifications + </a> + for more details. + </p> +</span> +{%endmacro%} +{{upload_progress_indicator()}} + +<div id="resumable-file-display-template" + class="panel panel-info" + style="display: none"> + <div class="panel-heading"></div> + <div class="panel-body"></div> +</div> + + +<h2 class="heading">Upload R/qtl2 Bundle</h2> + +<div id="resumable-drop-area" + style="display:none;background:#eeeeee;min-height:12em;border-radius:0.5em;padding:1em;"> + <p> + <a id="resumable-browse-button" href="#" + class="btn btn-info">Browse</a> + </p> + <p class="form-text text-muted"> + You can drag and drop your file here, or click the browse button. + Click on the file to remove it. + </p> + {{rqtl2_file_help()}} + <div id="resumable-selected-files" + style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"></div> + <div id="resumable-class-buttons" style="text-align: right;"> + <button id="resumable-upload-button" + class="btn btn-primary" + style="display: none">start upload</button> + <button id="resumable-cancel-upload-button" + class="btn btn-danger" + style="display: none">cancel upload</button> + </div> + <div id="resumable-progress-bar" class="progress" style="display: none"> + <div class="progress-bar" + role="progress-bar" + aria-valuenow="60" + aria-valuemin="0" + aria-valuemax="100" + style="width: 0%;"> + Uploading: 60% + </div> + </div> +</div> + +<form id="frm-upload-rqtl2-bundle" + action="{{url_for('expression-data.rqtl2.upload_rqtl2_bundle', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data" + data-resumable-target="{{url_for( + 'expression-data.rqtl2.upload_rqtl2_bundle_chunked_post', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}"> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + + {{flash_all_messages()}} + + <div class="form-group"> + <legend class="heading">file upload</legend> + <label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label> + <input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file" + accept="application/zip, .zip" + required="required" + class="form-control" /> + {{rqtl2_file_help()}} + </div> + + <button type="submit" + class="btn btn-primary" + data-toggle="modal" + data-target="#upload-progress-indicator">upload R/qtl2 bundle</button> +</form> + +{%endblock%} + +{%block javascript%} +<script src="{{url_for('base.node_modules', + filename='resumablejs/resumable.js')}}"></script> +<script type="text/javascript" src="/static/js/upload_progress.js"></script> +<script type="text/javascript"> + function readBinaryFile(file) { + return new Promise((resolve, reject) => { + var _reader = new FileReader(); + _reader.onload = (event) => {resolve(_reader.result);}; + _reader.readAsArrayBuffer(file); + }); + } + + function computeFileChecksum(file) { + return readBinaryFile(file) + .then((content) => { + return window.crypto.subtle.digest( + "SHA-256", new Uint8Array(content)); + }).then((digest) => { + return Uint8ArrayToHex(new Uint8Array(digest)) + }); + } + + function Uint8ArrayToHex(arr) { + var toHex = (val) => { + _hex = val.toString(16); + if(_hex.length < 2) { + return "0" + val; + } + return _hex; + }; + _hexstr = "" + arr.forEach((val) => {_hexstr += toHex(val)}); + return _hexstr + } + + var r = Resumable({ + target: $("#frm-upload-rqtl2-bundle").attr("data-resumable-target"), + fileType: ["zip"], + maxFiles: 1, + forceChunkSize: true, + generateUniqueIdentifier: (file, event) => { + return computeFileChecksum(file).then((checksum) => { + var _relativePath = (file.webkitRelativePath + || file.relativePath + || file.fileName + || file.name); + return checksum + "-" + _relativePath.replace( + /[^a-zA-Z0-9_-]/img, ""); + }); + } + }); + + if(r.support) { + //Hide form and display drag&drop UI + $("#frm-upload-rqtl2-bundle").css("display", "none"); + $("#resumable-drop-area").css("display", "block"); + + // Define UI elements for browse and drag&drop + r.assignDrop(document.getElementById("resumable-drop-area")); + r.assignBrowse(document.getElementById("resumable-browse-button")); + + // Event handlers + + function display_files(files) { + displayArea = $("#resumable-selected-files") + displayArea.empty(); + files.forEach((file) => { + var displayElement = $( + "#resumable-file-display-template").clone(); + displayElement.removeAttr("id"); + displayElement.css("display", ""); + displayElement.find(".panel-heading").text(file.fileName); + list = $("<ul></ul>"); + list.append($("<li><strong>Name</strong>: " + + (file.name + || file.fileName + || file.relativePath + || file.webkitRelativePath) + + "</li>")); + list.append($("<li><strong>Size</strong>: " + + (file.size / (1024*1024)).toFixed(2) + + " MB</li>")); + list.append($("<li><strong>Unique Identifier</strong>: " + + file.uniqueIdentifier + "</li>")); + list.append($("<li><strong>Mime</strong>: " + + file.file.type + + "</li>")); + displayElement.find(".panel-body").append(list); + displayElement.appendTo("#resumable-selected-files"); + }); + } + + r.on("filesAdded", function(files) { + display_files(files); + $("#resumable-upload-button").css("display", ""); + $("#resumable-upload-button").on("click", (event) => { + r.upload(); + }); + }); + + r.on("uploadStart", (event) => { + $("#resumable-upload-button").css("display", "none"); + $("#resumable-cancel-upload-button").css("display", ""); + $("#resumable-cancel-upload-button").on("click", (event) => { + r.files.forEach((file) => { + if(file.isUploading()) { + file.abort(); + } + }); + $("#resumable-cancel-upload-button").css("display", "none"); + $("#resumable-upload-button").on("click", (event) => { + r.files.forEach((file) => {file.retry();}); + }); + $("#resumable-upload-button").css("display", ""); + }); + }); + + r.on("progress", () => { + var progress = (r.progress() * 100).toFixed(2); + var pbar = $("#resumable-progress-bar > .progress-bar"); + $("#resumable-progress-bar").css("display", ""); + pbar.css("width", progress+"%"); + pbar.attr("aria-valuenow", progress); + pbar.text("Uploading: " + progress + "%"); + }) + + r.on("fileSuccess", (file, message) => { + if(message != "OK") { + var uri = (window.location.protocol + + "//" + + window.location.host + + message); + window.location.replace(uri); + } + }); + + r.on("error", (message, file) => { + filename = (file.webkitRelativePath + || file.relativePath + || file.fileName + || file.name); + jsonmsg = JSON.parse(message); + alert("There was an error while uploading your file '" + + filename + + "'. The error message was:\n\n\t" + + jsonmsg.error + + " (" + + jsonmsg.statuscode + + "): " + jsonmsg.message); + }) + } else { + setup_upload_handlers( + "frm-upload-rqtl2-bundle", make_data_uploader( + function (form) { + var formdata = new FormData(); + formdata.append( + "species_id", + form.querySelector('input[name="species_id"]').value); + formdata.append( + "population_id", + form.querySelector('input[name="population_id"]').value); + formdata.append( + "rqtl2_bundle_file", + form.querySelector("#file-rqtl2-bundle").files[0]); + return formdata; + })); + } +</script> +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html new file mode 100644 index 0000000..8210ed0 --- /dev/null +++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html @@ -0,0 +1,33 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Upload R/qtl2 Bundle</h2> + +<div class="row"> + <p>You have successfully uploaded the zipped bundle of R/qtl2 files.