grnsight 6.0.7 → 7.2.0

package/web-client/views/upload.pug

@@ -57,10 +57,21 @@ html
 
                 li(class='divider')
 
+                li
+                  span(class='menu-subheader') Network Mode
+                  
+                li(class='startDisabled disabled')
+                  a(href='#' id='network-mode-grn-menu' class="menu-submenu network-mode")
+                    span(class='glyphicon')
+                    |   Gene Regulatory Network
+                li(class='startDisabled disabled')
+                  a(href='#' id='network-mode-protein-protein-physical-interaction-menu' class="menu-submenu network-mode")
+                    span(class='glyphicon')
+                    |   Protein-Protein Physical Interaction Network
                 li
                   span(class='menu-subheader') Species
                 li
-                  p(id='Saccharomyces-cerevisiae')
+                  p(id='Saccharomyces-cerevisiae', class="menu-submenu")
                     span(class='glyphicon glyphicon-ok')
                     |   Saccharomyces cerevisiae
 
@@ -70,35 +81,33 @@ html
               ul(class='dropdown-menu' role='menu')
                 span(class='menu-subheader') Graph Options
                 li
-                  a(href='#' id='forceGraph' class='layout' checked)
-                    span(class='glyphicon glyphicon-ok')
-                    |   Force Graph
+                  a(href='#' id='forceGraph' class='layout')
+                    |      Force Graph
                   a(href='#' id='gridLayout' class='layout')
-                    span(class='glyphicon')
-                    |   Grid Layout
+                    |      Grid Layout
                 li(class='divider')
                 li
                   a(href='#' id='lockSlidersMenu' class="lockSliders")
                     span(class='glyphicon invisible')
-                    |   Lock Force Graph Parameters
+                    |Lock Force Graph Parameters
                 li
                   a(href='#' id='resetSlidersMenu' class="resetSliders")
                     span(class='glyphicon invisible')
-                    |   Reset Force Graph Parameters
+                    |Reset Force Graph Parameters
                 li(class='disabled')
                   a(href='#' id='undoResetMenu' class="undoSliderReset")
                     span(class='glyphicon invisible')
-                    |   Undo Reset
+                    |Undo Reset
                 li(class='divider')
                 li
                   a(href='#' id='link-distance' class='with-input')
                     span(class='glyphicon invisible')
-                    |   Link Distance (1 - 1000)  
+                    |Link Distance (1 - 1000)  
                     input(type='number' id='link-distance-menu' class='keepopen' value='500' aria-describedby='basic-addon1')
                 li
                   a(href='#' id='charge' class='with-input')
                     span(class='glyphicon invisible')
-                    |   Charge (-2000 - 0)  
+                    |Charge (-2000 - 0)  
                     input(type='number' id='charge-menu' class='keepopen' value='-50' aria-describedby='basic-addon1')
 
