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execute script to change top unbarcodes to integer #276

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execute script to change top unbarcodes to integer #276

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88d87cc
Displayed recorded samples per researcher
luissian May 5, 2024
38b75d0
added recorded samples vs other researchers
luissian May 5, 2024
0d66585
Implemented sample states graphic
luissian May 5, 2024
9bbbc9c
litin
luissian May 5, 2024
c375988
fetching lab list to use in form
luissian May 5, 2024
f53a00f
fetching lab list to use in form
luissian May 5, 2024
b168f3a
Included samples from lab
luissian May 6, 2024
95e06ca
included state samples in lab
luissian May 6, 2024
ad594f6
included samples in lab vs others
luissian May 6, 2024
aff1f5f
Added the remining graphics for lob
luissian May 8, 2024
2ba6815
Solved issue #266 Too many emails are sent during crontab process
luissian May 8, 2024
26cc50d
corrected litin
luissian May 8, 2024
29d80f3
change Pre-Recorded state to snake style
luissian May 17, 2024
ad6fc5e
Fixed bug after changed the relation of library_pool-runprocess to ma…
luissian May 17, 2024
483ddc5
fixing litin
luissian May 17, 2024
c3de17f
Do not allow to import sample sheet if not library kits are defined
luissian May 17, 2024
e6191e1
Changes in run state values from issue #260
luissian May 18, 2024
1b14557
Fixed error messages display
luissian May 18, 2024
bda3039
added num samples per run and pending changes
luissian May 22, 2024
b77ae0d
fixed litin
luissian May 22, 2024
c721fa4
added num samples per lab statistics
luissian May 22, 2024
43c27d6
fixin lint
luissian May 25, 2024
159fc8c
Implement in api that samples cannot be repeated
luissian May 25, 2024
09ab409
Changed sample name to lowercase to compare with the exisiting samples
luissian May 25, 2024
b6aea2b
Added analyzed samples in run graphic
luissian Jun 9, 2024
8fa149c
Completed graphic statistics for drylab
luissian Jun 9, 2024
69ceb0e
litin
luissian Jun 9, 2024
0d76ee6
Changes because PR review
luissian Jun 10, 2024
c0a9e6f
Include script to convert top_unbarcode to integers
luissian Jul 19, 2024
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2 changes: 1 addition & 1 deletion core/utils/samples.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,7 @@ def validate_sample_data(
app_name: str,
repeat_allowed: bool = False,
allow_user_repeat: bool = False,
) -> tuple:
) -> tuple:
"""sample data validation

Args:
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4 changes: 4 additions & 0 deletions install.sh
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Expand Up @@ -561,6 +561,10 @@ if [ $upgrade == true ]; then
echo "Done migrate command."

else
# change required only during the upgrade to 3.1.0
echo "Convert the count column in wetlab RawTopUnknowBarcodes to integer"
python manage.py runscript convert_rawtop_counter_to_int
# checking for database changes
echo "checking for database changes"
if python manage.py makemigrations | grep -q "No changes"; then
# check for pending migrations
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2 changes: 1 addition & 1 deletion wetlab/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -767,7 +767,7 @@
]

# ERROR TEXT FOR SEACHING #############################################
ERROR_INVALID_FORMAT_FOR_DATES = ["Invalid date format. Use the format (DD-MM-YYYY)"]
ERROR_INVALID_FORMAT_FOR_DATES = [["Invalid date format. Use the format (DD-MM-YYYY)"]]


