From: Diane Trout Date: Tue, 12 May 2015 18:38:12 +0000 (-0700) Subject: move experiment templates into the experiments app X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=90bc1912d92ccb7f3295be258d0eaf61a3a2e088 move experiment templates into the experiments app --- diff --git a/experiments/templates/experiments/detail.html b/experiments/templates/experiments/detail.html new file mode 100644 index 0000000..65d3c00 --- /dev/null +++ b/experiments/templates/experiments/detail.html @@ -0,0 +1,7 @@ +{% if run_f %} + +{% else %} +

Run folder not found.

+{% endif %} diff --git a/experiments/templates/experiments/email_preview.html b/experiments/templates/experiments/email_preview.html new file mode 100644 index 0000000..9c35c6d --- /dev/null +++ b/experiments/templates/experiments/email_preview.html @@ -0,0 +1,38 @@ +{% extends "base.html" %} +{% load i18n %} + +{% block breadcrumbs %} +
+ {% trans 'Home' %} › + Experiments › + flowcell › + {{ flowcell.flowcell_id }} +
+{% endblock %} + +{% block content %} +{% if warnings %} +
+

+{% for user_admin_url, username in warnings %} +Warning: User {{ username }} has no +email address
+{% endfor %} +{% endif %} +

+{% for to, subject, body, sending in emails %} +
+{% if sending %}Message: {{ sending }}
{% endif %} +From: {{ from }}
+To: {{ to }}
+Subject: {{ subject }}
+
+{{ body }}
+
+{% endfor %}
+
+ +
+ + +{% endblock %} \ No newline at end of file diff --git a/experiments/templates/experiments/flowcellSheet.html b/experiments/templates/experiments/flowcellSheet.html new file mode 100644 index 0000000..103b045 --- /dev/null +++ b/experiments/templates/experiments/flowcellSheet.html @@ -0,0 +1,87 @@ +{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG + + +{% if fc %} + + + + + + + + + + + + + + + + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + + + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + + +{% for lane in fc.lane_set.all %} + +{% endfor %} + + +
GA SEQUENCING (SOLEXA) LOG       
         
Date Run Started{{ fc.run_date }}      
         
Cluster station used{{ fc.cluster_station.name }}      
GA used{{ fc.sequencer.name }}      
         
Flowcell number{{ fc.flowcell_id }}      
Number of Tiles per Lane100       
Number of Cycles{{ fc.read_length }}       
         
         
SAMPLE INFORMATION        
 FC#     FC bar code
Lane{{ lane.lane_number }}
Solexa Library Number{{ lane.library.id }}
Sample Name{{ lane.library.library_name }}
Organism{{ lane.library.library_species.scientific_name }}
Submitter{{ lane.library.made_for }}
First time run?
Gel Cut Size (bp){{ lane.library.gel_cut_size }}
Template Concentration (ng/ul){{ lane.library.undiluted_concentration }}
Run Concentration (pM){{ lane.pM }}
+ +{% else %} +

Flowcell object missing. Can't create sheet.

+{% endif %} + + + + + + {% block additional_javascript %} + {% endblock %} +{% endblock %} + +{% block content %} +
+ {% include "experiments/flowcell_header.html" %} +
+

Lanes

+ + + + + + + + + + + + {% for lane in lanes %} + + + + + + + + {% endfor %} + +
LaneLibrary IDLibrary NameSpeciesComment
+ + {{lane.lane_number}} + + + + {{lane.library.id}} + {% if user.is_staff %} + + + {% endif %} + + + {{lane.library.library_name}} + + + + {{ lane.library.library_species.scientific_name }} + + {{lane.comment}} +
+
+ {% for run in flowcell.datarun_set.all %} +