 
@@ -109,32 +118,33 @@ html
                   a(href='#' id='node-coloring-toggle-menu' class='nodeColoringToggle')
                     span(class='glyphicon')
                     |   Enable Node Coloring
-                li(class='divider')
-                li(class='node-coloring-menu dropdown-submenu disabled')
-                  a(href='#')
-                    span(class='glyphicon invisible')
-                    |   Select Top Dataset
-                  ul(class='dropdown-menu' id='topDatasetDropdownMenu')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' id='averageDataTopMenu' class='nodeColoring')
-                    span(class='glyphicon')
-                    |   Average Replicate Values for Top Dataset
-                li(class='divider')
-                li(class='node-coloring-menu dropdown-submenu disabled')
-                  a(href='#')
-                    span(class='glyphicon invisible')
-                    |   Select Bottom Dataset
-                  ul(class='dropdown-menu' id='bottomDatasetDropdownMenu')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' id='averageDataBottomMenu' class='viewportOption')
-                    span(class='glyphicon')
-                    |   Average Replicate Values for Bottom Dataset
-                li(class='divider')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' class='nodeOptions with-input')
-                    span(class='glyphicon invisible')
-                    |   Log Fold Change Max Value (0.01 - 100):  
-                    input(type='number' min="0.01" max="100" id='log-fold-change-max-value-menu' class='logFoldChangeMaxValue keepopen' aria-describedby='basic-addon1')                  
+                div(id='node-coloring-navbar-options' class='disabled')
+                  li(class='divider')
+                  li(class='node-coloring-menu dropdown-submenu disabled')
+                    a(href='#')
+                      span(class='glyphicon invisible')
+                      |   Select Top Dataset
+                    ul(class='dropdown-menu' id='topDatasetDropdownMenu')
+                  li(class='node-coloring-menu disabled')
+                    a(href='#' id='averageDataTopMenu' class='nodeColoring')
+                      span(class='glyphicon')
+                      |   Average Replicate Values for Top Dataset
+                  li(class='divider')
+                  li(class='node-coloring-menu dropdown-submenu disabled')
+                    a(href='#')
+                      span(class='glyphicon invisible')
+                      |   Select Bottom Dataset
+                    ul(class='dropdown-menu' id='bottomDatasetDropdownMenu')
+                  li(class='node-coloring-menu disabled')
+                    a(href='#' id='averageDataBottomMenu' class='viewportOption')
+                      span(class='glyphicon')
+                      |   Average Replicate Values for Bottom Dataset
+                  li(class='divider')
+                  li(class='node-coloring-menu disabled')
+                    a(href='#' class='nodeOptions with-input')
+                      span(class='glyphicon invisible')
+                      |   Log Fold Change Max Value (0.01 - 100):  
+                      input(type='number' min="0.01" max="100" id='log-fold-change-max-value-menu' class='logFoldChangeMaxValue keepopen' aria-describedby='basic-addon1')                  
 
             li(class='dropdown')
               a(href='#' class='dropdown-toggle' data-toggle='dropdown') Edge
@@ -200,7 +210,7 @@ html
                     |   Fit To Window
                 li(class='divider')
                 li
-                  a(href='#' id='restrict-graph-to-viewport' class='viewportOption')
+                  a(href='#' id='restrict-graph-to-viewport' class='viewport')
                     span(class='glyphicon')
                     |   Restrict Graph to Viewport
                 li(class='divider')
@@ -234,15 +244,11 @@ html
                     li(class='startDisabled disabled weighted export')
                       a(href='#' id='exportAsWeightedSif') To Weighted SIF
                     li(class='divider')
-                    li(class='startDisabled disabled unweighted export')
+                    li(class='startDisabled disabled unweighted export' id='unweightedGraphmlContainer')
                       a(href='#' id='exportAsUnweightedGraphMl') To Unweighted GraphML
                     li(class='startDisabled disabled weighted export')
                       a(href='#' id='exportAsWeightedGraphMl') To Weighted GraphML
                     li(class='divider')
-                    //- li(class='startDisabled disabled unweighted export')
-                      a(href='#' id='exportAsUnweightedExcel') To Unweighted Excel
-                    //- li(class='startDisabled disabled weighted export')
-                    //-   a(href='#' id='exportAsWeightedExcel') To Weighted Excel
                     li(class='startDisabled disabled export')
                       a(href='#' id='exportAsExcel') To Excel
 