</p> + <p>The next step is to select the various extra information we need to figure + out what to do with the data. You will select/create the relevant studies + and/or datasets to organise the data in the steps that follow.</p> + <p>Click "Continue" below to proceed.</p> + + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('expression-data.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + {{flash_all_messages()}} + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html new file mode 100644 index 0000000..b23caeb --- /dev/null +++ b/uploader/templates/populations/view-population.html @@ -0,0 +1,102 @@ +{%extends "populations/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="view-population"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.view_population', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}">view</a> +</li> +{%endblock%} + + +{%block contents%} +<div class="row"> + <h2>Population Details</h2> + + {{flash_all_messages()}} + + <dl> + <dt>Name</dt> + <dd>{{population.Name}}</dd> + + <dt>FullName</dt> + <dd>{{population.FullName}}</dd> + + <dt>Code</dt> + <dd>{{population.InbredSetCode}}</dd> + + <dt>Genetic Type</dt> + <dd>{{population.GeneticType}}</dd> + + <dt>Family</dt> + <dd>{{population.Family}}</dd> + + <dt>Description</dt> + <dd><pre>{{population.Description or "-"}}</pre></dd> + </dl> +</div> + +<div class="row"> + … maybe provide a way to organise populations in the same family here … +</div> + +<div class="row"> + <h3>Actions</h3> + + <p> + Click any of the following links to use this population in performing the + subsequent operations. + </p> + + <nav class="nav"> + <ul> + <li> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Manage samples: Add new or delete existing."> + manage samples</a> + </li> + <li> + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Manage genotypes for {{species.FullName}}">Manage Genotypes</a> + </li> + <li> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Manage phenotype data.">manage phenotype data</a> + </li> + <li> + <a href="#" title="Manage expression data" + class="not-implemented">manage expression data</a> + </li> + <li> + <a href="#" title="Manage individual data" + class="not-implemented">manage individual data</a> + </li> + <li> + <a href="#" title="Manage RNA-Seq data" + class="not-implemented">manage RNA-Seq data</a> + </li> + </ul> + </nav> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/publications/base.html b/uploader/templates/publications/base.html new file mode 100644 index 0000000..db80bfa --- /dev/null +++ b/uploader/templates/publications/base.html @@ -0,0 +1,12 @@ +{%extends "base.html"%} + +{%block lvl1_breadcrumbs%} +<li {%if activelink=="publications"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('publications.index')}}">Publications</a> +</li> +{%block lvl2_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/publications/create-publication.html b/uploader/templates/publications/create-publication.html new file mode 100644 index 0000000..3f828a9 --- /dev/null +++ b/uploader/templates/publications/create-publication.html @@ -0,0 +1,191 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-create-publication" + method="POST" + action="{{url_for('publications.create_publication', **request.args)}}" + class="form-horizontal"> + + <div class="row mb-3"> + <label for="txt-pubmed-id" class="col-sm-2 col-form-label"> + PubMed ID</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + id="txt-pubmed-id" + name="pubmed-id" + class="form-control"/> + <div class="input-group-text"> + <button class="btn btn-outline-primary" + id="btn-search-pubmed-id">search</button> + </div> + </div> + <span id="search-pubmed-id-error" + class="form-text text-muted text-danger visually-hidden"> + </span> + <span class="form-text text-muted">This is the publication's ID on + <a href="https://pubmed.ncbi.nlm.nih.gov/" + title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a> + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-title" class="col-sm-2 col-form-label"> + Title</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-title" + name="publication-title" + class="form-control" /> + <span class="form-text text-muted">Provide the publication's title here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-authors" class="col-sm-2 col-form-label"> + Authors</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-authors" + name="publication-authors" + required="required" + class="form-control" /> + <span class="form-text text-muted"> + A publication <strong>MUST</strong> have an author. You <em>must</em> + provide a value for the authors field. + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-journal" class="col-sm-2 col-form-label"> + Journal</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-journal" + name="publication-journal" + class="form-control" /> + <span class="form-text text-muted">Provide the name journal where the + publication was done, here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="select-publication-month" + class="col-sm-2 col-form-label"> + Month</label> + <div class="col-sm-4"> + <select class="form-control" + id="select-publication-month" + name="publication-month"> + <option value="">Select a month</option> + <option value="january">January</option> + <option value="february">February</option> + <option value="march">March</option> + <option value="april">April</option> + <option value="may">May</option> + <option value="june">June</option> + <option value="july">July</option> + <option value="august">August</option> + <option value="september">September</option> + <option value="october">October</option> + <option value="november">November</option> + <option value="december">December</option> + </select> + <span class="form-text text-muted">Month of publication</span> + </div> + + <label for="txt-publication-year" + class="col-sm-2 col-form-label"> + Year</label> + <div class="col-sm-4"> + <input type="number" + id="txt-publication-year" + name="publication-year" + class="form-control" + min="1960" /> + <span class="form-text text-muted">Year of publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-volume" + class="col-sm-2 col-form-label"> + Volume</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-volume" + name="publication-volume" + class="form-control"> + <span class="form-text text-muted">Journal volume</span> + </div> + + <label for="txt-publication-pages" + class="col-sm-2 col-form-label"> + Pages</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-pages" + name="publication-pages" + class="form-control" /> + <span class="form-text text-muted">Journal pages for the publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" + name="publication-abstract" + class="form-control" + rows="7"></textarea> + </div> + </div> + + <div class="row mb-3"> + <div class="col-sm-2"></div> + <div class="col-sm-8"> + <input type="submit" class="btn btn-primary" value="Add" /> + <input type="reset" class="btn btn-danger" /> + </div> + </div> + +</form> +</div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/pubmed.js"></script> +<script