Run {{ run.runfolder_name }}

+ {% if run.lane_files %} + + + + + + + + + + + + + {% for lane_id, lane_file_set in run.lane_files.items %} + {% if lane_file_set.ivc_all %} + + + + + + + + + {% endif %} + {% endfor %} + +
LaneIVC AllIVC CallIVC Percent BaseIVC Percent Base AllIVC Percent Base Called
{{ lane_id }} + + Lane {{lane_id }} IVC All + + + Lane {{lane_id }} IVC Call + + + + Lane {{lane_id }} IVC % Base + + + + Lane {{lane_id }} IVC % Base All + + + + Lane {{lane_id }} IVC % Base Called + +
+ {% endif %} + {% endfor %} +
+
+
+ +{% endblock %} diff --git a/experiments/templates/experiments/flowcell_header.html b/experiments/templates/experiments/flowcell_header.html new file mode 100644 index 0000000..f0cb470 --- /dev/null +++ b/experiments/templates/experiments/flowcell_header.html @@ -0,0 +1,43 @@ +{% load staticfiles %} +
+

About this Flowcell

+ Flowcell: + {{flowcell.flowcell_id}}{% if user.is_staff %}Edit{% endif%} +
+
+
+ Instrument: + {{ flowcell.sequencer.name }} + {% if flowcell.sequencer.instrument_name %} + ({{ flowcell.sequencer.instrument_name}}) + {% endif %} +
+ Instrument Model: + {{flowcell.sequencer.model}} +
+
+
+ {% for datarun in flowcell.datarun_set.all %} + Image Analysis: + {{datarun.image_software}} + {{datarun.image_version}}
+ Base Caller: + {{datarun.basecall_software}} + {{datarun.basecall_version}}
+ Alignment: + {{datarun.alignment_software}} + {{datarun.alignment_version}}
+ {% endfor %} + Run Date: + {{ flowcell.run_date }}
+ Type: + {{flowcell.flowcell_type}}
+ Read Length: + {{flowcell.read_length}}
+ Control Lane: + {{flowcell.control_lane}}
+ + Notes: + 
{{flowcell.notes}}
+
diff --git a/experiments/templates/experiments/flowcell_lane_detail.html b/experiments/templates/experiments/flowcell_lane_detail.html new file mode 100644 index 0000000..ebe2c59 --- /dev/null +++ b/experiments/templates/experiments/flowcell_lane_detail.html @@ -0,0 +1,98 @@ +{% extends "base_site.html" %} +{% load humanize i18n %} +{% load staticfiles %} +{% block extrahead %} + + + + + {% block additional_javascript %} + {% endblock %} +{% endblock %} + +{% block content %} +
+
+ {% include "experiments/flowcell_header.html" %} +
+
+

About this lane

+ Lane: + {{lane.lane_number}}
+ pM: + {{ lane.pM }}
+ {% if lane.cluster_estimate %} + Cluster Estimate: + {{ lane.cluster_estimate|intcomma }}
{% endif %} + {% if lane.status %} + Lane Status: + {{ lane.status }}
{% endif %} + {% if lane.comment %} + Comments: + {{ lane.comment }}
{% endif %} +
+
+ {% include "sample_header.html" %} +
+
+ {% for run in flowcell.datarun_set.all %} +

Run {{ run.runfolder_name }}

+ + + + + + + + + + + + + {% for run, lane_number, lane_file_set in filtered_dataruns %} + {% if lane_file_set.ivc_all %} + + + + + + + + + {% else %} + + {% endif %} + {% endfor %} + +
LaneIVC AllIVC CallIVC Percent BaseIVC Percent Base AllIVC Percent Base Called
{{lane_number}} + + Lane {{lane_id }} IVC All + + + Lane {{lane_id }} IVC Call + + + + Lane {{lane_id }} IVC % Base + + + + Lane {{lane_id }} IVC % Base All + + + + Lane {{lane_id }} IVC % Base Called + +
No data
+ {% endfor %} +
+
+ +{% endblock %} diff --git a/experiments/templates/experiments/index.html b/experiments/templates/experiments/index.html new file mode 100644 index 0000000..28c24bf --- /dev/null +++ b/experiments/templates/experiments/index.html @@ -0,0 +1,14 @@ +{% if data_run_list %} + + {% for run in data_run_list %} + + + + + + + {% endfor %} +
{{run.run_folder}}sheetstarted emailfinished email
+{% else %} +

No data runs are available.

