From 754e8f214b940e05298cb360ed829f5c685d55a5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 25 Jul 2024 11:07:33 -0500 Subject: Rename module: qc_app --> uploader --- qc_app/templates/base.html | 51 ---- qc_app/templates/cli-output.html | 8 - qc_app/templates/continue_from_create_dataset.html | 52 ---- qc_app/templates/continue_from_create_study.html | 52 ---- qc_app/templates/data_review.html | 85 ------- qc_app/templates/dbupdate_error.html | 12 - qc_app/templates/dbupdate_hidden_fields.html | 29 --- qc_app/templates/errors_display.html | 47 ---- qc_app/templates/final_confirmation.html | 47 ---- qc_app/templates/flash_messages.html | 25 -- qc_app/templates/http-error.html | 18 -- qc_app/templates/index.html | 81 ------ qc_app/templates/insert_error.html | 32 --- qc_app/templates/insert_progress.html | 46 ---- qc_app/templates/insert_success.html | 19 -- qc_app/templates/job_progress.html | 40 --- qc_app/templates/no_such_job.html | 14 -- qc_app/templates/parse_failure.html | 26 -- qc_app/templates/parse_results.html | 30 --- .../rqtl2/create-geno-dataset-success.html | 55 ---- .../rqtl2/create-probe-dataset-success.html | 59 ----- .../rqtl2/create-probe-study-success.html | 49 ---- qc_app/templates/rqtl2/create-tissue-success.html | 106 -------- qc_app/templates/rqtl2/index.html | 36 --- qc_app/templates/rqtl2/no-such-job.html | 13 - qc_app/templates/rqtl2/rqtl2-job-error.html | 39 --- qc_app/templates/rqtl2/rqtl2-job-results.html | 24 -- qc_app/templates/rqtl2/rqtl2-job-status.html | 20 -- qc_app/templates/rqtl2/rqtl2-qc-job-error.html | 120 --------- qc_app/templates/rqtl2/rqtl2-qc-job-results.html | 66 ----- qc_app/templates/rqtl2/rqtl2-qc-job-status.html | 41 --- qc_app/templates/rqtl2/rqtl2-qc-job-success.html | 37 --- qc_app/templates/rqtl2/select-geno-dataset.html | 144 ----------- qc_app/templates/rqtl2/select-population.html | 136 ---------- .../templates/rqtl2/select-probeset-dataset.html | 191 -------------- .../templates/rqtl2/select-probeset-study-id.html | 143 ----------- qc_app/templates/rqtl2/select-tissue.html | 115 --------- qc_app/templates/rqtl2/summary-info.html | 65 ----- .../rqtl2/upload-rqtl2-bundle-step-01.html | 276 --------------------- .../rqtl2/upload-rqtl2-bundle-step-02.html | 33 --- qc_app/templates/samples/select-population.html | 99 -------- qc_app/templates/samples/select-species.html | 30 --- qc_app/templates/samples/upload-failure.html | 27 -- qc_app/templates/samples/upload-progress.html | 22 -- qc_app/templates/samples/upload-samples.html | 139 ----------- qc_app/templates/samples/upload-success.html | 18 -- qc_app/templates/select_dataset.html | 161 ------------ qc_app/templates/select_platform.html | 82 ------ qc_app/templates/select_species.html | 92 ------- qc_app/templates/select_study.html | 108 -------- qc_app/templates/stdout_output.html | 8 - qc_app/templates/unhandled_exception.html | 21 -- qc_app/templates/upload_progress_indicator.html | 35 --- qc_app/templates/worker_failure.html | 24 -- 54 files changed, 3348 deletions(-) delete mode 100644 qc_app/templates/base.html delete mode 100644 qc_app/templates/cli-output.html delete mode 100644 qc_app/templates/continue_from_create_dataset.html delete mode 100644 qc_app/templates/continue_from_create_study.html delete mode 100644 qc_app/templates/data_review.html delete mode 100644 qc_app/templates/dbupdate_error.html delete mode 100644 qc_app/templates/dbupdate_hidden_fields.html delete mode 100644 qc_app/templates/errors_display.html delete mode 100644 qc_app/templates/final_confirmation.html delete mode 100644 qc_app/templates/flash_messages.html delete mode 100644 qc_app/templates/http-error.html delete mode 100644 qc_app/templates/index.html delete mode 100644 qc_app/templates/insert_error.html delete mode 100644 qc_app/templates/insert_progress.html delete mode 100644 qc_app/templates/insert_success.html delete mode 100644 qc_app/templates/job_progress.html delete mode 100644 qc_app/templates/no_such_job.html delete mode 100644 qc_app/templates/parse_failure.html delete mode 100644 qc_app/templates/parse_results.html delete mode 100644 qc_app/templates/rqtl2/create-geno-dataset-success.html delete mode 100644 qc_app/templates/rqtl2/create-probe-dataset-success.html delete mode 100644 qc_app/templates/rqtl2/create-probe-study-success.html delete mode 100644 qc_app/templates/rqtl2/create-tissue-success.html delete mode 100644 qc_app/templates/rqtl2/index.html delete mode 100644 qc_app/templates/rqtl2/no-such-job.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-job-error.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-job-results.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-job-status.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-error.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-results.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-status.html delete mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-success.html delete mode 100644 qc_app/templates/rqtl2/select-geno-dataset.html delete mode 100644 qc_app/templates/rqtl2/select-population.html delete mode 100644 qc_app/templates/rqtl2/select-probeset-dataset.html delete mode 100644 qc_app/templates/rqtl2/select-probeset-study-id.html delete mode 100644 qc_app/templates/rqtl2/select-tissue.html delete mode 100644 qc_app/templates/rqtl2/summary-info.html delete mode 100644 qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html delete mode 100644 qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html delete mode 100644 qc_app/templates/samples/select-population.html delete mode 100644 qc_app/templates/samples/select-species.html delete mode 100644 qc_app/templates/samples/upload-failure.html delete mode 100644 qc_app/templates/samples/upload-progress.html delete mode 100644 qc_app/templates/samples/upload-samples.html delete mode 100644 qc_app/templates/samples/upload-success.html delete mode 100644 qc_app/templates/select_dataset.html delete mode 100644 qc_app/templates/select_platform.html delete mode 100644 qc_app/templates/select_species.html delete mode 100644 qc_app/templates/select_study.html delete mode 100644 qc_app/templates/stdout_output.html delete mode 100644 qc_app/templates/unhandled_exception.html delete mode 100644 qc_app/templates/upload_progress_indicator.html delete mode 100644 qc_app/templates/worker_failure.html (limited to 'qc_app/templates') diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html deleted file mode 100644 index eb5e6b7..0000000 --- a/qc_app/templates/base.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - - - - {%block extrameta%}{%endblock%} - - GN Uploader: {%block title%}{%endblock%} - - - - - - - - - - - {%block css%}{%endblock%} - - - - -
- {%block contents%}{%endblock%} -
- - - - {%block javascript%}{%endblock%} - - diff --git a/qc_app/templates/cli-output.html b/qc_app/templates/cli-output.html deleted file mode 100644 index 33fb73b..0000000 --- a/qc_app/templates/cli-output.html +++ /dev/null @@ -1,8 +0,0 @@ -{%macro cli_output(job, stream)%} - -

