From 0b37b9b3fa4fead86787a705713645fa14530a54 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 23 Sep 2024 14:28:49 -0500 Subject: Initialise the "Expression Data" section. --- uploader/templates/data_review.html | 85 --------------- uploader/templates/expression-data/base.html | 13 +++ .../templates/expression-data/data-review.html | 85 +++++++++++++++ uploader/templates/expression-data/index.html | 82 ++------------- .../templates/expression-data/job-progress.html | 47 +++++++++ .../templates/expression-data/no-such-job.html | 15 +++ .../templates/expression-data/parse-failure.html | 26 +++++ .../templates/expression-data/parse-results.html | 39 +++++++ .../templates/expression-data/select-file.html | 115 +++++++++++++++++++++ .../expression-data/select-population.html | 29 ++++++ uploader/templates/job_progress.html | 40 ------- uploader/templates/no_such_job.html | 14 --- uploader/templates/parse_failure.html | 26 ----- uploader/templates/parse_results.html | 30 ------ uploader/templates/select_species.html | 92 ----------------- 15 files changed, 379 insertions(+), 359 deletions(-) delete mode 100644 uploader/templates/data_review.html create mode 100644 uploader/templates/expression-data/base.html create mode 100644 uploader/templates/expression-data/data-review.html create mode 100644 uploader/templates/expression-data/job-progress.html create mode 100644 uploader/templates/expression-data/no-such-job.html create mode 100644 uploader/templates/expression-data/parse-failure.html create mode 100644 uploader/templates/expression-data/parse-results.html create mode 100644 uploader/templates/expression-data/select-file.html create mode 100644 uploader/templates/expression-data/select-population.html delete mode 100644 uploader/templates/job_progress.html delete mode 100644 uploader/templates/no_such_job.html delete mode 100644 uploader/templates/parse_failure.html delete mode 100644 uploader/templates/parse_results.html delete mode 100644 uploader/templates/select_species.html (limited to 'uploader/templates') diff --git a/uploader/templates/data_review.html b/uploader/templates/data_review.html deleted file mode 100644 index 4e5c586..0000000 --- a/uploader/templates/data_review.html +++ /dev/null @@ -1,85 +0,0 @@ -{%extends "base.html"%} - -{%block title%}Data Review{%endblock%} - -{%block contents%} -

data review

- -
-

Data Concerns

-

The following are some of the requirements that the data in your file - MUST fulfil before it is considered valid for this system: -

- -
    -
  1. File headings -
      -
    • 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.
      • -
    • Each heading value in the first row MUST appear in the first row - ONE AND ONLY ONE time
      • -
    • The sample/cases (previously 'strains') headers in your first row will be - against those in the - GeneNetwork database.
      - - 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 - Upload Samples/Cases - option on this system to upload them. - -
    -
    2. - -
  2. Data -
      -
    1. NONE of the data cells/fields is allowed to be empty. - All fields/cells MUST contain a value.
      2. -
    2. The first column of the data rows will be considered a textual field, - holding the "identifier" for that row
    3. -
    4. Except for the first column/field for each data row, - NONE of the data columns/cells/fields should contain - spurious characters like `eeeee`, `5.555iloveguix`, etc...
      - All of them should be decimal values
      5. -
    5. decimal numbers must conform to the following criteria: -
        -
      • when checking an average file decimal numbers must have exactly three - decimal places to the right of the decimal point.
        • -
      • when checking a standard error file decimal numbers must have six or - greater decimal places to the right of the decimal point.
        • -
      • there must be a number to the left side of the decimal place - (e.g. 0.55555 is allowed but .55555 is not).
        • -
      -
      6. -
    -
    3. -
-
- - -
-

Supported File Types

- We support the following file types: - - - -
-{%endblock%} 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%} +
  • + + Expression Data +
    • +{%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%} +

    data review

    + +
    +

    Data Concerns

    +

    The following are some of the requirements that the data in your file + MUST fulfil before it is considered valid for this system: +