@@ -341,6 +347,7 @@ html
                         option(href='#' id='demoSourceDropdown-weighted' class='weighted' value='weighted')  Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
                         option(href='#' id='demoSourceDropdown-schadeInput' class='schadeInput' value='schadeInput') Demo #3: Unweighted GRN (21 genes, 31 edges)
                         option(href='#' id='demoSourceDropdown-schadeOutput' class='schadeOutput' value='schadeOutput') Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data)
+                        option(href='#' id='demoSourceDropdown-ppi' class='ppi' value='ppi') Demo #5: PPI (18 proteins, 81 edges)
                     label(for='upload-network' class='open btn btn-default network-button' data-toggle='tooltip', title='(.xlsx, .sif, .graphml)')
                       span(class='glyphicon glyphicon-folder-open')
                       |   Open File 
@@ -354,6 +361,13 @@ html
                     span(class='glyphicon glyphicon-repeat sidebar-glyphicon')
                     |   Reload
                   div(class="long-sub-divider")
+                    form(class='panelDropdownContainer')
+                      label(for='speciesDropdown' class='info') Network Mode
+                      select(class="networkMode panelDropdown btn btn-default startDisabled disabled" id='networkModeDropdown' name="networkModeDropdown" href='#')
+                        option(value="none" selected="true" disabled hidden) Change Network Mode
+                        option(href='#' id='demoSourceDropdown-grn' value='grn') Gene Regulatory Network
+                        option(href='#' id='demoSourceDropdown-protein-protein-physical-interaction' value='protein-protein-physical-interaction') Protein-Protein Physical Interaction Network
+
                   label(for='species-info' class='info') Species: 
                     span(id='species' class='network-type') Saccharomyces cerevisiae
                   input(type="hidden" id='species-info')
@@ -488,7 +502,7 @@ html
                 tr(class='shortest-path-column-headers')
               tbody
 
-    div(id='errorModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+    div(id='errorModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')
         div(class='modal-content')
           div(class='modal-header')
@@ -499,9 +513,9 @@ html
             p(id='error')
           div(class='modal-footer')
             input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
-            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('.upload').click()")
+            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload-network').click()")
 
-    div(id='warningsModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+    div(id='warningsModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')
         div(class='modal-content')
           div(class='modal-header')
@@ -522,7 +536,7 @@ html
           div(class='modal-footer')
             input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
 
-    div(id='exportExcelModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+    div(id='exportExcelModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')
         div(class='modal-content')
           div(class='modal-header')
@@ -534,7 +548,7 @@ html
           div(class='modal-footer')
             div(id='exportExcelFooter-container')
           
-    div(id='generateNetworkModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+    div(id='generateNetworkModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')
         div(class='modal-content')
           div(class='modal-header')
@@ -546,7 +560,7 @@ html
           div(class='modal-footer')
             div(id='generateNetworkFooter-container')
 
-    div(id='warningsModalSpecies' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
+    div(id='warningsModalSpecies' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')
         div(class='modal-content')
           div(class='modal-header')
@@ -559,7 +573,7 @@ html
             input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
             //- input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('.upload').click()")
 
-    div(id='importErrorModal' class='modal fade' tab-index='-1' role='dialog' aria-hidden='true')
+    div(id='importErrorModal' class='modal fade' tab-index='-1' role='dialog' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')
         div(class='modal-content')
           div(class='modal-header')