{{stream | upper}} Output

-
- 
{{job.get(stream, "")}}
-
- -{%endmacro%} diff --git a/qc_app/templates/continue_from_create_dataset.html b/qc_app/templates/continue_from_create_dataset.html deleted file mode 100644 index 03bb49c..0000000 --- a/qc_app/templates/continue_from_create_dataset.html +++ /dev/null @@ -1,52 +0,0 @@ -{%extends "base.html"%} -{%from "dbupdate_hidden_fields.html" import hidden_fields%} - -{%block title%}Create Study{%endblock%} - -{%block css%} - -{%endblock%} - -{%block contents%} -

{{filename}}: create study

- -{%with messages = get_flashed_messages(with_categories=true)%} -{%if messages:%} - -{%endif%} -{%endwith%} - -
-
- continue with new dataset - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid, datasetid=datasetid, totallines=totallines)}} - - -
-
- -
-

OR

-
- -
-
- Select from existing dataset - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid, datasetid=datasetid, totallines=totallines)}} - - -
-
-{%endblock%} diff --git a/qc_app/templates/continue_from_create_study.html b/qc_app/templates/continue_from_create_study.html deleted file mode 100644 index 34e6e5e..0000000 --- a/qc_app/templates/continue_from_create_study.html +++ /dev/null @@ -1,52 +0,0 @@ -{%extends "base.html"%} -{%from "dbupdate_hidden_fields.html" import hidden_fields%} - -{%block title%}Create Study{%endblock%} - -{%block css%} - -{%endblock%} - -{%block contents%} -

{{filename}}: create study

- -{%with messages = get_flashed_messages(with_categories=true)%} -{%if messages:%} - -{%endif%} -{%endwith%} - -
-
- continue with new study - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid, totallines=totallines)}} - - -
-
- -
-

OR

-
- -
-
- Select from existing study - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid, totallines=totallines)}} - - -
-
-{%endblock%} diff --git a/qc_app/templates/data_review.html b/qc_app/templates/data_review.html deleted file mode 100644 index b7528fd..0000000 --- a/qc_app/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/qc_app/templates/dbupdate_error.html b/qc_app/templates/dbupdate_error.html deleted file mode 100644 index e1359d2..0000000 --- a/qc_app/templates/dbupdate_error.html +++ /dev/null @@ -1,12 +0,0 @@ -{%extends "base.html"%} - -{%block title%}DB Update Error{%endblock%} - -{%block contents%} -

database update error

- -

- Database Update Error: {{error_message}} -

- -{%endblock%} diff --git a/qc_app/templates/dbupdate_hidden_fields.html b/qc_app/templates/dbupdate_hidden_fields.html deleted file mode 100644 index ccbc299..0000000 --- a/qc_app/templates/dbupdate_hidden_fields.html +++ /dev/null @@ -1,29 +0,0 @@ -{%macro hidden_fields(filename, filetype):%} - - - - - -{%if kwargs.get("totallines")%} - -{%endif%} -{%if kwargs.get("species"):%} - -{%endif%} -{%if kwargs.get("genechipid"):%} - -{%endif%} -{%if kwargs.get("inbredsetid"):%} - -{%endif%} -{%if kwargs.get("tissueid"):%} - -{%endif%} -{%if kwargs.get("studyid"):%} - -{%endif%} -{%if kwargs.get("datasetid"):%} - -{%endif%} - -{%endmacro%} diff --git a/qc_app/templates/errors_display.html b/qc_app/templates/errors_display.html deleted file mode 100644 index 715cfcf..0000000 --- a/qc_app/templates/errors_display.html +++ /dev/null @@ -1,47 +0,0 @@ -{%macro errors_display(errors, no_error_msg, error_message, complete)%} - -{%if errors | length == 0 %} -{{no_error_msg}} -{%else %} -

