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The histogram is at /reports under the Growth tab.

We need to adjust the calculation we are using for the histogram on the backend. There are some calculations in app/lib/aggregates.rb, but we need to make sure they match the below requirements:

For histograms, bins to be by 1 cm increments, so 0-0.99 cm, 1-1.99 cm, etc. Our largest animal is just over 18 cm and the max listed size for a white abalone is 10 inches (25.4 cm), so it's probably safe to say we wouldn't ever have one over 30 cm. For a specific bar in the histogram, here is a scenario: Say I want to know X, the number of animals in the 4-4.99 cm bin, for the SF15-77 cohort animals:

N = the number of animals that were 4-4.99 cm in length in the most recent uploaded spreadsheet (Untagged AND Tagged animals) with length data for that cohort
S = the total number of animals measured in the same spreadsheet, i.e., the most recent uploaded spreadsheet with length data for that cohort (Untagged AND Tagged animals)
T = the total number of estimated animals in the cohort = the total number counted on the most recent count closest to the length measurement date minus the mortalities since then

X = (N/S)*T ... or the proportion of animals that were measured that were in that size bin, scaled up to the total predicted number of animals in that cohort.

The histogram calculations should have the following parameters (you should be able to pass in one or both):

1. cohort, or multiple cohorts
2. Optional date range

Use the module ImportJob for most of the logic.

Acceptance Criteria:
As a user, when I upload a CSV and it fails to process, I go the the page /file_uploads and:

1. See the failed file with name, date, category, 'failed' status, stats and initial errors
2. Click on the failed file
3. See detailed errors: which rows failed and why
4. Fix the errors on the original CSV on my machine
5. Click a button to re-upload my edited CSV.

BLOCKED by Issue #58 : We need the correct data on the backend first.

We need to make sure the Length Histogram is rendering correctly at /reports under the Growth tab. The current report has incorrect data AND incorrect formatting.

Acceptance Criteria:

• Y-axis: Count
• X-axis: Length in centimeters.
• Bins should be in 1 cm increments, so 0-0.99 cm, 1-1.99 cm, etc. from 0 to 30cm.
• Title: Size Distribution
• Tooltip: When hovering over a bar, user should see the count for that bin increment.

We use Highcharts, a JavaScript library for rendering all graphs and charts.

This issue builds on the devise work done in #76

We need a way for new users to be created through the app. This should be as lightweight and minimal as possible. There is no guarantee we can send email reliably, otherwise devise-invitable would be a good choice.

• Add administrate to Gemfile, bundle
• Create a User-admin dashboard: rails generate administrate:dashboard
  • You might need to create a user model
  • users table was already created in PR 76
  • If you need to create the user model, it should include name and email. Devise will probably want password and maybe some other stuff.
  • Make sure you can still login with the test user (from db/seed)

Confirm that you can do the following:

• Can login and logout with the test user from db/seed

As an authenticated user:

• Can create a new user and supply a name and email
• Can delete a user

Don't worry too much about roles - do whatever is simplest and least code. If that means everyone is an admin, start there.

Please pop into the #abalone channel in rubyforgood.slack.com if you have any questions or want to grab this issue.

Create a job to import the Spawning Success data.

Can we render the /file_uploads/#id page nicer? Currently headers and columns are cut off.

Tests need to be written for ImportJob, which is a module used by all the CSV import jobs.

Unit Tests
The following methods should be unit tested:

• #initialize_processed_file
• #validate_headers
• #import_records

Acceptance Criteria:

• As a user, I want to be able to upload all of the file types found in sample_date_files/wild_collection on the page /file_uploads/new.
• Tests should be written for each job similar to spec/jobs/tagged_animal_assessment_job_spec.rb
• Model Validations
• Unit tests for model validations

Notes:
Much of the logic for the file uploading/parsing is already written in the module concern ImportJob.

The heaviest lifting will be adding appropriate validations to the WildCollection model. Please refer to the data dictionary and the notes below for coding these.

**For columns that have the Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.)

WildCollection.rb

• Required: columns A-E, N
• See data dictionary for specific formats for tag, gonad score, predicted sex, initial holding facility, and final holding facility
• collection date, date of arrival, and OTC treatment completion date should be valid date with month, day, and year
• collection depth, length, weight should be float/integer
• Note from lab:
  I redacted some of the specific location info here, as the federal government is worried about disclosing where these endangered animals still exist in the wild, but I might not want that info in this database anyway, depending on how accessible it ends up being.

