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Fix links on sample page #164

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merged 16 commits into from
Oct 11, 2017
Merged

Fix links on sample page #164

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08b4fbf
put pipeline runs back
yunfangjuan Oct 6, 2017
f35ae08
Merge branch 'master' into add_pipeline_runs_page
yunfangjuan Oct 6, 2017
61c4acf
Merge branch 'master' of github.com:chanzuckerberg/idseq-web into add…
yunfangjuan Oct 6, 2017
5095f29
users clean up
yunfangjuan Oct 6, 2017
3681856
Merge branch 'master' into users_clean_up
yunfangjuan Oct 7, 2017
9231cbf
fix conflicts
yunfangjuan Oct 10, 2017
bce44ef
fix all the failures
yunfangjuan Oct 10, 2017
1d6b83d
add more tests
yunfangjuan Oct 10, 2017
6f4204a
more tests
yunfangjuan Oct 10, 2017
5c6b6c7
Merge branch 'master' into users_clean_up
yunfangjuan Oct 10, 2017
0c93c8c
Merge branch 'master' of github.com:chanzuckerberg/idseq-web into use…
yunfangjuan Oct 10, 2017
f8d7135
fix the right section for samples
yunfangjuan Oct 11, 2017
4ead9b7
fix a typo
yunfangjuan Oct 11, 2017
40ac0d6
fix rubocop
yunfangjuan Oct 11, 2017
d645851
fix rubocop
yunfangjuan Oct 11, 2017
60a005d
Merge branch 'master' into fix_links_on_sample_page
yunfangjuan Oct 11, 2017
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27 changes: 19 additions & 8 deletions app/assets/javascripts/components/PipelineSampleReads.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ class PipelineSampleReads extends React.Component {
}

let pipeline_run = null;
let download_section = null;
if (this.pipelineOutput) {
pipeline_run = (
<div className="data">
Expand Down Expand Up @@ -80,7 +81,22 @@ class PipelineSampleReads extends React.Component {
</div>
</div>
</div>
)
);

download_section = (
<div>
<a className="custom-button" href= { this.sampleInfo.sample_annotated_fasta_url }>
<i className="fa fa-cloud-download left"></i> DOWNLOAD NON HUMAN READS
</a>
<a className="custom-button" href= { this.sampleInfo.sample_output_folder_url }>
<i className="fa fa-cloud-download left"></i> GO TO RESULTS FOLDER
</a>
<a className="custom-button" href= { '/reports/new?report[pipeline_output_id]=' + this.pipelineOutput.id }>
<i className="fa fa-file-text-o left"></i> GENERATE REPORT
</a>
</div>
);

} else {
pipeline_run = (
<div className="center">
Expand Down Expand Up @@ -192,16 +208,11 @@ class PipelineSampleReads extends React.Component {
</div>

<div className="col s3 download-area">
<a className="custom-button">
<a className="custom-button" href={ this.sampleInfo.sample_input_folder_url }>
<i className="fa fa-cloud-download left"></i> DOWNLOAD ALL READS
</a>
{ download_section }

<a className="custom-button">
<i className="fa fa-user-times left"></i> DOWNLOAD NON HUMAN READS
</a>
<a onClick={this.gotoReport} className="custom-button">
<i className="fa fa-file-text-o left"></i> GENERATE REPORT
</a>
</div>

</div>
Expand Down
6 changes: 5 additions & 1 deletion app/controllers/reports_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,11 @@ def show

# GET /reports/new
def new
@report = Report.new
@report = if params[:report]
Report.new(params.require(:report).permit(:pipeline_output_id))
else
Report.new
end
end

# GET /reports/1/edit
Expand Down
8 changes: 8 additions & 0 deletions app/models/sample.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,14 @@ def sample_output_folder_url
"https://s3.console.aws.amazon.com/s3/object/#{SAMPLES_BUCKET_NAME}/#{sample_path}/results/"
end

def sample_input_folder_url
"https://s3.console.aws.amazon.com/s3/object/#{SAMPLES_BUCKET_NAME}/#{sample_path}/fastqs/"
end

def as_json(_options = {})
super(methods: [:sample_input_folder_url, :sample_output_folder_url, :sample_annotated_fasta_url])
end

def pipeline_command
script_name = File.basename(IdSeqPipeline::S3_SCRIPT_LOC)
batch_command_env_variables = "INPUT_BUCKET=#{sample_input_s3_path} OUTPUT_BUCKET=#{sample_output_s3_path} " \
Expand Down