{{error_message}}

- - - - - - - - - - - - - {%for error in errors%} - - - - - - - {%endfor%} - -
line numbercolumn(s)errorerror message
{{error["line"]}} - {%if isinvalidvalue(error):%} - {{error.column}} - {%elif isduplicateheading(error): %} - {{error.columns}} - {%else: %} - - - {%endif %} - - {%if isinvalidvalue(error):%} - Invalid Value - {%elif isduplicateheading(error): %} - Duplicate Header - {%else%} - Inconsistent Columns - {%endif %} - {{error["message"]}}
-{%endif%} - -{%endmacro%} diff --git a/qc_app/templates/final_confirmation.html b/qc_app/templates/final_confirmation.html deleted file mode 100644 index 0727fc8..0000000 --- a/qc_app/templates/final_confirmation.html +++ /dev/null @@ -1,47 +0,0 @@ -{%extends "base.html"%} -{%from "dbupdate_hidden_fields.html" import hidden_fields%} - -{%block title%}Confirmation{%endblock%} - -{%macro display_item(item_name, item_data):%} -
  • - {{item_name}} - {%if item_data%} - - {%endif%} -
    • -{%endmacro%} - -{%block contents%} -

    Final Confirmation

    - -
    -

    Selected Data

    - -
    - -
    - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid,datasetid=datasetid, totallines=totallines)}} -
    - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/flash_messages.html b/qc_app/templates/flash_messages.html deleted file mode 100644 index b7af178..0000000 --- a/qc_app/templates/flash_messages.html +++ /dev/null @@ -1,25 +0,0 @@ -{%macro flash_all_messages()%} -{%with messages = get_flashed_messages(with_categories=true)%} -{%if messages:%} - -{%endif%} -{%endwith%} -{%endmacro%} - -{%macro flash_messages(filter_class)%} -{%with messages = get_flashed_messages(with_categories=true)%} -{%if messages:%} - -{%endif%} -{%endwith%} -{%endmacro%} diff --git a/qc_app/templates/http-error.html b/qc_app/templates/http-error.html deleted file mode 100644 index 374fb86..0000000 --- a/qc_app/templates/http-error.html +++ /dev/null @@ -1,18 +0,0 @@ -{%extends "base.html"%} - -{%block title%}HTTP Error: {{exc.code}}{%endblock%} - -{%block contents%} -

    {{exc.code}}: {{exc.description}}

    - -
    -

    - You attempted to access {{request_url}} which failed with the following - error: -

    -
    - -
    - 
    {{"\n".join(trace)}}
    -
    -{%endblock%} diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html deleted file mode 100644 index 89d2ae9..0000000 --- a/qc_app/templates/index.html +++ /dev/null @@ -1,81 +0,0 @@ -{%extends "base.html"%} - -{%block title%}Data Upload{%endblock%} - -{%block contents%} -
    -

    data upload

    - -
    -

    Each of the sections below gives you a different option for data upload. - 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

    - -
    -

    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 -
    - -
    -

    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 -
    - -{%endblock%} diff --git a/qc_app/templates/insert_error.html b/qc_app/templates/insert_error.html deleted file mode 100644 index 5301288..0000000 --- a/qc_app/templates/insert_error.html +++ /dev/null @@ -1,32 +0,0 @@ -{%extends "base.html"%} - -{%block title%}Data Insertion Failure{%endblock%} - -{%block contents%} -

    Insertion Failure

    - -
    -

    - There was an error inserting data into the database -

    - -

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

    - -

    Debugging Information

    - - -
    - -
    -

    STDERR Output

    - 
    -    {{job["stderr"]}}
-
    -
    - -{%endblock%} diff --git a/qc_app/templates/insert_progress.html b/qc_app/templates/insert_progress.html deleted file mode 100644 index 52177d6..0000000 --- a/qc_app/templates/insert_progress.html +++ /dev/null @@ -1,46 +0,0 @@ -{%extends "base.html"%} -{%from "stdout_output.html" import stdout_output%} - -{%block extrameta%} - -{%endblock%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    {{job_name}}

    - -
    -
    -
    - - {{job_status}}: {{message}} -
    - -{%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%} - -
    - - {{fraction*100}} - - {{"%.2f" | format(fraction * 100 | float)}}% -
    -
    -
    - - -{{stdout_output(job)}} - -{%endblock%} diff --git a/qc_app/templates/insert_success.html b/qc_app/templates/insert_success.html deleted file mode 100644 index 7e1fa8d..0000000 --- a/qc_app/templates/insert_success.html +++ /dev/null @@ -1,19 +0,0 @@ -{%extends "base.html"%} -{%from "stdout_output.html" import stdout_output%} - -{%block title%}Insertion Success{%endblock%} - -{%block contents%} -

    Insertion Success

    - -
    -

    Data inserted successfully!

    - -

    The following queries were run:

    -
    - -
    - {{stdout_output(job)}} -
    - -{%endblock%} diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html deleted file mode 100644 index 1af0763..0000000 --- a/qc_app/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/qc_app/templates/no_such_job.html b/qc_app/templates/no_such_job.html deleted file mode 100644 index 42a2d48..0000000 --- a/qc_app/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/qc_app/templates/parse_failure.html b/qc_app/templates/parse_failure.html deleted file mode 100644 index 31f6be8..0000000 --- a/qc_app/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/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html deleted file mode 100644 index e2bf7f0..0000000 --- a/qc_app/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/qc_app/templates/rqtl2/create-geno-dataset-success.html b/qc_app/templates/rqtl2/create-geno-dataset-success.html deleted file mode 100644 index 1b50221..0000000 --- a/qc_app/templates/rqtl2/create-geno-dataset-success.html +++ /dev/null @@ -1,55 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Select Genotypes Dataset

    - -
    -

    You successfully created the genotype dataset with the following - information. -