    + +
      +
    1. File headings +
        +
      • 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.
        • +
      • Each heading value in the first row MUST appear in the first row + ONE AND ONLY ONE time
        • +
      • The sample/cases (previously 'strains') headers in your first row will be + against those in the + GeneNetwork database.
        + + 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 + Upload Samples/Cases + option on this system to upload them. + +
      +
      2. + +
    2. Data +
        +
      1. NONE of the data cells/fields is allowed to be empty. + All fields/cells MUST contain a value.
        2. +
      2. The first column of the data rows will be considered a textual field, + holding the "identifier" for that row
      3. +
      4. Except for the first column/field for each data row, + NONE of the data columns/cells/fields should contain + spurious characters like `eeeee`, `5.555iloveguix`, etc...
        + All of them should be decimal values
        5. +
      5. decimal numbers must conform to the following criteria: +
          +
        • when checking an average file decimal numbers must have exactly three + decimal places to the right of the decimal point.
          • +
        • when checking a standard error file decimal numbers must have six or + greater decimal places to the right of the decimal point.
          • +
        • there must be a number to the left side of the decimal place + (e.g. 0.55555 is allowed but .55555 is not).
          • +
        +
        6. +
      +
      3. +
    +
    + + +
    +

    Supported File Types

    + We support the following file types: + + + +
    +{%endblock%} diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html index ed5d8dd..9ba3582 100644 --- a/uploader/templates/expression-data/index.html +++ b/uploader/templates/expression-data/index.html @@ -1,5 +1,6 @@ -{%extends "base.html"%} +{%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%} @@ -10,86 +11,23 @@ Home
  • - Expression Data + + Expression Data
    • {%endblock%} {%block contents%} -
    - {{flash_all_messages()}} - -

    data upload

    - -
    -

    Each of the sections below gives you a different option for data expression-data. - Please read the documentation for each section carefully to understand what - each section is about.

    -
    -
    - -
    -

    R/qtl2 Bundles

    - -
    -

    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.

    -

    The R/qtl2 bundle, additionally, can contain extra metadata, that neither - of the methods below can handle.

    - - - -
    -
    - -

    Expression Data

    + {{flash_all_messages()}} -
    -

    This feature enables you to upload expression data. It expects the data to - be in tab-separated values (TSV) files. The data should be - a simple matrix of phenotype × sample, i.e. The first column is a - list of the phenotypes and the first row is a list of - samples/cases.

    - -

    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.

    - -
      -
    1. PLEASE REVIEW YOUR DATA.Make sure your data complies - with our system requirements. ( - Help - )
      2. -
    2. UPLOAD YOUR DATA FOR DATA VERIFICATION. We accept - .csv, .txt and .zip - files (Help)
      3. -
    -
    - - upload expression data +

    This section allows you to enter the expression data for your experiment. + You will need to select the species that your data concerns below.

    -

    samples/cases

    - -
    -

    For the expression data above, you need the samples/cases in your file to - already exist in the GeneNetwork database. If there are any samples that do - not already exist the upload of the expression data will fail.

    -

    This section gives you the opportunity to upload any missing samples

    -
    - - upload Samples/Cases + {{select_species_form(url_for("species.populations.expression-data.index"), + species)}}
    - {%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%} + +{%endblock%} + +{%block title%}Job Status{%endblock%} + +{%block contents%} +

    {{job_name}}

    + +
    +
    + Status +
    + + {{job_status}}: {{message}}
    +
    + +
    + + + {{progress}} + {{"%.2f" | format(progress)}}% +
    + + + + +
    +
    + +
    + {{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}} +
    + +{%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%} + +{%endblock%} + +{%block title%}No Such Job{%endblock%} + +{%block contents%} +

    No Such Job: {{job_id}}

    + +

    No job, with the id '{{job_id}}' was found!

    + +{%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%} +

    Worker Failure

    + +

    + There was an error while parsing your file. +

    + +

    + Please notify the developers of this issue when you encounter it, + providing the information below. +

    + +

    Debugging Information

    + + + +{%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%} + +
    +

    {{job_name}}: parse results

    + + {%if user_aborted%} + Job aborted by the user + {%endif%} + + {{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} + + {%if errors | length == 0 and not user_aborted %} +
    + + +
    + {%endif%} + + {%if errors | length > 0 or user_aborted %} +
    + Go back + + {%endif%} +
    +{%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()}} + +
    +

    Upload Expression Data

    + +

    This feature enables you to upload expression data. It expects the data to + be in tab-separated values (TSV) files. The data should be + a simple matrix of phenotype × sample, i.e. The first column is a + list of the phenotypes and the first row is a list of + samples/cases.