type="text/javascript"> + $(function() { + $("#btn-search-pubmed-id").on("click", (event) => { + event.preventDefault(); + var search_button = event.target; + var pubmed_id = $("#txt-pubmed-id").val().trim(); + remove_class($("#txt-pubmed-id").parent(), "has-error"); + if(pubmed_id == "") { + add_class($("#txt-pubmed-id").parent(), "has-error"); + return false; + } + + search_button.disabled = true; + // Fetch publication details + fetch_publication_details(pubmed_id, + [() => {search_button.disabled = false;}]); + return false; + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/publications/index.html b/uploader/templates/publications/index.html new file mode 100644 index 0000000..369812b --- /dev/null +++ b/uploader/templates/publications/index.html @@ -0,0 +1,100 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Publications{%endblock%} + +{%block pagetitle%}Publications{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row" style="padding-bottom: 1em;"> + <a href="{{url_for('publications.create_publication')}}" + class="btn btn-primary"> + add new publication</a> +</div> + +<div class="row"> + <table id="tbl-list-publications" class="table compact stripe"> + <thead> + <tr> + <th>#</th> + <th>PubMed ID</th> + <th>Title</th> + <th>Authors</th> + </tr> + </thead> + + <tbody></tbody> + </table> +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var publicationsDataTable = buildDataTable( + "#tbl-list-publications", + [], + [ + {data: "index"}, + { + searchable: true, + data: (pub) => { + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; + } + }, + { + searchable: true, + data: (pub) => { + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + return `<a href="/publications/view/${pub.Id}" ` + + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; + } + }, + { + searchable: true, + data: (pub) => { + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; + } + } + ], + { + serverSide: true, + ajax: { + url: "/publications/list", + dataSrc: "publications" + }, + scrollY: 700, + scroller: true, + scrollCollapse: true, + paging: true, + deferRender: true, + layout: { + topStart: "info", + topEnd: "search", + bottomStart: "pageLength", + bottomEnd: false + } + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/publications/view-publication.html b/uploader/templates/publications/view-publication.html new file mode 100644 index 0000000..388547a --- /dev/null +++ b/uploader/templates/publications/view-publication.html @@ -0,0 +1,78 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <table class="table"> + <tr> + <th>PubMed</th> + <td> + {%if publication.PubMed_ID%} + <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/" + target="_blank">{{publication.PubMed_ID}}</a> + {%else%} + — + {%endif%} + </td> + </tr> + <tr> + <th>Title</th> + <td>{{publication.Title or "—"}}</td> + </tr> + <tr> + <th>Authors</th> + <td>{{publication.Authors or "—"}}</td> + </tr> + <tr> + <th>Journal</th> + <td>{{publication.Journal or "—"}}</td> + </tr> + <tr> + <th>Published</th> + <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td> + </tr> + <tr> + <th>Volume</th> + <td>{{publication.Volume or "—"}}</td> + </tr> + <tr> + <th>Pages</th> + <td>{{publication.Pages or "—"}}</td> + </tr> + <tr> + <th>Abstract</th> + <td> + {%for line in (publication.Abstract or "—").replace("\r\n", "<br />").replace("\n", "<br />").split("<br />")%} + <p>{{line}}</p> + {%endfor%} + </td> + </tr> + </table> +</div> + +<div class="row"> + <form id="frm-edit-delete-publication" method="POST" action="#"> + <input type="hidden" name="publication_id" value="{{publication.Id}}" /> + <div class="form-group"> + <input type="submit" value="edit" class="btn btn-primary not-implemented" /> + {%if linked_phenotypes | length == 0%} + <input type="submit" value="delete" class="btn btn-danger not-implemented" /> + {%endif%} + </div> + </form> +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() {}); +</script> +{%endblock%} diff --git a/uploader/templates/samples/base.html b/uploader/templates/samples/base.html new file mode 100644 index 0000000..291782b --- /dev/null +++ b/uploader/templates/samples/base.html @@ -0,0 +1,12 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="samples"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.samples.index')}}">Samples</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html new file mode 100644 index 0000000..ee98734 --- /dev/null +++ b/uploader/templates/samples/index.html @@ -0,0 +1,23 @@ +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>GeneNetwork has a selection of different species of organisms to choose from. Within those species, there are the populations of interest for a variety of experiments, from which you, the researcher, picked your samples (or individuals or cases) from. Here you can provide some basic details about your samples.</p> + <p>To start off, we will need to know what species and population your samples belong to. Please provide that information in the next sections.</p> + + {{select_species_form(url_for("species.populations.samples.index"), species)}} +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html new file mode 100644 index 0000000..aed27c3 --- /dev/null +++ b/uploader/templates/samples/list-samples.html @@ -0,0 +1,130 @@ +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Samples — List Samples{%endblock%} + +{%block pagetitle%}Samples — List Samples{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-samples"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}">List</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p> + You selected the population "{{population.FullName}}" from the + "{{species.FullName}}" species. + </p> +</div> + +<div class="row"> + <p> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Add samples for population '{{population.FullName}}' from species + '{{species.FullName}}'." + class="btn btn-primary"> + add samples + </a> + </p> +</div> + +{%if samples | length > 0%} +<div class="row"> + <p> + This population already has <strong>{{total_samples}}</strong> + samples/individuals entered. You can explore the list of samples in this + population in the table below. + </p> +</div> + +<div class="row"> + <div class="col-md-2"> + {%if offset > 0:%} + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id, + from=offset-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + + <div class="col-md-8" style="text-align: center;"> + Samples {{offset}} — {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}} + </div> + + <div class="col-md-2"> + {%if offset + count < total_samples:%} + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id, + from=offset+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> +</div> +<div class="row"> + <table class="table"> + <thead> + <tr> + <th></th> + <th>Name</th> + <th>Auxilliary Name</th> + <th>Symbol</th> + <th>Alias</th> + </tr> + </thead> + + <tbody> + {%for sample in samples%} + <tr> + <td>{{sample.sequence_number}}</td> + <td>{{sample.Name}}</td> + <td>{{sample.Name2}}</td> + <td>{{sample.Symbol or "-"}}</td> + <td>{{sample.Alias or "-"}}</td> + </tr> + {%endfor%} + </tbody> + </table> + + <p> + <a href="#" + title="Delete samples from population '{{population.FullName}}' from species + '{{species.FullName}}'." + class="btn btn-danger not-implemented"> + delete all samples + </a> + </p> +</div> +{%else%} +<div class="row"> + <p>There are no samples entered for this population. Click the "Add Samples" + button above, to add some new samples.