    -
    ID
    -
    {{geno_dataset.id}}
    - -
    Name
    -
    {{geno_dataset.name}}
    - -
    Full Name
    -
    {{geno_dataset.fname}}
    - -
    Short Name
    -
    {{geno_dataset.sname}}
    - -
    Created On
    -
    {{geno_dataset.today}}
    - -
    Public?
    -
    {%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}
    -
    -

    -
    - -
    -
    - select from existing genotype datasets - - - - - - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/create-probe-dataset-success.html b/qc_app/templates/rqtl2/create-probe-dataset-success.html deleted file mode 100644 index 790d174..0000000 --- a/qc_app/templates/rqtl2/create-probe-dataset-success.html +++ /dev/null @@ -1,59 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Create ProbeSet Dataset

    - -
    -

    You successfully created the ProbeSet dataset with the following - information. -

    -
    Averaging Method
    -
    {{avgmethod.Name}}
    - -
    ID
    -
    {{dataset.datasetid}}
    - -
    Name
    -
    {{dataset.name2}}
    - -
    Full Name
    -
    {{dataset.fname}}
    - -
    Short Name
    -
    {{dataset.sname}}
    - -
    Created On
    -
    {{dataset.today}}
    - -
    DataScale
    -
    {{dataset.datascale}}
    -
    -

    -
    - -
    -
    - Create ProbeSet dataset - - - - - - - - - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/create-probe-study-success.html b/qc_app/templates/rqtl2/create-probe-study-success.html deleted file mode 100644 index d0ee508..0000000 --- a/qc_app/templates/rqtl2/create-probe-study-success.html +++ /dev/null @@ -1,49 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Create ProbeSet Study

    - -
    -

    You successfully created the ProbeSet study with the following - information. -

    -
    ID
    -
    {{study.id}}
    - -
    Name
    -
    {{study.name}}
    - -
    Full Name
    -
    {{study.fname}}
    - -
    Short Name
    -
    {{study.sname}}
    - -
    Created On
    -
    {{study.today}}
    -
    -

    - -
    - Create ProbeSet study - - - - - - - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/create-tissue-success.html b/qc_app/templates/rqtl2/create-tissue-success.html deleted file mode 100644 index 5f2c5a0..0000000 --- a/qc_app/templates/rqtl2/create-tissue-success.html +++ /dev/null @@ -1,106 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Select Tissue

    - -
    -

    You have successfully added a new tissue, organ or biological material with - the following details:

    -
    - -
    - {{flash_all_messages()}} - -
    - Create Tissue - - - - - - - -
    - - -
    - -
    - - -
    - - {%if tissue.BIRN_lex_ID%} -
    - - -
    - {%endif%} - - {%if tissue.BIRN_lex_Name%} -
    - - -
    - {%endif%} -
    - -
    - -
    - - - - - - - - -
    -
    -
    - -
    -

    - OR -

    -
    - -
    -
    - - - - - - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/index.html b/qc_app/templates/rqtl2/index.html deleted file mode 100644 index f3329c2..0000000 --- a/qc_app/templates/rqtl2/index.html +++ /dev/null @@ -1,36 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Data Upload{%endblock%} - -{%block contents%} -

    R/qtl2 data upload

    - -

    R/qtl2 Upload

    - -
    - upload R/qtl2 bundle - {{flash_messages("error-rqtl2")}} - -
    - - - - 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. - -
    - - -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/no-such-job.html b/qc_app/templates/rqtl2/no-such-job.html deleted file mode 100644 index b17004f..0000000 --- a/qc_app/templates/rqtl2/no-such-job.html +++ /dev/null @@ -1,13 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    R/qtl2 job status

    - -

    R/qtl2 Upload: No Such Job

    - -

    No job with ID {{jobid}} was found.

    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-job-error.html b/qc_app/templates/rqtl2/rqtl2-job-error.html deleted file mode 100644 index 9817518..0000000 --- a/qc_app/templates/rqtl2/rqtl2-job-error.html +++ /dev/null @@ -1,39 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    R/qtl2 job status

    - -

    R/qtl2 Upload: Job Status

    - -
    -

    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.

    -

    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: -

    -

    -
    - -

    stdout

    -{{cli_output(job, "stdout")}} - -

    stderr

    -{{cli_output(job, "stderr")}} - -

    Log

    -
    - {%for msg in messages%} - {{msg}}
    - {%endfor%} -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-job-results.html b/qc_app/templates/rqtl2/rqtl2-job-results.html deleted file mode 100644 index 4ecd415..0000000 --- a/qc_app/templates/rqtl2/rqtl2-job-results.html +++ /dev/null @@ -1,24 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    R/qtl2 job status

    - -

    R/qtl2 Upload: Job Status

    - -
    -

    The processing of the R/qtl2 bundle you uploaded has completed - successfully.

    -

    You should now be able to use GeneNetwork to run analyses on your data.

    -
    - -

    Log

    -
    - {%for msg in messages%} - {{msg}}
    - {%endfor%} -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-job-status.html b/qc_app/templates/rqtl2/rqtl2-job-status.html deleted file mode 100644 index e896f88..0000000 --- a/qc_app/templates/rqtl2/rqtl2-job-status.html +++ /dev/null @@ -1,20 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Job Status{%endblock%} - -{%block extrameta%} - -{%endblock%} - -{%block contents%} -

    R/qtl2 job status

    - -

    R/qtl2 Upload: Job Status

    - -

    Log

    -
    - 
    {{"\n".join(messages)}}
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html deleted file mode 100644 index 90e8887..0000000 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html +++ /dev/null @@ -1,120 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}R/qtl2 bundle: QC Job Error{%endblock%} - -{%macro errors_table(tableid, errors)%} - - - - - - - - - - - - {%for error in errors%} - - - - - - - {%else%} - - - - {%endfor%} - -
    {{caption}}
    LineColumnValueMessage
    {{error.line}}{{error.column}}{{error.value}}{{error.message}}
    No errors to display here.
    -{%endmacro%} - -{%block contents%} -

    R/qtl2 bundle: QC job Error

    - -
    -

    The R/qtl2 bundle has failed some Quality Control checks.