+{% endif %} diff --git a/experiments/templates/experiments/sequencer.html b/experiments/templates/experiments/sequencer.html new file mode 100644 index 0000000..411288c --- /dev/null +++ b/experiments/templates/experiments/sequencer.html @@ -0,0 +1,25 @@ +{% extends "base_site.html" %} +{% load humanize i18n %} +{% load staticfiles %} +{% block extrahead %} + + + + + {% block additional_javascript %} + {% endblock %} +{% endblock %} + +{% block content %} +

Sequencer

+
+
Name
+
{{sequencer.name}}
+
Instrument Name
+
{{sequencer.instrument_name}}
+
Model
+
{{sequencer.model}}
+
Comment
+
+
+{% endblock %} diff --git a/experiments/templates/experiments/started_email.html b/experiments/templates/experiments/started_email.html new file mode 100644 index 0000000..180cde6 --- /dev/null +++ b/experiments/templates/experiments/started_email.html @@ -0,0 +1,19 @@ +

+The following libraries are on the flowcell {{ flowcell.flowcell_id }} +which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell. +

+

{% for lane in lanes %} +Lane #{{ lane.lane_number }} : + +{{ lane.library.id }} +{{ lane.library.library_name }}
+{% endfor %}

+

+The data should be available at the following link when +the pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }} +days from {{ now|date:"D, M d Y" }} +

+

+ +https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer }} +

diff --git a/experiments/templates/experiments/started_email.txt b/experiments/templates/experiments/started_email.txt new file mode 100644 index 0000000..7337ef8 --- /dev/null +++ b/experiments/templates/experiments/started_email.txt @@ -0,0 +1,19 @@ +The following libraries are on the flowcell {{ flowcell.flowcell_id }} +which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell. + +Lane : (Library Id) Library Name (Cluster Estimate) +{% for lane in lanes %} +Lane #{{ lane.lane_number }} : ({{ lane.library.id }}) {{ lane.library.library_name }} ({{ lane.cluster_estimate }}) + https://jumpgate.caltech.edu/library/{{ lane.library.id }} +{% endfor %} + +The raw data should be available at the following link when the +pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }} +days from {{ now|date:"D, M d Y" }} + +https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer}} + +Username: gec +Password: gecilluminadata + +- Jumpgate diff --git a/htsworkflow/templates/experiments/detail.html b/htsworkflow/templates/experiments/detail.html deleted file mode 100644 index 65d3c00..0000000 --- a/htsworkflow/templates/experiments/detail.html +++ /dev/null @@ -1,7 +0,0 @@ -{% if run_f %} - -{% else %} -

Run folder not found.

-{% endif %} diff --git a/htsworkflow/templates/experiments/email_preview.html b/htsworkflow/templates/experiments/email_preview.html deleted file mode 100644 index 9c35c6d..0000000 --- a/htsworkflow/templates/experiments/email_preview.html +++ /dev/null @@ -1,38 +0,0 @@ -{% extends "base.html" %} -{% load i18n %} - -{% block breadcrumbs %} -
- {% trans 'Home' %} › - Experiments › - flowcell › - {{ flowcell.flowcell_id }} -
-{% endblock %} - -{% block content %} -{% if warnings %} -
-

-{% for user_admin_url, username in warnings %} -Warning: User {{ username }} has no -email address
-{% endfor %} -{% endif %} -

-{% for to, subject, body, sending in emails %} -
-{% if sending %}Message: {{ sending }}
{% endif %} -From: {{ from }}
-To: {{ to }}
-Subject: {{ subject }}
-
-{{ body }}
-
-{% endfor %}
- - -
- - -{% endblock %} \ No newline at end of file diff --git a/htsworkflow/templates/experiments/flowcellSheet.html b/htsworkflow/templates/experiments/flowcellSheet.html deleted file mode 100644 index 103b045..0000000 --- a/htsworkflow/templates/experiments/flowcellSheet.html +++ /dev/null @@ -1,87 +0,0 @@ -{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG - - -{% if fc %} - - - - - - - - - - - - - - - - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - - - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - - -{% for lane in fc.lane_set.all %} - -{% endfor %} - - -
GA SEQUENCING (SOLEXA) LOG       
         
Date Run Started{{ fc.run_date }}      
         
Cluster station used{{ fc.cluster_station.name }}      
GA used{{ fc.sequencer.name }}      
         