</p> +</div> +{%endif%} + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html new file mode 100644 index 0000000..1cc7573 --- /dev/null +++ b/uploader/templates/samples/select-population.html @@ -0,0 +1,26 @@ +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Samples — Select Population{%endblock%} + +{%block pagetitle%}Samples — Select Population{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {{select_population_form( + url_for("species.populations.samples.select_population", species_id=species.SpeciesId), species, populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%endblock%} diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html new file mode 100644 index 0000000..2cf8053 --- /dev/null +++ b/uploader/templates/samples/upload-failure.html @@ -0,0 +1,37 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Samples Upload Failure{%endblock%} + +{%block contents%} +<div class="row"> +<h2 class="heading">{{job.job_name[0:50]}}…</h2> + +<p>There was a failure attempting to upload the samples.</p> + +<p>Here is some information to help with debugging the issue. Provide this + information to the developer/maintainer.</p> + +<h3>Debugging Information</h3> +<ul> + <li><strong>job id</strong>: {{job.jobid}}</li> + <li><strong>status</strong>: {{job.status}}</li> + <li><strong>job type</strong>: {{job["job-type"]}}</li> +</ul> +</div> + +<div class="row"> +<h4>stdout</h4> +{{cli_output(job, "stdout")}} +</div> + +<div class="row"> +<h4>stderr</h4> +{{cli_output(job, "stderr")}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html new file mode 100644 index 0000000..677d457 --- /dev/null +++ b/uploader/templates/samples/upload-progress.html @@ -0,0 +1,31 @@ +{%extends "samples/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5"> +{%endblock%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +<div class="row" style="overflow-x: clip;"> +<h2 class="heading">{{job.job_name[0:50]}}…</h2> + +<p> +<strong>status</strong>: +<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> +</p> + +<p>saving to database...</p> +</div> + +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html new file mode 100644 index 0000000..6422094 --- /dev/null +++ b/uploader/templates/samples/upload-samples.html @@ -0,0 +1,160 @@ +{%extends "samples/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-select-population.html" import select_population_form%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Samples — Upload Samples{%endblock%} + +{%block pagetitle%}Samples — Upload Samples{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="uploade-samples"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}">List</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p> + You can now upload the samples for the "{{population.FullName}}" population + from the "{{species.FullName}}" species here. + </p> + <p> + Upload a <strong>character-separated value (CSV)</strong> file that contains + details about your samples. The CSV file should have the following fields: + <dl> + <dt>Name</dt> + <dd>The primary name/identifier for the sample/individual.</dd> + + <dt>Name2</dt> + <dd>A secondary name for the sample. This can simply be the same as + <strong>Name</strong> above. This field <strong>MUST</strong> contain a + value.</dd> + + <dt>Symbol</dt> + <dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for + species that have strains. This field can be left empty for species like + Humans that do not have strains..</dd> + + <dt>Alias</dt> + <dd>An alias for the sample. Can be an empty field, or take on the same + value as that of the Symbol.</dd> + </dl> + </p> +</div> + +<div class="row"> + <form id="form-samples" + method="POST" + action="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + enctype="multipart/form-data"> + <legend class="heading">upload samples</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" value="{{population.Id}}" /> + + <div class="form-group"> + <label for="file-samples" class="form-label">select file</label> + <input type="file" name="samples_file" id="file:samples" + accept="text/csv, text/tab-separated-values, text/plain" + class="form-control" /> + </div> + + <div class="form-group"> + <label for="select:separator" class="form-label">field separator</label> + <select id="select:separator" + name="separator" + required="required" + class="form-control"> + <option value="">Select separator for your file: (default is comma)</option> + <option value="	">TAB</option> + <option value=" ">Space</option> + <option value=",">Comma</option> + <option value=";">Semicolon</option> + <option value="other">Other</option> + </select> + <input id="txt:separator" + type="text" + name="other_separator" + class="form-control" /> + <small class="form-text text-muted"> + If you select '<strong>Other</strong>' for the field separator value, + enter the character that separates the fields in your CSV file in the form + field below. + </small> + </div> + + <div class="form-group form-check"> + <input id="chk:heading" + type="checkbox" + name="first_line_heading" + class="form-check-input" /> + <label for="chk:heading" class="form-check-label"> + first line is a heading?</label> + <small class="form-text text-muted"> + Select this if the first line in your file contains headings for the + columns. + </small> + </div> + + <div class="form-group"> + <label for="txt:delimiter" class="form-label">field delimiter</label> + <input id="txt:delimiter" + type="text" + name="field_delimiter" + maxlength="1" + class="form-control" /> + <small class="form-text text-muted"> + If there is a character delimiting the string texts within particular + fields in your CSV, provide the character here. This can be left blank if + no such delimiters exist in your file. + </small> + </div> + + <button type="submit" + class="btn btn-primary">upload samples file</button> + </form> +</div> + +<div class="row"> + <h3>Preview File Content</h3> + + <table id="tbl:samples-preview" class="table"> + <caption class="heading">preview content</caption> + + <thead> + <tr> + <th>Name</th> + <th>Name2</th> + <th>Symbol</th> + <th>Alias</th> + </tr> + </thead> + + <tbody> + <tr id="default-row"> + <td colspan="4"> + Please make some selections in the form above to preview the data.</td> + </tr> + </tbody> + </table> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + +{%block javascript%} +<script src="/static/js/upload_samples.js" type="text/javascript"></script> +{%endblock%} diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html new file mode 100644 index 0000000..881d466 --- /dev/null +++ b/uploader/templates/samples/upload-success.html @@ -0,0 +1,36 @@ +{%extends "samples/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} + +<div class="row" style="overflow-x: clip;"> + <h2 class="heading">{{job.job_name[0:50]}}…</h2> + + <p> + <strong>status</strong>: + <span>{{job["status"]}} ({{job.get("message", "-")}})</span><br /> + </p> + + <p>Successfully uploaded the samples.