    -

    We list below some of the errors that need to be fixed before the data can - be uploaded onto GeneNetwork.

    -
    - -{%if errorsgeneric | length > 0%} -

    Generic Errors ({{errorsgeneric | length}})

    -
    - We found the following generic errors in your R/qtl2 bundle: -
    - -

    Missing Files

    -
    -

    These files are listed in the bundle's control file, but do not actually - exist in the bundle

    -
    - - - - - - - - - - {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%} - - - - - - {%endfor%} - -
    Control File KeyBundle File NameMessage
    {{error.controlfilekey}}{{error.filename}}{{error.message}}
    - -

    Other Generic Errors

    -{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}} -{%endif%} - -{%if errorsgeno | length > 0%} -

    Geno Errors ({{errorsgeno | length}})

    -
    - We found the following errors in the 'geno' file in your R/qtl2 bundle: -
    -{{errors_table("tbl-errors-geno", errorsgeno[0:50])}} -{%endif%} - -{%if errorspheno | length > 0%} -

    Pheno Errors ({{errorspheno | length}})

    -
    - We found the following errors in the 'pheno' file in your R/qtl2 bundle: -
    -{{errors_table("tbl-errors-pheno", errorspheno[0:50])}} -{%endif%} - -{%if errorsphenose | length > 0%} -

    Phenose Errors ({{errorsphenose | length}})

    -
    - We found the following errors in the 'phenose' file in your R/qtl2 bundle: -
    -{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}} -{%endif%} - -{%if errorsphenocovar | length > 0%} -

    Phenocovar Errors ({{errorsphenocovar | length}})

    -
    - We found the following errors in the 'phenocovar' file in your R/qtl2 bundle: -
    -{{errorsphenocovar}} -{%endif%} - -

    stdout

    -{{cli_output(job, "stdout")}} - -

    stderr

    -{{cli_output(job, "stderr")}} - -

    Log

    -
    - 
    {{"\n".join(messages)}}
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html deleted file mode 100644 index 59bc8cd..0000000 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html +++ /dev/null @@ -1,66 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}R/qtl2 bundle: QC job results{%endblock%} - -{%block contents%} -

    R/qtl2 bundle: QC job results

    - -
    -

    The R/qtl2 bundle you uploaded has passed all automated quality-control - checks successfully.

    -

    You may now continue to load the data into GeneNetwork for the bundle, with - the following details:

    -
    - -
    -
    -
    - Species - - - Name - {{species.Name | capitalize}} - - Scientific - {{species.FullName | capitalize}} -
    - -
    - population - - - Name - {{population.InbredSetName}} - - Full Name - {{population.FullName}} - - Genetic Type - {{population.GeneticType}} - - Description - {{population.Description or "-"}} -
    - -
    - R/qtl2 Bundle File - - - - Original Name - {{rqtl2bundleorig}} - - Internal Name - {{rqtl2bundle[0:25]}}… -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html b/qc_app/templates/rqtl2/rqtl2-qc-job-status.html deleted file mode 100644 index f4a6266..0000000 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html +++ /dev/null @@ -1,41 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Job Status{%endblock%} - -{%block extrameta%} - -{%endblock%} - -{%block contents%} -

    R/qtl2 bundle: QC job status

    - -{%if geno_percent%} -

    -

    Checking 'geno' file:

    - - {{geno_percent}}% - {{geno_percent}}%

    -{%endif%} - -{%if pheno_percent%} -

    -

    Checking 'pheno' file:

    - - {{pheno_percent}}% - {{pheno_percent}}%

    -{%endif%} - -{%if phenose_percent%} -

    -

    Checking 'phenose' file:

    - - {{phenose_percent}}% - {{phenose_percent}}%

    -{%endif%} - -

    Log

    -
    - 
    {{"\n".join(messages)}}
    -
    -{%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html deleted file mode 100644 index 2861a04..0000000 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html +++ /dev/null @@ -1,37 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%} - -{%block contents%} -

    R/qtl2 Bundle: Quality Control Successful

    - -
    -

    The R/qtl2 bundle you uploaded has passed all quality control - checks successfully, and is now ready for uploading into the database.

    -

    Click "Continue" below to proceed.

    -
    - - -
    -
    - {{flash_all_messages()}} - - - - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html deleted file mode 100644 index 873f9c3..0000000 --- a/qc_app/templates/rqtl2/select-geno-dataset.html +++ /dev/null @@ -1,144 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Select Genotypes Dataset

    - -
    -

    Your R/qtl2 files bundle contains a "geno" specification. You will - therefore need to select from one of the existing Genotype datasets or - create a new one.

    -

    This is the dataset where your data will be organised under.