Acceptance Criteria:

• As a user, I want to be able to upload a CSV of category found in sample_date_files/tagged_animal_assessment on the page /file_uploads/new with correct data formats. I should see errors if there are incorrect data formats.
• Model Validations
• Unit tests for model validations

Please refer to the data dictionary and the notes below for coding the model validations. For an example, please look at: Example of WildCollection model validations and spec

TaggedAnimalAssessment.rb

• Required: measurement_date, shl_case_number, spawning_date, tag, length
• See data dictionary for specific formats for shl_case_number, tag, predicted_sex and gonad_score
• length should be float not exceed 100
• measurement_date and spawning_date should be valid date with month, day, and year
• Columns E-J treated as a note/strings

**If there is a column for Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.)

This resulted from a conversation in this PR: #88

Currently, when a CSV is processed with some invalid rows, we reject the invalid rows and save the valid rows. However, we should not save any rows to the db because this risks the user of duplicating data. Let's reject the entire CSV and tell the user to fix the invalid rows and re-upload the file.

• total animals
• animals per facility
• animals per spawn date

Analytics:

• spawning history of the broodstock (i.e., when we attempted to spawn them, were they successful in releasing gametes)
• total egg, larval, or juvenile production by year (esp. how many year-old animals are produced annually)
• mortality within a cohort/population over time
• size distribution of animals within a population or within the entire captive breeding program
• average growth rates of tagged individuals within populations or size classes over time

We will need to work with Kristin's team to ensure that upload errors are not happening too frequently.

Render data

Related to counts, one graph I’d love to be able to produce easily is one that shows the total number of animals that make it to ~1 year old each year. We have a “first count” when the animals are between 10-12 months old.

BLOCKED: UntaggedAnimalAssessmentJob must be created first.

Tests need to be written for UntaggedAnimalAssessmentJob.

Please use a fixture file for testing in this directory: db/sample_data_files/untagged_animal_assessment/

Feature/Integration Tests
The following contexts and expected outcomes should be tested:

1. Context: The user uploads a CSV that has already been processed.
   Outcome:

• A new ProcessedFile record should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Failed"
  • File has Errors: "Already processed a file with the same name. Data not imported!"
  • File has Statistics: "{}"

2. Context: The user uploads a CSV with invalid headers.
   Outcome:

• A new ProcessedFile record should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Failed"
  • File has Errors: "Does not have valid headers. Data not imported!"
  • File has Statistics: "{}"

3. Context: The user successfully uploads a CSV with no errors:
   Outcome:

• A new ProcessedFile record should be created
• 201 new UntaggedAnimalAssessment records should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Processed"
  • File has no Errors
  • File has Statistics: "{row_count: 201, rows_imported: 201, rows_not_imported: 0, shl_case_numbers: {"SF16-9A": 100, "SF16-9B": 20, "SF16-9C": 10, "SF16-9D": 71}}"

4. Context: The user successfully uploads a CSV with errors for 2 rows:
   Outcome:

• A new ProcessedFile record should be created
• 199 new UntaggedAnimalAssessment records should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Processed"
  • File has Errors: "Does not have valid headers. Data not imported!"
  • File has Statistics: "{row_count: 201, rows_imported: 199, rows_not_imported: 2, shl_case_numbers: {"SF16-9A": 100, "SF16-9B": 20, "SF16-9C": 10, "SF16-9D": 69}}"

Acceptance Criteria:

• As a user, I want to be able to upload a CSV of category found in sample_date_files/mortality_tracking on the page /file_uploads/new.
• Test should be written for this job similar to spec/jobs/tagged_animal_assessment_job_spec.rb
• Model Validations
• Unit tests for model validations

Notes:
Much of the logic for the file uploading/parsing is already written in the module concern ImportJob.

The heaviest lifting will be adding appropriate validations for the MortalityTracking model. Please refer to the data dictionary and the notes below for coding these. For an example, please look at: Example of WildCollection model validations and spec

**If there is a column for Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.)

MortalityTracking.rb

• Required: mortality_date, cohort, shl_case_number, spawning_date, # of morts (some might be unknown see note from lab)
• See data dictionary for specific formats for cohort, shl_case_number, tag
• motality_date and spawning_date should be valid date with month, day, and year
• Note from lab:
  These are the data that are probably going to need the most attention and QA/QC on
  our end. One challenge here is that mortalities are currently being tracked on this
  datasheet via a single entry for each population/location collected from at a single time
  point. When there are multiple tagged animals collected at a single timepoint, all the
  tagged animals are all lumped together in a single entry on this data sheet, and their tags are listed in the Notes. One other challenge is that sometimes we don’t know exactly which population a dead animal was from (e.g., it was found dead on the floor or in a sump), but we have some guesses
  based on the animal size and/or where it was located. Not sure the best way to code for
  that.
  --> This brings up one question: for those animals that are lumped together in a single entry (#_of_morts > 1), can we create multiple entries in the db for each individual animal, and can we extract each animal's tag from the Note column??