</p> + <p> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View population samples"> + View samples + </a> + </p> +</div> + +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/select_dataset.html b/uploader/templates/select_dataset.html new file mode 100644 index 0000000..2f07de8 --- /dev/null +++ b/uploader/templates/select_dataset.html @@ -0,0 +1,161 @@ +{%extends "base.html"%} +{%from "dbupdate_hidden_fields.html" import hidden_fields%} + +{%block title%}Select Dataset{%endblock%} + +{%block css%} +<link rel="stylesheet" href="/static/css/two-column-with-separator.css" /> +{%endblock%} + +{%block contents%} +<h2 class="heading">{{filename}}: select dataset</h2> + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.final_confirmation')}}" + id="select-dataset-form" class="two-col-sep-col1"> + <legend class="heading">choose existing dataset</legend> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid, totallines=totallines)}} + + <div class="form-group"> + <label for="datasetid" class="form-label">dataset:</label> + <select id="datasetid" name="datasetid" class="form-control" + {%if datasets | length == 0:%} + disabled="disabled" + {%endif%}> + {%for dataset in datasets:%} + <option value="{{dataset['Id']}}"> + [{{dataset["Name"]}}] - {{dataset["FullName"]}} + </option> + {%endfor%} + </select> + </div> + + <button type="submit" class="btn btn-primary" + {%if datasets | length == 0:%} + disabled="disabled" + {%endif%} />update database</button> +</form> +</div> + +<div class="row"> + <p class="two-col-sep-separator">OR</p> +</div> + +<div class="row"> + <form method="POST" id="create-dataset-form" + action="{{url_for('dbinsert.create_dataset')}}" + class="two-col-sep-col2"> + <legend class="heading">create new dataset</legend> + {{hidden_fields( + filename, filetype, species=species, genechipid=genechipid, + studyid=studyid, totallines=totallines)}} + + {%with messages = get_flashed_messages(with_categories=true)%} + {%if messages:%} + <ul> + {%for category, message in messages:%} + <li class="{{category}}">{{message}}</li> + {%endfor%} + </ul> + {%endif%} + {%endwith%} + + <div class="form-group"> + <label for="avgid" class="form-label">average:</label> + <select id="avgid" name="avgid" required="required" class="form-control"> + <option value="">Select averaging method</option> + {%for method in avgmethods:%} + <option value="{{method['AvgMethodId']}}" + {%if avgid is defined and method['AvgMethodId'] | int == avgid | int%} + selected="selected" + {%endif%}> + {{method["Name"]}} + </option> + {%endfor%} + </select> + </div> + + <div class="form-group"> + <label for="datasetname" class="form-label">name:</label> + <input id="datasetname" name="datasetname" type="text" + class="form-control" + {%if datasetname is defined %} + value="{{datasetname}}" + {%endif%} /> + </div> + + <div class="form-group"> + <label for="datasetname2" class="form-label">name 2:</label> + <input id="datasetname2" name="datasetname2" type="text" + required="required" class="form-control" + {%if datasetname2 is defined %} + value="{{datasetname2}}" + {%endif%} /> + </div> + + <div class="form-group"> + <label for="datasetfullname" class="form-label">full name:</label> + <input id="datasetfullname" name="datasetfullname" type="text" + required="required" class="form-control" + {%if datasetfullname is defined %} + value="{{datasetfullname}}" + {%endif%} /> + </div> + + <div class="form-group"> + <label for="datasetshortname" class="form-label">short name:</label> + <input id="datasetshortname" name="datasetshortname" type="text" + required="required" class="form-control" + {%if datasetshortname is defined %} + value="{{datasetshortname}}" + {%endif%} /> + </div> + + <div class="form-group"> + <label for="datasetpublic" class="form-label">public:</label> + <input id="datasetpublic" name="datasetpublic" type="number" + required="required" min="0" max="2" + {%if datasetpublic is defined %} + value="{{datasetpublic | int}}" + {%else%} + value="0" + {%endif%} + class="form-control" /> + </div> + + <div class="form-group"> + <label for="datasetconfidentiality">confidentiality:</label> + <input id="datasetconfidentiality" name="datasetconfidentiality" + type="number" required="required" min="0" max="2" + {%if datasetconfidentiality is defined %} + value="{{datasetconfidentiality | int}}" + {%else%} + value="0" + {%endif%} + class="form-control" /> + </div> + + <div class="form-group"> + <label for="datasetdatascale" class="form-label">data scale:</label> + <select id="datasetdatascale" name="datasetdatascale" class="form-control"> + <option value="">None</option> + {%for dscale in datascales:%} + <option value="{{dscale}}" + {%if datasetdatascale is defined and dscale == datasetdatascale%} + selected="selected" + {%elif dscale == "log2":%} + selected="selected" + {%endif%}> + {{dscale}} + </option> + {%endfor%} + </select> + </div> + + <button type="submit" class="btn btn-primary">create new dataset</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/select_platform.html b/uploader/templates/select_platform.html new file mode 100644 index 0000000..d9bc68f --- /dev/null +++ b/uploader/templates/select_platform.html @@ -0,0 +1,82 @@ +{%extends "base.html"%} + +{%block title%}Select Dataset{%endblock%} + +{%block contents%} +<h2 class="heading">{{filename}}: select platform</h2> + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.select_study')}}" + id="select-platform-form" data-genechips="{{genechips_data}}"> + <input type="hidden" name="filename" value="{{filename}}" /> + <input type="hidden" name="filetype" value="{{filetype}}" /> + <input type="hidden" name="totallines" value="{{totallines}}" /> + + <div class="form-group"> + <label for="species" class="form-label">species</label> + <select id="species" name="species" class="form-control"> + {%for row in species:%} + <option value="{{row['SpeciesId']}}" + {%if row["Name"] == default_species:%} + selected="selected" + {%endif%}> + {{row["MenuName"]}} + </option> + {%endfor%} + </select> + </div> + + <table id="genechips-table" class="table"> + <caption>select platform</caption> + <thead> + <tr> + <th>Select</th> + <th>GeneChip ID</th> + <th>GeneChip Name</th> + </tr> + </thead> + + <tbody> + {%for chip in genechips:%} + <tr> + <td> + <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}" + required="required" /> + </td> + <td>{{chip["GeneChipId"]}}</td> + <td>{{chip["GeneChipName"]}}</td> + </tr> + {%else%} + <tr> + <td colspan="5">No chips found for selected species</td> + </tr> + {%endfor%} + </tbody> + </table> + + <button type="submit" class="btn btn-primary">submit platform</button> + </form> +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/utils.js"></script> +<script type="text/javascript" src="/static/js/select_platform.js"></script> +<script type="text/javascript"> + document.getElementById( + "species").addEventListener("change", update_genechips); + document.getElementById( + "genechips-table").getElementsByTagName( + "tbody")[0].addEventListener( + "click", + function(event) { + if(event.target.tagName.toLowerCase() == "td") { + return select_row_radio(event.target.parentElement); + } + if(event.target.tagName.toLowerCase() == "td") { + return select_row_radio(event.target); + } + return false; + }); +</script> +{%endblock%} diff --git