ERROR_MANY_USER_MATCHES_FOR_INPUT_CONDITIONS = [
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10 changes: 10 additions & 0 deletions wetlab/templates/wetlab/create_next_seq_run.html
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Expand Up @@ -86,13 +86,19 @@ <h3 class="text-center">Run creation progress</h3>
</div>
<label class="form-label" for="runindexlibraryname">Index Library Name :</label>
<div class="col">
<<<<<<< HEAD
<select class="form-select mb-3" name="libraryKit">
{% for value in get_user_names.used_libraryKit %}<option value="{{ value }}">{{ value }}</option>{% endfor %}
</select>
=======
<input class="form-control"
required="required"
type="text"
name="runindexlibraryname"
size="60"
maxlength="50"
value="{{ get_user_names.index_library_name }}" />
>>>>>>> 85461c1d (Fixed error messages display)
</div>
{% for key, values in get_user_names.projects_user %}
<p class="mt-3">Project name assigned to run :</p>
Expand Down Expand Up @@ -233,7 +239,11 @@ <h5>Run configuration have been sucessfully stored</h5>
{% else %}
<!-- Progress Step bar for the Form -->
<div class="row my-2">
<<<<<<< HEAD
<div class="col-sm-8 offset-2">
=======
<div class="col-sm-10 offset-2">
>>>>>>> 85461c1d (Fixed error messages display)
<ol class="track-progress" data-steps="3">
<li class="active">
<span>Upload Sample Sheet</span><i></i>
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833 changes: 715 additions & 118 deletions wetlab/templates/wetlab/stats_per_researcher.html
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173 changes: 112 additions & 61 deletions wetlab/templates/wetlab/stats_per_time.html
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Original file line number Diff line number Diff line change
Expand Up @@ -37,67 +37,118 @@ <h3 class="text-center">
role="tab"
aria-controls="overview"
aria-selected="true">Overview</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="quality-tab"
data-bs-toggle="tab"
data-bs-target="#quality"
type="button"
role="tab"
aria-controls="quality"
aria-selected="false">Sequence quality</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="runs-tab"
data-bs-toggle="tab"
data-bs-target="#runs"
type="button"
role="tab"
aria-controls="runs"
aria-selected="false">Runs</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="barcode-tab"
data-bs-toggle="tab"
data-bs-target="#barcode"
type="button"
role="tab"
aria-controls="barcode"
aria-selected="false">Unknown barcodes</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="samples-tab"
data-bs-toggle="tab"
data-bs-target="#samples"
type="button"
role="tab"
aria-controls="samples"
aria-selected="false">Sequenced samples</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="def-samples-tab"
data-bs-toggle="tab"
data-bs-target="#def-samples"
type="button"
role="tab"
aria-controls="def-samples"
aria-selected="false">Defined samples</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="other-graphic-tab"
data-bs-toggle="tab"
data-bs-target="#other-graphic"
type="button"
role="tab"
aria-controls="other-graphic"
aria-selected="false">Comparison graphics</button>
</li>
id="graphic-tab"
data-bs-toggle="tab"
data-bs-target="#overview"
type="button"
role="tab"
aria-controls="overview"
aria-selected="true">Overview
</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="quality-tab"
data-bs-toggle="tab"
data-bs-target="#quality"
type="button"
role="tab"
aria-controls="quality"
aria-selected="false">Sequence quality</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="runs-tab"
data-bs-toggle="tab"
data-bs-target="#runs"
type="button"
role="tab"
aria-controls="runs"
aria-selected="false">Runs</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="samples-tab"
data-bs-toggle="tab"
data-bs-target="#barcode"
type="button"
role="tab"
aria-controls="barcode"
aria-selected="false">Unknown barcodes</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="barcode-tab"
data-bs-toggle="tab"
data-bs-target="#barcode"
type="button"
role="tab"
aria-controls="barcode"
aria-selected="false">Unknown barcodes</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="samples-tab"
data-bs-toggle="tab"
data-bs-target="#samples"
type="button"
role="tab"
aria-controls="samples"
aria-selected="false">Sequenced samples</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="def-samples-tab"
data-bs-toggle="tab"
data-bs-target="#def-samples"
type="button"
role="tab"
aria-controls="def-samples"
aria-selected="false">Defined samples</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="other-graphic-tab"
data-bs-toggle="tab"
data-bs-target="#other-graphic"
type="button"
role="tab"
aria-controls="other-graphic"
aria-selected="false">Comparison graphics</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="samples-tab"
data-bs-toggle="tab"
data-bs-target="#samples"
type="button"
role="tab"
aria-controls="samples"
aria-selected="false">Sequenced samples</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="def-samples-tab"
data-bs-toggle="tab"
data-bs-target="#def-samples"
type="button"
role="tab"
aria-controls="def-samples"
aria-selected="false">Defined samples</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link "
id="other-graphic-tab"
data-bs-toggle="tab"
data-bs-target="#other-graphic"
type="button"
role="tab"
aria-controls="other-graphic"
aria-selected="false">Comparison graphics</button>
</li>
</ul>
<div class="tab-content bg-white border-tab p-2" id="nav-tabContent">
<div class="tab-pane fade show active" id="overview" =======
</ul>
<div class="tab-content bg-white border-tab p-2" id="nav-tabContent">
<div class="tab-pane fade show active"
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2 changes: 2 additions & 0 deletions wetlab/utils/samplesheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -361,6 +361,7 @@ def get_sample_with_user_owner(sample_sheet_path):
return sample_user


def get_projects_in_run(in_file: str) -> dict:
def get_projects_in_run(in_file: str) -> dict:
"""Funtion to check if the sample sheet has a valid heading. On valid file
get project names and the user names from description column
Expand All @@ -371,6 +372,7 @@ def get_projects_in_run(in_file: str) -> dict:
Returns:
dict: dictionary with the projects or error message
"""
"""
header_found = False
projects = {}
with open(in_file, "r") as fh:
Expand Down
1 change: 1 addition & 0 deletions wetlab/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1602,6 +1602,7 @@ def change_run_name(request, run_id):

@login_required
def stats_per_researcher(request):
lab_list = list(core.models.LabRequest.objects.all().values_list("pk", "lab_name"))
lab_list = list(core.models.LabRequest.objects.all().values_list("pk", "lab_name"))
if request.method == "POST":
r_name = request.POST["researchername"]
Expand Down
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