Users should be able to select multiple CSV files of the same type to be uploaded/parsed on this page: http://abalone.blrice.net/file_uploads/new.

Acceptance Criteria:
As a user, I can upload a maximum of 10 CSV files in bulk of the same type (e.g. Untagged Animal Assessment) from my computer.

Our deployed site is running on: http://abalone.blrice.net/

We need to get DelayedJob working in production. Maybe check out https://github.com/collectiveidea/delayed_job/wiki/Delayed-Job-tasks-for-Capistrano-3

Most of the code for this CSV import is already written in ImportJob. Import this module into an UntaggedAnimalAssessmentJob and write any custom methods; it should look similar to the TaggedAnimalAssessmentJob.

How many animals do I have from each spawning date right now?

• Look into postgres version... do we need to upgrade?
• Decide and obtain new domain name
• Set up continuous integration to run tests automatically
• Set up continuous deployment (3 applications are: database, background jobs and main application)

Acceptance Criteria:

• As a user, I want to be able to upload a CSV of category found in sample_date_files/tagged_animal_assessment on the page /file_uploads/new.
• Tests should be written for this job similar to spec/jobs/tagged_animal_assessment_job_spec.rb
• Model Validations
• Unit tests for model validations

Notes:
Much of the logic for the file uploading/parsing is already written in the module concern ImportJob.

The heaviest lifting will be adding appropriate validations for the UntaggedAnimalAssessment model. Please refer to the data dictionary and the notes below for coding these. For an example, please look at: Example of WildCollection model validations and spec

**If there is a column for Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.)

UntaggedAnimalAssessment.rb

• *cohort column should be changed to shl_case_number on sample data CSVs (this is an error; cohort is something different)
• Required: measurement_date, shl_case_number, spawning_date, length
• See data dictionary for specific formats for shl_case_number, predicted_sex and gonad_score
• length should not exceed 100
• length/mass should be float
• measurement_date and spawning_date should be valid date with month, day, and year
• Columns E-G treated as a note/strings

Acceptance Criteria:

• As a user, I want to be able to upload a CSV of category found in sample_date_files/population_estimate on the page /file_uploads/new.
• Test should be written for this job similar to spec/jobs/tagged_animal_assessment_job_spec.rb
• Model Validations
• Unit tests for model validations

Notes:
Much of the logic for the file uploading/parsing is already written in the module concern ImportJob.

The heaviest lifting will be adding appropriate validations for the PopulationEstimate model. Please refer to the data dictionary and the notes below for coding these. For an example, please look at: Example of WildCollection model validations and spec

**If there is a column for Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.)

PopulationEstimate.rb

• Required: sample_date, shl_case_number, spawning_date, lifestage, abundance and facility
• shl_case_number, lifestage, and facility should have specific format/options (see example CSV)
• sample_date and spawning_date should be valid date with month, day, and year
• abundance should be Integer

We need basic authentication for at least one user. Login page.

ActiveStorage will not work on Heroku for temp file storage for reasons listed here:
https://devcenter.heroku.com/articles/active-storage-on-heroku. Currently file uploading breaks on production for this reason :(

Let's just use a good ole' postgresql table instead called TemporaryFile to temporarily store the CSV. Workflow should be:

1. When a user uploads a file, add the raw data to this table
2. Kick off the job that processes the file and saves the cleaned data to the db
3. Delete the raw data when the job finishes

Add Tagged Animal Assessment file upload category.
Add data import job for Tagged Animal Assessment spreadsheets.

What sizes are animals from each spawning date? I'd like to be able to select a measurement event (a certain population on a certain date) or a group of measuring events (different populations near the same dates or same population over time) to generate a histogram of lengths ideally binned in 1-cm increments.

There should be an area where the user can select parameters in the upper right hand side of the histogram chart at /reports under the Growth tab. The user should have the ability to select a measuring event (i.e. a certain population on a certain date) or a group of measuring events (different populations near the same date).

Acceptance Criteria:

• Backend - returns a list of cohorts
• Frontend - Multiple select list of cohorts
• Frontend - Date picker

We use Highcharts, a JavaScript library for rendering all graphs and charts.

We want to have a basic linter set up and enforced for new PRs.