a/uploader/templates/select_study.html b/uploader/templates/select_study.html new file mode 100644 index 0000000..648ad4c --- /dev/null +++ b/uploader/templates/select_study.html @@ -0,0 +1,108 @@ +{%extends "base.html"%} +{%from "dbupdate_hidden_fields.html" import hidden_fields%} + +{%block title%}Select Dataset{%endblock%} + +{%block css%} +<link rel="stylesheet" href="/static/css/two-column-with-separator.css" /> +{%endblock%} + +{%block contents%} +<h2 class="heading">{{filename}}: select study</h2> + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.select_dataset')}}" + id="select-platform-form" data-genechips="{{genechips_data}}" + class="two-col-sep-col1"> + <legend class="heading">Select from existing study</legend> + {{hidden_fields(filename, filetype, species=species, genechipid=genechipid, + totallines=totallines)}} + + <div class="form-group"> + <label class="form-label" for="study">study:</label> + <select id="study" name="studyid" class="form-control"> + {%for study in studies:%} + <option value="{{study['Id']}}">{{study["Name"]}}</option> + {%endfor%} + </select> + </div> + + <button type="submit" + class="btn btn-primary" + {%if studies | length == 0:%} + disabled="disabled" + {%endif%} />submit selected study</button> +</form> +</div> + +<div class="row"> + <p class="two-col-sep-separator">OR</p> +</div> + +<div class="row"> + <form method="POST" action="{{url_for('dbinsert.create_study')}}" + id="select-platform-form" data-genechips="{{genechips_data}}" + class="two-col-sep-col2"> + {%with messages = get_flashed_messages(with_categories=true)%} + {%if messages:%} + <ul> + {%for category, message in messages:%} + <li class="{{category}}">{{message}}</li> + {%endfor%} + </ul> + {%endif%} + {%endwith%} + <legend class="heading">Create new study</legend> + {{hidden_fields(filename, filetype, species=species, genechipid=genechipid, + totallines=totallines)}} + + <div class="form-group"> + <label class="form-label" for="studyname">name:</label> + <input type="text" id="studyname" name="studyname" class="form-control" + required="required" + {%if studyname:%} + value="{{studyname}}" + {%endif%} /> + </div> + + <div class="form-group"> + <label class="form-label" for="group">group:</label> + <select id="group" name="inbredsetid" class="form-control" + required="required"> + <option value="">Select group</option> + {%for family in groups:%} + <optgroup label="{{family}}"> + {%for group in groups[family]:%} + <option value="{{group['InbredSetId']}}" + {%if group["InbredSetId"] == selected_group:%} + selected="selected" + {%endif%}> + {{group["FullName"]}} + </option> + {%endfor%} + </optgroup> + {%endfor%} + </select> + </div> + + <div class="form-group"> + <label class="form-label" for="tissue">tissue:</label> + <select id="tissue" name="tissueid" class="form-control" + required="required"> + <option value="">Select type</option> + {%for tissue in tissues:%} + <option value="{{tissue['TissueId']}}" + {%if tissue["TissueId"] == selected_tissue:%} + selected="selected" + {%endif%}> + {{tissue["Name"]}} + </option> + {%endfor%} + </select> + </div> + + <button type="submit" class="btn btn-primary">create study</button> + </form> +</div> + +{%endblock%} diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html new file mode 100644 index 0000000..f64f72b --- /dev/null +++ b/uploader/templates/species/base.html @@ -0,0 +1,17 @@ +{%extends "base.html"%} + +{%block lvl1_breadcrumbs%} +<li {%if activelink=="species"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + {%if species is mapping%} + <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}"> + {{species.Name}}</a> + {%else%} + <a href="{{url_for('species.list_species')}}">Species</a> + {%endif%} +</li> +{%block lvl2_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html new file mode 100644 index 0000000..138dbaa --- /dev/null +++ b/uploader/templates/species/create-species.html @@ -0,0 +1,148 @@ +{%extends "species/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Create Species{%endblock%} + +{%block pagetitle%}Create Species{%endblock%} + +{%block lvl2_breadcrumbs%} +<li {%if activelink=="create-species"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.create_species')}}">Create</a> +</li> +{%endblock%} + +{%block contents%} +<div class="row"> + <form id="frm-create-species" + method="POST" + action="{{url_for('species.create_species', return_to=return_to)}}" + class="form-horizontal"> + <legend>Create Species</legend> + + {{flash_all_messages()}} + + <input type="hidden" name="return_to" value="{{return_to}}"> + + <div class="form-group"> + <label for="txt-taxonomy-id" class="control-label col-sm-2"> + Taxonomy ID</label> + <div class="col-sm-10"> + <div class="input-group"> + <input id="txt-taxonomy-id" + name="species_taxonomy_id" + type="text" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-search-taxonid" class="btn btn-info">Search</button> + </span> + </div> + <small class="form-text text-small text-muted"> + Use + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/" + title="NCBI's Taxonomy Browser homepage" + target="_blank"> + NCBI's Taxonomy Browser homepage</a> to search for the species you + want. If the species exists on NCBI, they will have a Taxonomy ID. Copy + that Taxonomy ID to this field, and click "Search" to auto-fill the + details.<br /> + This field is optional.</small> + </div> + </div> + + <div class="form-group"> + <label for="txt-species-name" class="control-label col-sm-2">Common Name</label> + <div class="col-sm-10"> + <input id="txt-species-name" + name="common_name" + type="text" + class="form-control" + required="required" /> + <small class="form-text text-muted">This is the day-to-day term used by + laymen, e.g. Mouse (instead of Mus musculus), round worm (instead of + Ascaris lumbricoides), etc.<br /> + For species without this, just enter the scientific name. + </small> + </div> + </div> + + <div class="form-group"> + <label for="txt-species-scientific" class="control-label col-sm-2"> + Scientific Name</label> + <div class="col-sm-10"> + <input id="txt-species-scientific" + name="scientific_name" + type="text" + class="form-control" + required="required" /> + <small class="form-text text-muted">This is the scientific name for the + species e.g. Homo sapiens, Mus musculus, etc.</small> + </div> + </div> + + <div class="form-group"> + <label for="select-species-family" class="control-label col-sm-2">Family</label> + <div class="col-sm-10"> + <select id="select-species-family" + name="species_family" + required="required" + class="form-control"> + <option value="ungrouped">I do not know what to pick</option> + {%for family in families%} + <option value="{{family}}">{{family}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + This is a rough grouping of the species.