Flowcell number{{ fc.flowcell_id }}      
Number of Tiles per Lane100       
Number of Cycles{{ fc.read_length }}       
         
         
SAMPLE INFORMATION        
 FC#     FC bar code
Lane{{ lane.lane_number }}
Solexa Library Number{{ lane.library.id }}
Sample Name{{ lane.library.library_name }}
Organism{{ lane.library.library_species.scientific_name }}
Submitter{{ lane.library.made_for }}
First time run?
Gel Cut Size (bp){{ lane.library.gel_cut_size }}
Template Concentration (ng/ul){{ lane.library.undiluted_concentration }}
Run Concentration (pM){{ lane.pM }}
- -{% else %} -

Flowcell object missing. Can't create sheet.

-{% endif %} - - - - - - {% block additional_javascript %} - {% endblock %} -{% endblock %} - -{% block content %} -
- {% include "experiments/flowcell_header.html" %} -
-

Lanes

- - - - - - - - - - - - {% for lane in lanes %} - - - - - - - - {% endfor %} - -
LaneLibrary IDLibrary NameSpeciesComment
- - {{lane.lane_number}} - - - - {{lane.library.id}} - {% if user.is_staff %} - - - {% endif %} - - - {{lane.library.library_name}} - - - - {{ lane.library.library_species.scientific_name }} - - {{lane.comment}} -
-
- {% for run in flowcell.datarun_set.all %} -

Run {{ run.runfolder_name }}

- {% if run.lane_files %} - - - - - - - - - - - - - {% for lane_id, lane_file_set in run.lane_files.items %} - {% if lane_file_set.ivc_all %} - - - - - - - - - {% endif %} - {% endfor %} - -
LaneIVC AllIVC CallIVC Percent BaseIVC Percent Base AllIVC Percent Base Called
{{ lane_id }} - - Lane {{lane_id }} IVC All - - - Lane {{lane_id }} IVC Call - - - - Lane {{lane_id }} IVC % Base - - - - Lane {{lane_id }} IVC % Base All - - - - Lane {{lane_id }} IVC % Base Called - -
- {% endif %} - {% endfor %} -
-
-
- -{% endblock %} diff --git a/htsworkflow/templates/experiments/flowcell_header.html b/htsworkflow/templates/experiments/flowcell_header.html deleted file mode 100644 index f0cb470..0000000 --- a/htsworkflow/templates/experiments/flowcell_header.html +++ /dev/null @@ -1,43 +0,0 @@ -{% load staticfiles %} -
-

About this Flowcell

- Flowcell: - {{flowcell.flowcell_id}}{% if user.is_staff %}Edit{% endif%} -
-
-
- Instrument: - {{ flowcell.sequencer.name }} - {% if flowcell.sequencer.instrument_name %} - ({{ flowcell.sequencer.instrument_name}}) - {% endif %} -
- Instrument Model: - {{flowcell.sequencer.model}} -
-
-
- {% for datarun in flowcell.datarun_set.all %} - Image Analysis: - {{datarun.image_software}} - {{datarun.image_version}}
- Base Caller: - {{datarun.basecall_software}} - {{datarun.basecall_version}}
- Alignment: - {{datarun.alignment_software}} - {{datarun.alignment_version}}
- {% endfor %} - Run Date: - {{ flowcell.run_date }}
- Type: - {{flowcell.flowcell_type}}
- Read Length: - {{flowcell.read_length}}
- Control Lane: - {{flowcell.control_lane}}
- - Notes: - 
{{flowcell.notes}}
-
diff --git a/htsworkflow/templates/experiments/flowcell_lane_detail.html b/htsworkflow/templates/experiments/flowcell_lane_detail.html deleted file mode 100644 index ebe2c59..0000000 --- a/htsworkflow/templates/experiments/flowcell_lane_detail.html +++ /dev/null @@ -1,98 +0,0 @@ -{% extends "base_site.html" %} -{% load humanize i18n %} -{% load staticfiles %} -{% block extrahead %} - - - - - {% block additional_javascript %} - {% endblock %} -{% endblock %} - -{% block content %} -
-
- {% include "experiments/flowcell_header.html" %} -
-
-

