diff options
| -rw-r--r-- | uploader/population/views.py | 3 | ||||
| -rw-r--r-- | uploader/samples/views.py | 5 | ||||
| -rw-r--r-- | uploader/templates/populations/create-population.html | 32 |
3 files changed, 38 insertions, 2 deletions
diff --git a/uploader/population/views.py b/uploader/population/views.py index e870c85..f9041be 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -151,6 +151,9 @@ def create_population(species_id: int): species_id=species["SpeciesId"], error_values=values)) + # TODO: Setup auth + # 1. Create new resource in gn-auth and add this population to it + # 2. Assign active user the "resource-creator" rights to the new resource new_population = save_population(conn, { "SpeciesId": species["SpeciesId"], "Name": population_name, diff --git a/uploader/samples/views.py b/uploader/samples/views.py index f444497..4332c21 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -200,6 +200,11 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma redisuri = app.config["REDIS_URL"] with Redis.from_url(redisuri, decode_responses=True) as rconn: + #TODO: Add a QC step here — what do we check? + # 1. Does any sample in the uploaded file exist within the database? + # If yes, what is/are its/their species and population? + # 2. If yes 1. above, provide error with notes on which species and + # populations already own the samples. the_job = jobs.launch_job( jobs.initialise_job( rconn, diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html index b57afba..b05ce37 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -107,7 +107,10 @@ value="{{error_values.population_code or ''}}" class="form-control" /> <small class="form-text text-muted"> - … document what this field is for … + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + What is this field is for? Confirm with Arthur and the rest. + </p> </small> </div> @@ -159,7 +162,10 @@ {%endfor%} </select> <small class="form-text text-muted"> - <p>… provide some documentation on what this field does …</p> + <p> + This is a rough grouping of the populations in GeneNetwork into lists + of common types of populations. + </p> </small> </div> @@ -207,6 +213,28 @@ {%endif%}>{{gtype}}</option> {%endfor%} </select> + <small class="form-text text-muted text-danger"> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + This might be a poorly named field. + </p> + <p> + It probably has more to do with the mating crosses/crossings used to + produce the individuals in the population. I am no biologist, however, + and I'm leaving this here to remind myself to confirm this. + </p> + <p> + I still don't know what riset is.<br /> + … probably something to do with Recombinant Inbred Strains + </p> + <p> + Possible resources for this: + <ul> + <li>https://www.informatics.jax.org/silver/chapters/3-2.shtml</li> + <li>https://www.informatics.jax.org/silver/chapters/9-2.shtml</li> + </ul> + </p> + </small> </div> <div class="form-group"> |