Acceptance Criteria:

• As a user, I want to be able to upload a CSV of category found in sample_date_files/spawning_success on the page /file_uploads/new.
• Tests should be written for this job similar to spec/jobs/tagged_animal_assessment_job_spec.rb
• Model Validations
• Unit tests for model validations

Notes:
Much of the logic for the file uploading/parsing is already written in the module concern ImportJob.

The heaviest lifting will be adding appropriate validations for the SpawningSuccess model. Please refer to the data dictionary and the notes below for coding these. For an example, please look at: Example of WildCollection model validations and spec

**If there is a column for Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.)

SpawningSuccess.rb

• Required: tag, shl_case_number, spawning_date, date_attempted, spawning_success
• See data dictionary for specific formats for tag, shl_case_number, spawning_success
• spawning_date and date_attempted should be valid date with month, day, and year
• #_of_eggs spawned should be Integer
• #_of_eggs spawned should be populated in the sample data CSV (lab forgot to do this)
• Note from lab:
  My primary concern here is how to differentiate between the date that an animal was
  spawned (i.e., it’s birthday) and the date the animal spawned (i.e., it released gametes)
  without causing confusion.
  --> We should probably change the header name for spawning_date for this CSV...

Tests need to be written for TaggedAnimalAssessmentJob.

Please use this fixture file for testing: db/sample_data_files/tagged_animal_assessment/Tagged_assessment_12172018 (original).csv

Feature/Integration Tests
The following contexts and expected outcomes should be tested:

1. Context: The user uploads a CSV that has already been processed.
   Outcome:

• A new ProcessedFile record should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Failed"
  • File has Errors: "Already processed a file with the same name. Data not imported!"
  • File has Statistics: "{}"

2. Context: The user uploads a CSV with invalid headers.
   Outcome:

• A new ProcessedFile record should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Failed"
  • File has Errors: "Does not have valid headers. Data not imported!"
  • File has Statistics: "{}"

3. Context: The user successfully uploads a CSV with no errors:
   Outcome:

• A new ProcessedFile record should be created
• 201 new TaggedAnimalAssessment records should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Processed"
  • File has no Errors
  • File has Statistics: "{row_count: 201, rows_imported: 201, rows_not_imported: 0, shl_case_numbers: {"SF16-9A": 100, "SF16-9B": 21, "SF16-9C": 11, "SF16-9D": 69}}"

4. Context: The user successfully uploads a CSV with errors for 2 rows:
   Outcome:

• A new ProcessedFile record should be created
• 199 new TaggedAnimalAssessment records should be created
• On the /file_uploads page, the user should see:
  • File has Status: "Processed"
  • File has Errors: "Does not have valid headers. Data not imported!"
  • File has Statistics: "{row_count: 201, rows_imported: 199, rows_not_imported: 2, shl_case_numbers: {"SF16-9A": 100, "SF16-9B": 21, "SF16-9C": 11, "SF16-9D": 69}}"

Use Capybara or MiniTest? See https://chriskottom.com/blog/2015/11/testing-rails-background-workers/

Set up a deploy pipeline via DigitalOcean.

Acceptance Criteria:

• As a user, I want to be able to upload all of the file types found in sample_date_files/pedigree/ on the page /file_uploads/new.
• Tests should be written for each job similar to spec/jobs/tagged_animal_assessment_job_spec.rb
• Model Validations
• Unit tests for model validations

Notes:
Much of the logic for the file uploading/parsing is already written in the module concern ImportJob.

The heaviest lifting will be adding appropriate validations to both models. Please refer to the data dictionary and the notes below for coding these.

**If there are columns that have Facility, let's make these foreign keys to the Facility.rb model we already have. There should only be certain facilities (see the seeds.rb file and users have the ability to add new ones.) For an example, please look at: Example of WildCollection model validations and spec

Pedigree.rb

• Required: cohort, shl_case_number, spawning_date
• Mother, Father, and Separate crosses within cohort are a list of tags and EACH of these should follow the correct tag format. We could store these in an array and array of arrays for the crosses?

PedigreeParents.rb
**Need model and migration for this

• See data dictionary for specific formats for Sex (M/F), Origin, Holding Facility
• Fertilization date, Collection date should be valid date with month, day, and year

We need to make sure the Length Histogram is rendering correctly: http://abalone.blrice.net/reports.

This should create bins of 1 cm increments, so 0-0.99 cm, 1-1.99 cm, etc up to 30cm.

We also need to be able to input parameters of 1) Cohort or multiple cohorts and 2) Date range (optional - default is the most recent).
--> Will need to model a select dropdown of cohorts