    + +

    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.

    + +
      +
    1. PLEASE REVIEW YOUR DATA.Make sure your data complies + with our system requirements. ( + Help + )
      2. +
    2. UPLOAD YOUR DATA FOR DATA VERIFICATION. We accept + .csv, .txt and .zip + files (Help)
      3. +
    +
    + +
    +
    + {{flash_messages("error-expr-data")}} + +
    + File Type + +
    + +

    + The averages data …

    +
    + +
    + +

    + The standard errors computed from the averages …

    +
    +
    + +
    + + + +

    + Select the file to upload.

    +
    + + +
    +
    +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + +{%block javascript%} + + +{%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()}} + +
    +

    You have selected the species. Now you need to select the population that + the expression data belongs to.

    +
    + +
    + {{select_population_form(url_for( + "species.populations.expression-data.select_population", + species_id=species.SpeciesId), + populations)}} +
    +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/job_progress.html b/uploader/templates/job_progress.html deleted file mode 100644 index 2feaa89..0000000 --- a/uploader/templates/job_progress.html +++ /dev/null @@ -1,40 +0,0 @@ -{%extends "base.html"%} -{%from "errors_display.html" import errors_display%} - -{%block extrameta%} - -{%endblock%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    {{job_name}}

    - -
    -
    - Status -
    - - {{job_status}}: {{message}}
    -
    - -
    - - - {{progress}} - {{"%.2f" | format(progress)}}% -
    - - - - -
    -
    - -
    - {{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}} -
    - -{%endblock%} diff --git a/uploader/templates/no_such_job.html b/uploader/templates/no_such_job.html deleted file mode 100644 index 874d047..0000000 --- a/uploader/templates/no_such_job.html +++ /dev/null @@ -1,14 +0,0 @@ -{%extends "base.html"%} - -{%block extrameta%} - -{%endblock%} - -{%block title%}No Such Job{%endblock%} - -{%block contents%} -

    No Such Job: {{job_id}}

    - -

    No job, with the id '{{job_id}}' was found!

    - -{%endblock%} diff --git a/uploader/templates/parse_failure.html b/uploader/templates/parse_failure.html deleted file mode 100644 index 31f6be8..0000000 --- a/uploader/templates/parse_failure.html +++ /dev/null @@ -1,26 +0,0 @@ -{%extends "base.html"%} - -{%block title%}Worker Failure{%endblock%} - -{%block contents%} -

    Worker Failure

    - -

    - There was an error while parsing your file. -

    - -

    - Please notify the developers of this issue when you encounter it, - providing the information below. -

    - -

    Debugging Information

    - - - -{%endblock%} diff --git a/uploader/templates/parse_results.html b/uploader/templates/parse_results.html deleted file mode 100644 index 46fbaaf..0000000 --- a/uploader/templates/parse_results.html +++ /dev/null @@ -1,30 +0,0 @@ -{%extends "base.html"%} -{%from "errors_display.html" import errors_display%} - -{%block title%}Parse Results{%endblock%} - -{%block contents%} -

    {{job_name}}: parse results

    - -{%if user_aborted%} -Job aborted by the user -{%endif%} - -{{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} - -{%if errors | length == 0 and not user_aborted %} -
    - - -
    -{%endif%} - -{%if errors | length > 0 or user_aborted %} -
    - - Go back - -{%endif%} - -{%endblock%} diff --git a/uploader/templates/select_species.html b/uploader/templates/select_species.html deleted file mode 100644 index 1642401..0000000 --- a/uploader/templates/select_species.html +++ /dev/null @@ -1,92 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} -{%from "upload_progress_indicator.html" import upload_progress_indicator%} - -{%block title%}expression data: select species{%endblock%} - -{%block contents%} -{{upload_progress_indicator()}} - -

    expression data: select species

    - -
    -
    - upload expression data - {{flash_messages("error-expr-data")}} - -
    - - -
    - -
    - file type - -
    - - -
    - -
    - - -
    -
    - -
    - - - -
    - - -
    -
    -{%endblock%} - - -{%block javascript%} - - -{%endblock%} -- cgit v1.2.3