From d89e5f48d12479b25d7e85adfd924189a7c0c7a8 Mon Sep 17 00:00:00 2001 From: chen42 Date: Mon, 11 Jan 2021 10:49:59 -0600 Subject: [PATCH] minor wording tweaks --- server.py | 12 ++++++------ templates/cytoscape.html | 2 -- templates/index.html | 5 +++-- 3 files changed, 9 insertions(+), 10 deletions(-) diff --git a/server.py b/server.py index 14d06de..59bc620 100755 --- a/server.py +++ b/server.py @@ -546,7 +546,7 @@ def tableview(): gene_name = gene_name+added num_gene = gene_name.count(',')+1 - message3=" Actions:
  • Click on the abstract count to read sentences linking the keyword and the gene
  • Click on a keyword to see the terms included in the search.
  • View the results in a graph.".format(rnd_url,genes_url) + message3=" Links will be preserved when the table is copy-n-pasted into a spreadsheet.".format(rnd_url,genes_url) return render_template('tableview.html', genes_session_tmp = genes_session_tmp, nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message3=message3, rnd_url=rnd_url, genes_url=genes_url) @app.route("/tableview0/") @@ -605,7 +605,7 @@ def tableview0(): gene_name=gene_name.replace("'","") gene_name = gene_name+added num_gene = gene_name.count(',')+1 - message4=" Notes:
  • These are the keywords that have zero abstract counts.
  • View all the results in a graph.".format(rnd_url,genes_url) + message4=" Notes:
  • These are the keywords that have zero abstract counts.
  • View all the results in a graph. ".format(rnd_url,genes_url) return render_template('tableview0.html',nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message4=message4) @app.route("/userarchive") @@ -640,7 +640,7 @@ def sorted_alphanumeric(data): filename=filename[0:4]+"-"+filename[5:7]+"-"+filename[8:13]+":"+filename[14:16]+":"+filename[17:19] directory_list.append(filename) len_dir = len(directory_list) - message3=" Actions:
  • Click on the Date/Time to view archived results.
  • The Date/Time are based on US Central time zone. " + message3=" " return render_template('userarchive.html', len_dir=len_dir, gene_list = gene_list, folder_list=folder_list, directory_list=directory_list, session_id=session_id, message3=message3) # delete this search @@ -674,7 +674,7 @@ def date(): for line in file_edges.readlines(): if ':' not in line: nodata_temp = 1 - else: + else: nodata_temp = 0 with open(tf_path+"/"+str(session['hashed_email'])+"/"+select_date+"/edges.json", "r") as edgesjsonfile: jedges = json.load(edgesjsonfile) @@ -709,7 +709,7 @@ def date(): else: flash("You logged out!") return render_template('index.html') - message3=" Actions:
  • Click on the abstract count to read sentences linking the keyword and the gene
  • Click on a keyword to see the terms included in the search.
  • View the results in a graph.".format(select_date,genes_session) + message3=" Links will be preserved when the table is copy-n-pasted into a spreadsheet.".format(select_date,genes_session) return render_template('tableview.html',nodata_temp=nodata_temp, num_gene=num_gene,genes_session_tmp = genes_session_tmp, rnd_url=select_date ,jedges=jedges, jnodes=jnodes,gene_name=gene_name, genes_url=genes_session, message3=message3) @app.route('/cytoscape/') @@ -719,7 +719,7 @@ def cytoscape(): tf_path=tempfile.gettempdir() genes_session_tmp=tf_path + "/" + genes_url - message2=" Actions:
  • Click on a line to read the sentences
  • Click on a keyword to see the terms included in the search
  • Hover a pointer over a node to hide other links
  • Move the nodes around to adjust visibility, reload the page to restore the default layout
  • View the results in a table. ".format(rnd_url,genes_url) + message2="".format(rnd_url,genes_url) if ('email' in session): filename = rnd_url.split("_0_")[0] rnd_url_tmp = datadir+"/user/"+str(session['hashed_email'])+"/"+rnd_url+"/"+filename diff --git a/templates/cytoscape.html b/templates/cytoscape.html index 48ff3ef..c1daf56 100644 --- a/templates/cytoscape.html +++ b/templates/cytoscape.html @@ -13,9 +13,7 @@

    {{ message |safe}}

    -
    • {{ message2 |safe}} -


    diff --git a/templates/index.html b/templates/index.html index 840b50f..5af610e 100644 --- a/templates/index.html +++ b/templates/index.html @@ -6,7 +6,7 @@

    Relationship with Addiction Through Searches of

    -

    RatsPub is a tool to efficiently and comprehensively answer the question "What do we know about these genes and addiction?". RatsPub answers this question by searching PubMed to find sentences containing the query terms (i.e., gene symbols) and over 300 drug addiction-related keywords that are organized into seven categories. Data from NHGRI-EBI GWAS catalog are also included in the search. These gene-keyword relationships are presented as an interactive graph and a table.Gene alias often include non-specific words and are thus not included in the initial search. However, a list of alias can be found by clicking on the gene symbol in the results section. These alias then can be searched with a single click. +

    RatsPub is a tool to efficiently and comprehensively answer the question "What do we know about these genes and addiction?". RatsPub answers this question by searching PubMed to find sentences containing the query terms (i.e., gene symbols) and over 300 drug addiction-related keywords that are organized into seven categories. Data from NHGRI-EBI GWAS catalog are also included in the search. These gene-keyword relationships are presented as an interactive graph and a table. Gene alias often include non-specific words and are thus not included in the initial search. However, a list of alias can be found by clicking on the gene symbol in the results section. These alias then can be searched with a single click.

    Up to 200 gene symbols can be entered in the box below. Gene symbols can be separated by a space, a comma or a semicolon. User accounts (free) can be created if you prefer to save the results. @@ -24,7 +24,7 @@

    Relationship with Addiction Through Searches of
    - Please choose keyword categories to be included in the search: + Please choose keyword categories to be included in the search: +