package/database/network-database/scripts/filter_genes.py

@@ -1,76 +0,0 @@
-import psycopg2
-import csv
-import os
-
-PROCESSED_GENES = "../script-results/processed-loader-files/gene.csv"
-MISSING_GENE_DESTINATION = '../script-results/processed-loader-files/missing-genes.csv'
-UPDATE_GENE_DESTINATION = '../script-results/processed-loader-files/update-genes.csv'
-
-try:
-    connection = psycopg2.connect(user="postgres",
-                                  password="",
-                                  host="grnsight2.cfimp3lu6uob.us-west-1.rds.amazonaws.com",
-                                  port="5432",
-                                  database="postgres")
-    cursor = connection.cursor()
-    postgreSQL_select_Query = "select * from gene_regulatory_network.gene"
-
-    cursor.execute(postgreSQL_select_Query)
-    print("Selecting rows from gene table using cursor.fetchall")
-    gene_records = cursor.fetchall()
-
-    db_genes = {}
-    missing_genes = {}
-    genes_to_update = {}
-    for gene in gene_records:
-        # key = (gene_id, taxon_id)
-        key = (gene[0], gene[3])
-        value = {"display_gene_id": gene[1], "species": gene[2], "regulator": gene[4]}
-        db_genes[key] = value
-
-    print(f'Processing file {PROCESSED_GENES}')
-    with open(PROCESSED_GENES, 'r+', encoding="UTF-8") as f:
-        i = 0
-        reader = csv.reader(f)
-        for row in reader:
-            if i != 0:
-                row = row[0].split('\t')
-                gene_id = row[0]
-                display_gene_id = row[1]
-                species = row[2]
-                taxon_id = row[3]
-                regulator = row[4]
-                key = (gene_id, taxon_id)
-                value = {"display_gene_id": display_gene_id , "species": species, "regulator": regulator}
-                if key not in db_genes:
-                    missing_genes[key] = value
-                elif db_genes[key]["display_gene_id"] != display_gene_id:
-                    # the display gene id got updated, so lets update our db to account for that
-                    genes_to_update[key] = value
-            i+=1
-            
-    print(f'Creating missing-genes.csv\n')
-    gene_file = open(MISSING_GENE_DESTINATION, 'w')
-    headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator'
-    gene_file.write(f'{headers}\n')
-    for gene in missing_genes:
-        gene_file.write(f'{gene[0]}\t{missing_genes[gene]["display_gene_id"]}\t{missing_genes[gene]["species"]}\t{gene[1]}\t{missing_genes[gene]["regulator"]}\n')
-    gene_file.close()
-
-    print(f'Creating update-genes.csv\n')
-    gene_file = open(UPDATE_GENE_DESTINATION, 'w')
-    headers = f'Gene ID\tDisplay Gene ID\tSpecies\tTaxon ID\tRegulator'
-    gene_file.write(f'{headers}\n')
-    for gene in genes_to_update:
-        gene_file.write(f'{gene[0]}\t{genes_to_update[gene]["display_gene_id"]}\t{genes_to_update[gene]["species"]}\t{gene[1]}\t{genes_to_update[gene]["regulator"]}\n')
-    gene_file.close()
-
-except (Exception, psycopg2.Error) as error:
-    print("Error while fetching data from PostgreSQL", error)
-
-finally:
-    # closing database connection.
-    if connection:
-        cursor.close()
-        connection.close()
-        print("PostgreSQL connection is closed")

package/database/network-database/scripts/loader.py

@@ -1,79 +0,0 @@
-import csv
-import re
-# Usage
-# python3 loader.py | psql postgresql://localhost/postgres
-"""
-This program generates direct SQL statements from the source files in order
-to populate a relational database with those files’ data.
-
-By taking the approach of emitting SQL statements directly, we bypass the need to import
-some kind of database library for the loading process, instead passing the statements
-directly into a database command line utility such as `psql`.
-"""
-
-"""
-This function Loads Network Data Sources into the database
-"""
-def LOAD_SOURCES():
-    print('COPY gene_regulatory_network.source (time_stamp, source, display_name) FROM stdin;')
-    NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv'
-    with open(NETWORK_DATA_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                time_stamp = r[0]
-                source = r[1]
-                display_name = r[2]
-                print(f'{time_stamp}\t{source}\t{display_name}')
-            row_num += 1
-    print('\\.')
-
-
-"""
-This function Loads Gene ID Mapping into the database
-"""
-def LOAD_GENES():
-    print('COPY gene_regulatory_network.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;')
-    GENE_SOURCE = '../script-results/processed-loader-files/gene.csv'
-    with open(GENE_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                gene_id = r[0]
-                display_gene_id= r[1]
-                species = r[2]
-                taxon_id = r[3]
-                regulator = r[4]
-                print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}')
-            row_num += 1
-    print('\\.')
-
-
-"""
-This function Loads the Network Matrix into the database
-"""
-def LOAD_NETWORK():
-    print('COPY gene_regulatory_network.network (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source) FROM stdin;')
-    NETWORK_SOURCE = '../script-results/processed-loader-files/network.csv'
-    with open(NETWORK_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                regulator_gene_id = r[0]
-                target_gene_id= r[1]
-                taxon_id = r[2]
-                time_stamp = r[3]
-                source = r[4]
-                print(f'{regulator_gene_id}\t{target_gene_id}\t{taxon_id}\t{time_stamp}\t{source}')
-            row_num += 1
-    print('\\.')
-
-LOAD_SOURCES()
-LOAD_GENES()
-LOAD_NETWORK()