    -
    - -
    -
    - select from existing genotype datasets - - - - - - {{flash_messages("error-rqtl2-select-geno-dataset")}} - -
    - Datasets - - - - Select from the existing genotype datasets for species - {{species.SpeciesName}} ({{species.FullName}}). - -
    - - -
    -
    - -
    -

    OR

    -
    - -
    -
    - create a new genotype dataset - - - - - - {{flash_messages("error-rqtl2-create-geno-dataset")}} - -
    - - - - Provide the new name for the genotype dataset, e.g. "BXDGeno" - -
    - -
    - - - - - Provide a longer name that better describes the genotype dataset, e.g. - "BXD Genotypes" - -
    - -
    - - - - - Provide a short name for the genotype dataset. This is optional. If not - provided, we'll default to the same value as the "Name" above. - -
    - -
    - - - - - Specify whether the dataset will be available publicly. Check to make the - dataset publicly available and uncheck to limit who can access the dataset. - -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/select-population.html b/qc_app/templates/rqtl2/select-population.html deleted file mode 100644 index 37731f0..0000000 --- a/qc_app/templates/rqtl2/select-population.html +++ /dev/null @@ -1,136 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Select Grouping/Population{%endblock%} - -{%block contents%} -

    Select grouping/population

    - -
    -

    The data is organised in a hierarchical form, beginning with - species at the very top. Under species the data is - organised by population, sometimes referred to as grouping. - (In some really old documents/systems, you might see this referred to as - InbredSet.)

    -

    In this section, you get to define what population your data is to be - organised by.

    -
    - -
    - select grouping/population - {{flash_messages("error-select-population")}} - - - -
    - - - If you are adding data to an already existing - population, simply pick the population from this drop-down selector. If - you cannot find your population from this list, try the form below to - create a new one.. -
    - - -
    - -

    OR

    - -
    - create new grouping/population - {{flash_messages("error-create-population")}} - - - -
    - mandatory - -
    - - - This is a short name that identifies the - population. Useful for menus, and quick scanning. -
    - -
    - - - This can be the same as the name above, or can - be longer. Useful for documentation, and human communication. -
    -
    - -
    - optional - -
    - - - This determines whether the - population/grouping will appear on the menus for users. -
    - -
    - - - I do not currently know what this is about. - This is a failure on my part to figure out what this is and provide a - useful description. Please feel free to remind me. -
    - -
    - - - - A long-form description of what the population consists of. Useful for - humans. -
    -
    - - -
    - -{%endblock%} - - -{%block javascript%} -{%endblock%} diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html deleted file mode 100644 index 26f52ed..0000000 --- a/qc_app/templates/rqtl2/select-probeset-dataset.html +++ /dev/null @@ -1,191 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Phenotype(ProbeSet) Dataset

    - -
    -

    The R/qtl2 bundle you uploaded contains (a) "pheno" - file(s). This data needs to be organised under a dataset.

    -

    This page gives you the ability to do that.

    -
    - -{%if datasets | length > 0%} -
    -
    - Select from existing ProbeSet datasets - {{flash_messages("error-rqtl2")}} - - - - - - - - -
    - - - - - Select from existing ProbeSet datasets. -
    - - -
    -
    - -
    -

    OR

    -
    -{%endif%} - -
    -

    Create an entirely new ProbeSet dataset for your data.

    -
    - -
    -
    - Create a new ProbeSet dataset - {{flash_messages("error-rqtl2-create-probeset-dataset")}} - - - - - - - - -
    - - - - - Select the averaging method used for your data. - -
    - -
    - - - - - Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This - is mandatory MUST be provided. - -
    - -
    - - - - - Provide a longer, more descriptive name for the dataset e.g. - "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and - MUST be provided. - -
    - -
    - - - - - Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". - This is optional. - -
    - -
    - - - - - Check to specify that the dataset will be publicly available. Uncheck to - limit access to the dataset. - -
    - -
    - - - - - Select from a list of scaling methods. - -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html deleted file mode 100644 index b9bf52e..0000000 --- a/qc_app/templates/rqtl2/select-probeset-study-id.html +++ /dev/null @@ -1,143 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages %} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Phenotype(ProbeSet) Study

    - -
    -

    The R/qtl2 bundle you uploaded contains (a) "pheno" - file(s). This data needs to be organised under a study.

    -

    In this page, you can either select from a existing dataset:

    - -
    - Select from existing ProbeSet studies - {{flash_messages("error-rqtl2-select-probeset-study")}} - - - - - - - -
    - - - - Select from existing ProbeSet studies. - -
    - - -
    -
    - -
    -

    OR

    -
    - -
    - -

    Create a new ProbeSet dataset below:

    - -
    - Create new ProbeSet study - - {{flash_messages("error-rqtl2-create-probeset-study")}} - - - - - - - -
    - - - - Select from a list of known genomics platforms. - -
    - -
    - - - - Provide a name for the study. -
    - -
    - - - - Provide a longer, more descriptive name for the study. This is optional - and you can leave it blank. - -
    - -
    - - - - Provide a shorter name for the study. This is optional and you can leave - it blank. - -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/select-tissue.html b/qc_app/templates/rqtl2/select-tissue.html deleted file mode 100644 index 34e1758..0000000 --- a/qc_app/templates/rqtl2/select-tissue.html +++ /dev/null @@ -1,115 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Tissue

    - -
    -

    The data you are uploading concerns a tissue, cell, organ, or other - biological material used in an experiment.

    -

    Select the appropriate biological material below

    -
    - -{%if tissues | length > 0%} -
    -
    - Select from existing ProbeSet datasets - {{flash_messages("error-select-tissue")}} - - - - - - -
    - - - - - Select from existing biological material. -
    - - -
    -
    - -
    -

    OR

    -
    -{%endif%} - -
    -

    If you cannot find the biological material in the drop-down above, add it - to the system below.

    - -
    - Add new tissue, organ or biological material - {{flash_messages("error-create-tissue")}} - - - - - - -
    - - - - - A name to identify the tissue, organ or biological material. - -
    - -
    - - - - - Provide a short name for the tissue, organ or biological material used in - the experiment. - -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html deleted file mode 100644 index 1be87fa..0000000 --- a/qc_app/templates/rqtl2/summary-info.html +++ /dev/null @@ -1,65 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Summary

    - -
    -

    This is the information you have provided to accompany the R/qtl2 bundle - you have uploaded. Please verify the information is correct before - proceeding.