About this lane

- Lane: - {{lane.lane_number}}
- pM: - {{ lane.pM }}
- {% if lane.cluster_estimate %} - Cluster Estimate: - {{ lane.cluster_estimate|intcomma }}
{% endif %} - {% if lane.status %} - Lane Status: - {{ lane.status }}
{% endif %} - {% if lane.comment %} - Comments: - {{ lane.comment }}
{% endif %} -
-
- {% include "sample_header.html" %} -
-
- {% for run in flowcell.datarun_set.all %} -

Run {{ run.runfolder_name }}

- - - - - - - - - - - - - {% for run, lane_number, lane_file_set in filtered_dataruns %} - {% if lane_file_set.ivc_all %} - - - - - - - - - {% else %} - - {% endif %} - {% endfor %} - -
LaneIVC AllIVC CallIVC Percent BaseIVC Percent Base AllIVC Percent Base Called
{{lane_number}} - - Lane {{lane_id }} IVC All - - - Lane {{lane_id }} IVC Call - - - - Lane {{lane_id }} IVC % Base - - - - Lane {{lane_id }} IVC % Base All - - - - Lane {{lane_id }} IVC % Base Called - -
No data
- {% endfor %} -
-
- -{% endblock %} diff --git a/htsworkflow/templates/experiments/index.html b/htsworkflow/templates/experiments/index.html deleted file mode 100644 index 28c24bf..0000000 --- a/htsworkflow/templates/experiments/index.html +++ /dev/null @@ -1,14 +0,0 @@ -{% if data_run_list %} - - {% for run in data_run_list %} - - - - - - - {% endfor %} -
{{run.run_folder}}sheetstarted emailfinished email
-{% else %} -

No data runs are available.

-{% endif %} diff --git a/htsworkflow/templates/experiments/sequencer.html b/htsworkflow/templates/experiments/sequencer.html deleted file mode 100644 index 411288c..0000000 --- a/htsworkflow/templates/experiments/sequencer.html +++ /dev/null @@ -1,25 +0,0 @@ -{% extends "base_site.html" %} -{% load humanize i18n %} -{% load staticfiles %} -{% block extrahead %} - - - - - {% block additional_javascript %} - {% endblock %} -{% endblock %} - -{% block content %} -

Sequencer

-
-
Name
-
{{sequencer.name}}
-
Instrument Name
-
{{sequencer.instrument_name}}
-
Model
-
{{sequencer.model}}
-
Comment
-
-
-{% endblock %} diff --git a/htsworkflow/templates/experiments/started_email.html b/htsworkflow/templates/experiments/started_email.html deleted file mode 100644 index 180cde6..0000000 --- a/htsworkflow/templates/experiments/started_email.html +++ /dev/null @@ -1,19 +0,0 @@ -

-The following libraries are on the flowcell {{ flowcell.flowcell_id }} -which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell. -

-

{% for lane in lanes %} -Lane #{{ lane.lane_number }} : - -{{ lane.library.id }} -{{ lane.library.library_name }}
-{% endfor %}

-

-The data should be available at the following link when -the pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }} -days from {{ now|date:"D, M d Y" }} -

-

- -https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer }} -

diff --git a/htsworkflow/templates/experiments/started_email.txt b/htsworkflow/templates/experiments/started_email.txt deleted file mode 100644 index 7337ef8..0000000 --- a/htsworkflow/templates/experiments/started_email.txt +++ /dev/null @@ -1,19 +0,0 @@ -The following libraries are on the flowcell {{ flowcell.flowcell_id }} -which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell. - -Lane : (Library Id) Library Name (Cluster Estimate) -{% for lane in lanes %} -Lane #{{ lane.lane_number }} : ({{ lane.library.id }}) {{ lane.library.library_name }} ({{ lane.cluster_estimate }}) - https://jumpgate.caltech.edu/library/{{ lane.library.id }} -{% endfor %} - -The raw data should be available at the following link when the -pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }} -days from {{ now|date:"D, M d Y" }} - -https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer}} - -Username: gec -Password: gecilluminadata - -- Jumpgate