package/database/network-database/scripts/loader_updates.py

@@ -1,99 +0,0 @@
-import csv
-import re
-# Usage
-# python3 loader.py | psql postgresql://localhost/postgres
-"""
-This program generates direct SQL statements from the source files in order
-to populate a relational database with those files’ data.
-
-By taking the approach of emitting SQL statements directly, we bypass the need to import
-some kind of database library for the loading process, instead passing the statements
-directly into a database command line utility such as `psql`.
-"""
-
-"""
-This function Loads Network Data Sources into the database
-"""
-def LOAD_SOURCES():
-    print('COPY gene_regulatory_network.source (time_stamp, source, display_name) FROM stdin;')
-    NETWORK_DATA_SOURCE = '../script-results/processed-loader-files/source.csv'
-    with open(NETWORK_DATA_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                time_stamp = r[0]
-                source = r[1]
-                display_name = r[2]
-                print(f'{time_stamp}\t{source}\t{display_name}')
-            row_num += 1
-    print('\\.')
-
-
-"""
-This function Loads Gene ID Mapping into the database
-"""
-def LOAD_GENES():
-    print('COPY gene_regulatory_network.gene (gene_id, display_gene_id, species, taxon_id, regulator) FROM stdin;')
-    GENE_SOURCE = '../script-results/processed-loader-files/gene.csv'
-    with open(GENE_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                gene_id = r[0]
-                display_gene_id= r[1]
-                species = r[2]
-                taxon_id = r[3]
-                regulator = r[4]
-                print(f'{gene_id}\t{display_gene_id}\t{species}\t{taxon_id}\t{regulator}')
-            row_num += 1
-    print('\\.')
-    
-"""
-This Updates to Gene ID Mapping into the database
-"""
-def UPDATE_GENES():
-    print('BEGIN;')
-    GENE_SOURCE = '../script-results/processed-loader-files/gene_update.csv'
-    with open(GENE_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                gene_id = r[0]
-                display_gene_id= r[1]
-                regulator = r[2]
-                print(f"UPDATE gene_regulatory_network.gene\nSET display_gene_id = '{display_gene_id}', regulator={regulator}\nWHERE gene_id = '{gene_id}';")
-            row_num += 1
-    print('COMMIT;')
-
-"""
-This function Loads the Network Matrix into the database
-"""
-def LOAD_NETWORK():
-    print('COPY gene_regulatory_network.network (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source) FROM stdin;')
-    NETWORK_SOURCE = '../script-results/processed-loader-files/network.csv'
-    with open(NETWORK_SOURCE, 'r+') as f:
-        reader = csv.reader(f)
-        row_num = 0
-        for row in reader:
-            if row_num != 0:
-                r= ','.join(row).split('\t')
-                regulator_gene_id = r[0]
-                target_gene_id= r[1]
-                taxon_id = r[2]
-                time_stamp = r[3]
-                source = r[4]
-                print(f'{regulator_gene_id}\t{target_gene_id}\t{taxon_id}\t{time_stamp}\t{source}')
-            row_num += 1
-    print('\\.')
-
-
-UPDATE_GENES()
-LOAD_SOURCES()
-LOAD_GENES()
-LOAD_NETWORK()