    -
    - -
    -
    -
    Species
    -
    {{species.SpeciesName}} ({{species.FullName}})
    - -
    Population
    -
    {{population.InbredSetName}}
    - - {%if geno_dataset%} -
    Genotype Dataset
    -
    {{geno_dataset.Name}} ({{geno_dataset.FullName}})
    - {%endif%} - - {%if tissue%} -
    Tissue
    -
    {{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})
    - {%endif%} - - {%if probe_study%} -
    ProbeSet Study
    -
    {{probe_study.Name}} ({{probe_study.FullName}})
    - {%endif%} - - {%if probe_dataset%} -
    ProbeSet Dataset
    -
    {{probe_dataset.Name2}} ({{probe_dataset.FullName}})
    - {%endif%} -
    -
    - -
    -
    - Create ProbeSet dataset - - - - - - - - - -
    -
    -{%endblock%} diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html deleted file mode 100644 index 07c240f..0000000 --- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html +++ /dev/null @@ -1,276 +0,0 @@ -{%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()%} - -

    - 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. -

    -

    - The control file can be either a YAML or JSON file. ALL other data - files in the zip bundle should be CSV files. -

    -

    See the - - R/qtl2 file format specifications - - for more details. -

    -     -{%endmacro%} -{{upload_progress_indicator()}} - - - - -

    Upload R/qtl2 Bundle

    - - - -
    - - - - {{flash_all_messages()}} - -
    - file upload - - - {{rqtl2_file_help()}} -
    - - -
    - -{%endblock%} - -{%block javascript%} - - - -{%endblock%} diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html deleted file mode 100644 index 93b1dc9..0000000 --- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html +++ /dev/null @@ -1,33 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -

    Upload R/qtl2 Bundle

    - -
    -

    You have successfully uploaded the zipped bundle of R/qtl2 files.

    -

    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.

    -

    Click "Continue" below to proceed.

    - -
    - {{flash_all_messages()}} - - - - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html deleted file mode 100644 index da19ddc..0000000 --- a/qc_app/templates/samples/select-population.html +++ /dev/null @@ -1,99 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Select Grouping/Population{%endblock%} - -{%block contents%} -

    Select grouping/population

    - -
    -

    We organise the samples/cases/strains in a hierarchichal form, starting - with species at the very top. Under species, we have a - grouping in terms of the relevant population - (e.g. Inbred populations, cell tissue, etc.)

    -
    - -
    - select grouping/population - {{flash_messages("error-select-population")}} - - - -
    - - -
    - - -
    - -

    OR

    - -
    - create new grouping/population - {{flash_messages("error-create-population")}} - - -
    - mandatory - - - - - - -
    -
    - Optional - - - - - - - - - -
    - - -
    - -{%endblock%} - - -{%block javascript%} -{%endblock%} diff --git a/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html deleted file mode 100644 index edadc61..0000000 --- a/qc_app/templates/samples/select-species.html +++ /dev/null @@ -1,30 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Select Grouping/Population{%endblock%} - -{%block contents%} -

    upload samples/cases

    - -

    We need to know what species your data belongs to.

    - -{{flash_all_messages()}} - -
    - upload samples -
    - - -
    - - -
    -{%endblock%} diff --git a/qc_app/templates/samples/upload-failure.html b/qc_app/templates/samples/upload-failure.html deleted file mode 100644 index 09e2ecf..0000000 --- a/qc_app/templates/samples/upload-failure.html +++ /dev/null @@ -1,27 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}Samples Upload Failure{%endblock%} - -{%block contents%} -

    {{job.job_name}}

    - -

    There was a failure attempting to upload the samples.

    - -

    Here is some information to help with debugging the issue. Provide this - information to the developer/maintainer.

    - -

    Debugging Information

    - - -

    stdout

    -{{cli_output(job, "stdout")}} - -

    stderr

    -{{cli_output(job, "stderr")}} - -{%endblock%} diff --git a/qc_app/templates/samples/upload-progress.html b/qc_app/templates/samples/upload-progress.html deleted file mode 100644 index 7bb02be..0000000 --- a/qc_app/templates/samples/upload-progress.html +++ /dev/null @@ -1,22 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block extrameta%} - -{%endblock%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    {{job.job_name}}

    - -

    -status: -{{job["status"]}} ({{job.get("message", "-")}})
    -

    - -

    saving to database...

    - -{{cli_output(job, "stdout")}} - -{%endblock%} diff --git a/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html deleted file mode 100644 index e62de57..0000000 --- a/qc_app/templates/samples/upload-samples.html +++ /dev/null @@ -1,139 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload Samples{%endblock%} - -{%block css%}{%endblock%} - -{%block contents%} -

    upload samples

    - -{{flash_messages("alert-success")}} - -

    You can now upload a character-separated value (CSV) file that contains - details about your samples. The CSV file should have the following fields: -

    -
    Name
    -
    The primary name for the sample
    - -
    Name2
    -
    A secondary name for the sample. This can simply be the same as - Name above. This field MUST contain a - value.
    - -
    Symbol
    -
    A symbol for the sample. Can be an empty field.
    - -
    Alias
    -
    An alias for the sample. Can be an empty field.
    -
    -

    - -
    - upload samples - -
    - - - {{species.SpeciesName}} [{{species.MenuName}}] -
    - -
    - - - {{population.Name}} [{{population.FullName}}] -
    - -
    - - -
    - -
    - - - - - If you select 'Other' for the field separator value, - enter the character that separates the fields in your CSV file in the form - field below. - -
    - -
    - - - - Select this if the first line in your file contains headings for the - columns. - -
    - -
    - - - - 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. - -
    - - -
    - - - - - - - - - - - - - - - - - - -
    preview content
    NameName2SymbolAlias
    - Please make some selections to preview the data.
    - -{%endblock%} - - -{%block javascript%} - -{%endblock%} diff --git a/qc_app/templates/samples/upload-success.html b/qc_app/templates/samples/upload-success.html deleted file mode 100644 index cb745c3..0000000 --- a/qc_app/templates/samples/upload-success.html +++ /dev/null @@ -1,18 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}Job Status{%endblock%} - -{%block contents%} -

    {{job.job_name}}

    - -

    -status: -{{job["status"]}} ({{job.get("message", "-")}})
    -

    - -

    Successfully uploaded the samples.