</small> + </div> + </div> + + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + value="create new species" + class="btn btn-primary" /> + </div> + + </form> +</div> +{%endblock%} + +{%block javascript%} +<script> + var lastTaxonId = null; + + var fetch_taxonomy = (taxonId) => { + var uri = ( + "https://rest.uniprot.org/taxonomy/" + encodeURIComponent(taxonId)); + $.get( + uri, + {}, + (data, textStatus, jqXHR) => { + if(textStatus == "success") { + lastTaxonId = taxonId; + $("#txt-species-scientific").val(data.scientificName); + $("#txt-species-name").val(data.commonName); + return false; + } + msg = ( + "Request to '${uri}' failed with message '${textStatus}'. " + + "Please try again later, or fill the details manually."); + alert(msg); + console.error(msg, data, textStatus); + return false; + }, + "json"); + }; + + $("#btn-search-taxonid").on("click", (event) => { + event.preventDefault(); + taxonId = $("#txt-taxonomy-id").val(); + if((taxonId !== "") && (taxonId !== lastTaxonId)) { + fetch_taxonomy(taxonId); + } + }); +</script> +{%endblock%} diff --git a/uploader/templates/species/edit-species.html b/uploader/templates/species/edit-species.html new file mode 100644 index 0000000..5a26455 --- /dev/null +++ b/uploader/templates/species/edit-species.html @@ -0,0 +1,177 @@ +{%extends "species/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Edit Species{%endblock%} + +{%block pagetitle%}Edit Species{%endblock%} + +{%block css%} +<style type="text/css"> + .card { + margin-top: 0.3em; + border-width: 1px; + border-style: solid; + border-radius: 0.3em; + border-color: #AAAAAA; + padding: 0.5em; + } +</style> +{%endblock%} + +{%block lvl2_breadcrumbs%} +<li {%if activelink=="edit-species"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.edit_species_extra', + species_id=species.SpeciesId)}}">Edit</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} +<div class="row"> + <form id="frm-edit-species" + method="POST" + action="{{url_for('species.edit_species_extra', + species_id=species.SpeciesId)}}"> + + <legend>Edit Extra Detail for Species '{{species.FullName}}'</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + + <div class="form-group"> + <label for="lbl-species-taxonid" class="form-label"> + Taxonomy Id + </label> + <label id="lbl-species-taxonid" + disabled="disabled" + class="form-control">{{species.TaxonomyId}}</label> + </div> + + <div class="form-group"> + <label for="txt-species-name" class="form-label"> + Common Name + </label> + <input type="text" + id="txt-species-name" + name="species_name" + required="required" + value="{{species.SpeciesName}}" + class="form-control" /> + <small class="form-text text-muted"> + This is the layman's name for the species, e.g. mouse</mall> + </div> + + <div class="form-group"> + <label for="txt-species-fullname" class="form-label"> + Scientific Name + </label> + <input type="text" + id="txt-species-fullname" + name="species_fullname" + required="required" + value="{{species.FullName}}" + class="form-control" /> + <small class="form-text text-muted"> + A scientific name for the species that mostly adheres to the biological + binomial nomenclature system.</small> + </div> + + <div class="form-group"> + <label for="select-species-family" class="form-label"> + Family + </label> + <select id="select-species-family" + name="species_family" + class="form-control"> + <option value="">Select the family</option> + {%for family in families%} + <option value="{{family}}" + {%if species.Family == family%} + selected="selected" + {%endif%}>{{family}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + A general classification for the species. This is mostly for use in + GeneNetwork's menus.</small> + </div> + + <div class="form-group"> + <label for="txt-species-familyorderid" class="form-label"> + Family Order Id + </label> + <input type="number" + id="txt-species-familyorderid" + name="species_familyorderid" + value="{{species.FamilyOrderId}}" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + This is a number that determines the order of the "Family" groupings + above in the GeneNetwork menus. This is an integer value that's manually + assigned.</small> + </div> + + <div class="form-group"> + <label for="txt-species-orderid" class="form-label"> + Order Id + </label> + <input type="number" + id="txt-species-orderid" + name="species_orderid" + value="{{species.OrderId or (max_order_id + 5)}}" + class="form-control" /> + <small class="form-text text-muted"> + This integer value determines the order of the species in relation to + each other, but also within the respective "Family" groups.</small> + </div> + + <div class="form-group"> + <input type="submit" value="Submit Changes" class="btn btn-primary" /> + </div> + + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Family Order</h5> + <div class="card-text"> + <p>The current family order is as follows</p> + <table class="table"> + <thead> + <tr> + <th>Family Order Id</th> + <th>Family</th> + </tr> + </thead> + <tbody> + {%for item in family_order%} + <tr> + <td>{{item[0]}}</td> + <td>{{item[1]}}</td> + </tr> + {%endfor%} + </tbody> + </table> + </div> + </div> +</div> + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Order ID</h5> + <div class="card-text"> + <p>The current largest OrderID is: {{max_order_id}}</p> + <p>We recommend giving a new species an order ID that is five more than + the current highest i.e. {{max_order_id + 5}}.</p> + </div> + </div> +</div> +{%endblock%} diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html new file mode 100644 index 0000000..64084b0 --- /dev/null +++ b/uploader/templates/species/list-species.html @@ -0,0 +1,75 @@ +{%extends "species/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}List Species{%endblock%} + +{%block pagetitle%}List Species{%endblock%} + +{%block contents%} +{{flash_all_messages()}} +<div class="row"> + <p> + All data in GeneNetwork revolves around species. This is the core of the + system.</p> + <p>Here you can see a list of all the species available in GeneNetwork. + Click on the link besides each species to view greater detail on the species, + and access further operations that are possible for said species.</p> +</div> + +<div class="row"> + <p>If you cannot find the species you are looking for below, click the button + below to create it</p> + <p><a href="{{url_for('species.create_species')}}" + title="Add a new species to GeneNetwork" + class="btn btn-danger">Create Species</a></p> +</div> + +<div class="row"> + <table class="table"> + <caption>Available Species</caption> + <thead> + <tr> + <th></td> + <th title="A common, layman's name for the species.">Common Name</th> + <th title="The scientific name for the species">Organism Name</th> + <th title="An identifier for the species in the NCBI taxonomy database"> + Taxonomy ID + </th> + <th title="A generic grouping used internally by GeneNetwork for organising species."> + Family + </th> + </tr> + </thead> + <tbody> + {%for species in allspecies%} + <tr> + <td>{{species["sequence_number"]}}</td> + <td>{{species["SpeciesName"]}}</td> + <td> + <a href="{{url_for('species.view_species', + species_id=species['SpeciesId'])}}" + title="View details in GeneNetwork on {{species['FullName']}}"> + {{species["FullName"]}} + </a> + </td> + <td> + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species['TaxonomyId']}}" + title="View species details on NCBI" + target="_blank">{{species["TaxonomyId"]}}</a> + </td> + <td>{{species.Family}}</td> + </tr> + {%else%} + <tr> + <td colspan="3"> + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-mark"></span> + There were no species found! + </p> + </td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%endblock%} diff --git a/uploader/templates/species/macro-display-species-card.html b/uploader/templates/species/macro-display-species-card.html new file mode 100644 index 0000000..166c7b9 --- /dev/null +++ b/uploader/templates/species/macro-display-species-card.html @@ -0,0 +1,22 @@ +{%macro display_species_card(species)%} +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Species</h5> + <div class="card-text"> + <table class="table"> + <tbody> + <tr> + <td>Common Name</td> + <td>{{species.SpeciesName}}</td> + </tr> + + <tr> + <td>Scientific Name</td> + <td>{{species.FullName}}</td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html new file mode 100644 index 0000000..3714ae4 --- /dev/null +++ b/uploader/templates/species/macro-select-species.html @@ -0,0 +1,59 @@ +{%from "macro-step-indicator.html" import step_indicator%} + +{%macro select_species_form(form_action, species)%} +<form method="GET" action="{{form_action}}" class="form-horizontal"> + + <h2>{{step_indicator("1")}} What species do you want to work with?</h2> + + {%if species | length != 0%} + + <p class="form-text">Search for, and select the species from the table below + and click "Continue"</p> + + <div class="radio"> + <label for="rdo-cant-find-species" + style="font-weight: 1;"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + I could not find the species I want (create it). + </label> + </div> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary" + value="continue" /> + </div> + + <div style="margin-top:3em;"> + <table id="tbl-select-species" class="table compact stripe" + data-species-list='{{species | tojson}}'> + <div class=""> + <thead> + <tr> + <th></th> + <th>Species Name</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> + + {%else%} + + <label class="control-label" for="rdo-cant-find-species"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + There are no species to select from. Create the first one.</label> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary col-sm-offset-1" + value="continue" /> + </div> + + {%endif%} + +</form> +{%endmacro%} diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html new file mode 100644 index 0000000..2d02f7e --- /dev/null +++ b/uploader/templates/species/view-species.html @@ -0,0 +1,90 @@ +{%extends "species/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Species{%endblock%} + +{%block pagetitle%}View Species{%endblock%} + +{%block lvl2_breadcrumbs%} +<li {%if activelink=="view-species"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}">View</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} +<div class="row"> + <h2>Details on species {{species.FullName}}</h2> + + <dl> + <dt>Common Name</dt> + <dd>{{species.SpeciesName}}</dd> + + <dt>Scientific Name</dt> + <dd>{{species.FullName}}</dd> + + <dt>Taxonomy ID</dt> + <dd>{{species.TaxonomyId}}</dd> + </dl> + + <h3>Actions</h3> + + <p> + You can proceed to perform any of the following actions for species + {{species.FullName}} + </p> + + <ol> + <li> + <a href="{{url_for('species.populations.list_species_populations', + species_id=species.SpeciesId)}}" + title="Create/Edit populations for {{species.FullName}}"> + Manage populations</a> + </li> + <li> + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId)}}" + title="Create/Edit sequencing platforms for {{species.FullName}}"> + Manage sequencing platforms</a> + </li> + </ol> + + +</div> +{%endblock%} + +{%block sidebarcontents%} +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Species Extras</h5> + <div class="card-text"> + <p>Some extra internal-use details (mostly for UI concerns on GeneNetwork)</p> + <p> + <small> + If you do not understand what the following are about, simply ignore them + — + They have no bearing whatsoever on your data, or its analysis. + </small> + </p> + <dl> + <dt>Family</dt> + <dd>{{species.Family}}</dd> + + <dt>FamilyOrderId</dt> + <dd>{{species.FamilyOrderId}}</dd> + + <dt>OrderId</dt> + <dd>{{species.OrderId}}</dd> + </dl> + </div> + <a href="{{url_for('species.edit_species_extra', + species_id=species.SpeciesId)}}" + class="card-link" + title="Edit the species' internal-use details.">Edit</a> + </div> +</div> +{%endblock%} diff --git a/uploader/templates/stdout_output.html b/uploader/templates/stdout_output.html new file mode 100644 index 0000000..85345a9 --- /dev/null +++ b/uploader/templates/stdout_output.html @@ -0,0 +1,8 @@ +{%macro stdout_output(job)%} + +<h4>STDOUT Output</h4> +<div class="cli-output"> + <pre>{{job.get("stdout", "")}}</pre> +</div> + +{%endmacro%} diff --git a/uploader/templates/unhandled_exception.html b/uploader/templates/unhandled_exception.html new file mode 100644 index 0000000..cfb0c0b --- /dev/null +++ b/uploader/templates/unhandled_exception.html @@ -0,0 +1,24 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}System Error{%endblock%} + +{%block css%} +<link rel="stylesheet" href="/static/css/two-column-with-separator.css" /> +{%endblock%} + +{%block contents%} +<div class="row"> + {{flash_all_messages()}} + <h1>Exception!</h1> + + <p>An error has occured, and your request has been aborted. Please notify the + administrator to try and get this fixed.</p> + <p>The system has failed with the following error:</p> +</div> +<div class="row"> + <pre> + {{trace}} + </pre> +</div> +{%endblock%} diff --git a/uploader/templates/upload_progress_indicator.html b/uploader/templates/upload_progress_indicator.html new file mode 100644 index 0000000..e274e83 --- /dev/null +++ b/uploader/templates/upload_progress_indicator.html @@ -0,0 +1,35 @@ +{%macro upload_progress_indicator()%} +<div id="upload-progress-indicator" class="modal fade" tabindex="-1" role="dialog"> + <div class="modal-dialog" role="document"> + <div class="modal-content"> + <div class="modal-header"> + <h3 class="modal-title">Uploading file</h3> + </div> + + <div class="modal-body"> + <form id="frm-cancel-upload" style="border-style: none;"> + <div class="form-group"> + <span id="progress-filename" class="form-text">No file selected!</span> + <progress id="progress-bar" value="0" max="100" class="form-control"> + 0</progress> + </div> + + <div class="form-group"> + <span class="form-text text-muted" id="progress-text"> + Uploading 0%</span> + <span class="form-text text-muted" id="progress-extra-text"> + Processing</span> + </div> + </form> + </div> + + <div class="modal-footer"> + <button id="btn-cancel-upload" + type="button" + class="btn btn-danger" + data-dismiss="modal">Cancel</button> + </div> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/worker_failure.html b/uploader/templates/worker_failure.html new file mode 100644 index 0000000..b65b140 --- /dev/null +++ b/uploader/templates/worker_failure.html @@ -0,0 +1,24 @@ +{%extends "base.html"%} + +{%block title%}Worker Failure{%endblock%} + +{%block contents%} +<h1 class="heading">Worker Failure</h1> + +<p> + There was a critical failure launching the job to parse your file. + This is our fault and (probably) has nothing to do with the file you uploaded. +</p> + +<p> + Please notify the developers of this issue when you encounter it, + providing the link to this page, or the information below. +</p> + +<h4>Debugging Information</h4> + +<ul> + <li><strong>job id</strong>: {{job_id}}</li> +</ul> + +{%endblock%} |