    - -{{cli_output(job, "stdout")}} - -{%endblock%} diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html deleted file mode 100644 index 2f07de8..0000000 --- a/qc_app/templates/select_dataset.html +++ /dev/null @@ -1,161 +0,0 @@ -{%extends "base.html"%} -{%from "dbupdate_hidden_fields.html" import hidden_fields%} - -{%block title%}Select Dataset{%endblock%} - -{%block css%} - -{%endblock%} - -{%block contents%} -

    {{filename}}: select dataset

    - -
    -
    - choose existing dataset - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid, totallines=totallines)}} - -
    - - -
    - - -
    -
    - -
    -

    OR

    -
    - -
    -
    - create new dataset - {{hidden_fields( - filename, filetype, species=species, genechipid=genechipid, - studyid=studyid, totallines=totallines)}} - - {%with messages = get_flashed_messages(with_categories=true)%} - {%if messages:%} - - {%endif%} - {%endwith%} - -
    - - -
    - -
    - - -
    - -
    - - -
    - -
    - - -
    - -
    - - -
    - -
    - - -
    - -
    - - -
    - -
    - - -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html deleted file mode 100644 index d9bc68f..0000000 --- a/qc_app/templates/select_platform.html +++ /dev/null @@ -1,82 +0,0 @@ -{%extends "base.html"%} - -{%block title%}Select Dataset{%endblock%} - -{%block contents%} -

    {{filename}}: select platform

    - -
    -
    - - - - -
    - - -
    - - - - - - - - - - - - - {%for chip in genechips:%} - - - - - - {%else%} - - - - {%endfor%} - -
    select platform
    SelectGeneChip IDGeneChip Name
    - - {{chip["GeneChipId"]}}{{chip["GeneChipName"]}}
    No chips found for selected species
    - - -
    -
    -{%endblock%} - -{%block javascript%} - - - -{%endblock%} diff --git a/qc_app/templates/select_species.html b/qc_app/templates/select_species.html deleted file mode 100644 index 3b1a8a9..0000000 --- a/qc_app/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%} diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html deleted file mode 100644 index 648ad4c..0000000 --- a/qc_app/templates/select_study.html +++ /dev/null @@ -1,108 +0,0 @@ -{%extends "base.html"%} -{%from "dbupdate_hidden_fields.html" import hidden_fields%} - -{%block title%}Select Dataset{%endblock%} - -{%block css%} - -{%endblock%} - -{%block contents%} -

    {{filename}}: select study

    - -
    -
    - Select from existing study - {{hidden_fields(filename, filetype, species=species, genechipid=genechipid, - totallines=totallines)}} - -
    - - -
    - - -
    -
    - -
    -

    OR

    -
    - -
    -
    - {%with messages = get_flashed_messages(with_categories=true)%} - {%if messages:%} - - {%endif%} - {%endwith%} - Create new study - {{hidden_fields(filename, filetype, species=species, genechipid=genechipid, - totallines=totallines)}} - -
    - - -
    - -
    - - -
    - -
    - - -
    - - -
    -
    - -{%endblock%} diff --git a/qc_app/templates/stdout_output.html b/qc_app/templates/stdout_output.html deleted file mode 100644 index 85345a9..0000000 --- a/qc_app/templates/stdout_output.html +++ /dev/null @@ -1,8 +0,0 @@ -{%macro stdout_output(job)%} - -

    STDOUT Output

    -
    - 
    {{job.get("stdout", "")}}
    -
    - -{%endmacro%} diff --git a/qc_app/templates/unhandled_exception.html b/qc_app/templates/unhandled_exception.html deleted file mode 100644 index 6e6a051..0000000 --- a/qc_app/templates/unhandled_exception.html +++ /dev/null @@ -1,21 +0,0 @@ -{%extends "base.html"%} - -{%block title%}System Error{%endblock%} - -{%block css%} - -{%endblock%} - -{%block contents%} -

    - An error has occured, and your request has been aborted. Please notify the - administrator to try and get this sorted. -

    -

    - Provide the following information to help the administrator figure out and fix - the issue:
    -


    - {{trace}} -

    -

    -{%endblock%} diff --git a/qc_app/templates/upload_progress_indicator.html b/qc_app/templates/upload_progress_indicator.html deleted file mode 100644 index e274e83..0000000 --- a/qc_app/templates/upload_progress_indicator.html +++ /dev/null @@ -1,35 +0,0 @@ -{%macro upload_progress_indicator()%} - -{%endmacro%} diff --git a/qc_app/templates/worker_failure.html b/qc_app/templates/worker_failure.html deleted file mode 100644 index b65b140..0000000 --- a/qc_app/templates/worker_failure.html +++ /dev/null @@ -1,24 +0,0 @@ -{%extends "base.html"%} - -{%block title%}Worker Failure{%endblock%} - -{%block contents%} -

    Worker Failure

    - -

    - 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. -

    - -

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

    - -

    Debugging Information

    - - - -{%endblock%} -- cgit v1.2.3