diff --git a/clade/cmds.py b/clade/cmds.py index 3408ba4..888f626 100644 --- a/clade/cmds.py +++ b/clade/cmds.py @@ -123,8 +123,7 @@ def get_last_id(cmds_file, raise_exception=False): def get_all_cmds(cmds_file): """Get list of all intercepted build commands.""" - with open_cmds_file(cmds_file) as cmds_fp: - return list(iter_cmds(cmds_fp)) + return list(iter_cmds(cmds_file)) def get_stats(cmds_file): diff --git a/clade/db.py b/clade/db.py new file mode 100644 index 0000000..95da189 --- /dev/null +++ b/clade/db.py @@ -0,0 +1,156 @@ +# Copyright (c) 2019 ISP RAS (http://www.ispras.ru) +# Ivannikov Institute for System Programming of the Russian Academy of Sciences +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import os +import psycopg2 +import sys + +from psycopg2 import sql + +from clade import Clade +from clade.cmds import iter_cmds + + +class CladeDB: + # TODO: change it + USER = "clade" + DB = "clade" + PASSWORD = "clade" + + def __init__(self, work_dir): + self.clade = Clade(work_dir) + self.logger = self.clade.logger + + self.connection = psycopg2.connect(user=self.USER, password=self.PASSWORD, database=self.DB) + self.cursor = self.connection.cursor() + + def get_project_id(self): + return "clade-_" + self.clade.get_uuid().replace("-", "_") + + def __insert_path(self, path): + path_sql = "INSERT INTO paths (path) VALUES (%s) ON CONFLICT DO NOTHING" + + self.cursor.execute(path_sql, [path]) + + def __get_path_id(self, path): + select_path_id_sql = "SELECT id FROM paths WHERE path = %s" + + self.cursor.execute(select_path_id_sql, [path]) + + return self.cursor.fetchone()[0] + + def clear_tables(self): + tables = [ + "cmd_opts", + "cmd_in", + "cmd_out", + "cmd_graph", + "src_compiled_in", + "src_used_by", + "parsed_cmds", + "cmds", + "paths" + ] + + for table in tables: + self.cursor.execute(sql.SQL("DELETE FROM {}").format(sql.Identifier(table))) + + self.cursor.connection.commit() + + def import_cmds(self): + cmd_sql = "INSERT INTO cmds (id, pid, cwd_id, which_id, command) VALUES (%s, %s, %s, %s, %s)" + + for cmd in iter_cmds(self.clade.cmds_file): + self.__insert_path(cmd["cwd"]) + self.__insert_path(cmd["which"]) + + cwd_id = self.__get_path_id(cmd["cwd"]) + which_id = self.__get_path_id(cmd["which"]) + + self.cursor.execute(cmd_sql, [ + cmd["id"], + cmd["pid"], + cwd_id, + which_id, + cmd["command"] + ]) + + self.cursor.connection.commit() + + def import_cmd_graph(self): + # parsed_cmd_sql = sql.SQL("INSERT INTO parsed_cmds (id, cwd_id, in_id, out_id, opts) VALUES (%s, %s, %s, %s, %s)") + parsed_cmd_sql = "INSERT INTO parsed_cmds (id, type) VALUES (%s, %s)" + cmd_opts_sql = "INSERT INTO cmd_opts (id, opts) VALUES (%s, %s)" + cmd_in_sql = "INSERT INTO cmd_in (cmd_id, in_id) VALUES (%s, %s)" + cmd_out_sql = "INSERT INTO cmd_out (cmd_id, out_id) VALUES (%s, %s)" + cmd_graph_sql = "INSERT INTO cmd_graph (cmd_id, used_by) VALUES (%s, %s)" + + cmds = self.clade.get_cmds(with_opts=True) + + for cmd in cmds: + self.cursor.execute(parsed_cmd_sql, [cmd["id"], cmd["type"]]) + self.cursor.execute(cmd_opts_sql, [cmd["id"], cmd["opts"]]) + + for cmd_in in cmd["in"]: + self.__insert_path(cmd_in) + in_id = self.__get_path_id(cmd_in) + + self.cursor.execute(cmd_in_sql, [cmd["id"], in_id]) + + for cmd_out in cmd["out"]: + self.__insert_path(cmd_out) + out_id = self.__get_path_id(cmd_out) + + self.cursor.execute(cmd_out_sql, [cmd["id"], out_id]) + + for cmd_id in self.clade.cmd_graph: + for used_by in self.clade.cmd_graph[cmd_id]["used_by"]: + self.cursor.execute(cmd_graph_sql, [cmd_id, used_by]) + + self.cursor.connection.commit() + + def import_src_graph(self): + src_graph = self.clade.src_graph + + src_compiled_in_sql = "INSERT INTO src_compiled_in (path_id, cmd_id) VALUES (%s, %s)" + src_used_by_sql = "INSERT INTO src_used_by (path_id, cmd_id) VALUES (%s, %s)" + + for path in src_graph: + self.__insert_path(path) + path_id = self.__get_path_id(path) + + for cmd_id in src_graph[path]["compiled_in"]: + self.cursor.execute(src_compiled_in_sql, [path_id, cmd_id]) + + for cmd_id in src_graph[path]["used_by"]: + self.cursor.execute(src_used_by_sql, [path_id, cmd_id]) + + self.cursor.connection.commit() + + +if __name__ == "__main__": + if len(sys.argv) <= 1: + sys.exit("Please specify path to the Clade working directory") + + work_dir = sys.argv[1] + + if not os.path.isdir(work_dir): + sys.exit("Specified working directory does not exist") + + c = CladeDB(work_dir) + c.clear_tables() + c.import_cmds() + c.import_cmd_graph() + c.import_src_graph() diff --git a/clade/mirror/cmds/__init__.py b/clade/mirror/cmds/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/clade/mirror/cmds/admin.py b/clade/mirror/cmds/admin.py new file mode 100644 index 0000000..8c38f3f --- /dev/null +++ b/clade/mirror/cmds/admin.py @@ -0,0 +1,3 @@ +from django.contrib import admin + +# Register your models here. diff --git a/clade/mirror/cmds/apps.py b/clade/mirror/cmds/apps.py new file mode 100644 index 0000000..e85344b --- /dev/null +++ b/clade/mirror/cmds/apps.py @@ -0,0 +1,5 @@ +from django.apps import AppConfig + + +class CmdsConfig(AppConfig): + name = 'cmds' diff --git a/clade/mirror/cmds/migrations/__init__.py b/clade/mirror/cmds/migrations/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/clade/mirror/cmds/models.py b/clade/mirror/cmds/models.py new file mode 100644 index 0000000..42edfc7 --- /dev/null +++ b/clade/mirror/cmds/models.py @@ -0,0 +1,90 @@ +# This is an auto-generated Django model module. +# You'll have to do the following manually to clean this up: +# * Rearrange models' order +# * Make sure each model has one field with primary_key=True +# * Make sure each ForeignKey has `on_delete` set to the desired behavior. +# * Remove `managed = False` lines if you wish to allow Django to create, modify, and delete the table +# Feel free to rename the models, but don't rename db_table values or field names. +from django.db import models + + +class Paths(models.Model): + path = models.TextField(unique=True, blank=True, null=True) + + class Meta: + managed = False + db_table = 'paths' + + +class Cmds(models.Model): + pid = models.IntegerField(blank=True, null=True) + cwd = models.ForeignKey('Paths', models.DO_NOTHING, related_name='cwd_ids', blank=True, null=True) + which = models.ForeignKey('Paths', models.DO_NOTHING, related_name='which_ids', blank=True, null=True) + command = models.TextField(blank=True, null=True) # This field type is a guess. + + class Meta: + managed = False + db_table = 'cmds' + + +class ParsedCmds(models.Model): + id = models.ForeignKey(Cmds, models.DO_NOTHING, db_column='id', primary_key=True) + type = models.TextField(blank=True, null=True) + + class Meta: + managed = False + db_table = 'parsed_cmds' + + +class CmdGraph(models.Model): + cmd_id = models.ForeignKey('ParsedCmds', models.DO_NOTHING, db_column='cmd_id', related_name='cmd_ids', blank=True, null=True) + used_by = models.ForeignKey('ParsedCmds', models.DO_NOTHING, db_column='used_by', blank=True, null=True) + + class Meta: + managed = False + db_table = 'cmd_graph' + + +class CmdIn(models.Model): + cmd_id = models.ForeignKey('ParsedCmds', models.DO_NOTHING, db_column='cmd_id', blank=True, null=True) + in_id = models.ForeignKey('Paths', models.DO_NOTHING, db_column='in_id', blank=True, null=True) # Field renamed because it was a Python reserved word. + + class Meta: + managed = False + db_table = 'cmd_in' + + +class CmdOpts(models.Model): + id = models.ForeignKey('ParsedCmds', models.DO_NOTHING, db_column='id', primary_key=True) + opts = models.TextField(blank=True, null=True) # This field type is a guess. + + class Meta: + managed = False + db_table = 'cmd_opts' + + +class CmdOut(models.Model): + cmd_id = models.ForeignKey('ParsedCmds', models.DO_NOTHING, db_column='cmd_id', blank=True, null=True) + out_id = models.ForeignKey('Paths', models.DO_NOTHING, db_column='out_id', blank=True, null=True) + + class Meta: + managed = False + db_table = 'cmd_out' + + +class SrcCompiledIn(models.Model): + path_id = models.ForeignKey(Paths, models.DO_NOTHING, db_column='path_id', blank=True, null=True) + cmd_id = models.ForeignKey(ParsedCmds, models.DO_NOTHING, db_column='cmd_id', blank=True, null=True) + + class Meta: + managed = False + db_table = 'src_compiled_in' + + +class SrcUsedBy(models.Model): + path_id = models.ForeignKey(Paths, models.DO_NOTHING, db_column='path_id', blank=True, null=True) + cmd_id = models.ForeignKey(ParsedCmds, models.DO_NOTHING, db_column='cmd_id', blank=True, null=True) + + class Meta: + managed = False + db_table = 'src_used_by' diff --git a/clade/mirror/cmds/static/cmds/css/cmds.css b/clade/mirror/cmds/static/cmds/css/cmds.css new file mode 100644 index 0000000..5b4ebf8 --- /dev/null +++ b/clade/mirror/cmds/static/cmds/css/cmds.css @@ -0,0 +1,15 @@ +/* https://colorhunt.co/palette/156759 = color palette*/ + +.filter { + margin-bottom: 5px; +} + +input[type=text] { + width: 160px; + padding: 2px 5px; + border: 1px solid #3c70a4; + } + +/* .parsed:hover { + background-color: #feed95; +} */ diff --git a/clade/mirror/cmds/static/cmds/css/pid_graph.css b/clade/mirror/cmds/static/cmds/css/pid_graph.css new file mode 100644 index 0000000..a17d381 --- /dev/null +++ b/clade/mirror/cmds/static/cmds/css/pid_graph.css @@ -0,0 +1,38 @@ +.node { + cursor: pointer; +} + +.overlay{ + background-color:#EEE; +} + +.node circle { + fill: #fff; + stroke: steelblue; + stroke-width: 1.5px; +} + +.node text { + font-size:10px; + font-family:sans-serif; +} + +.link { + fill: none; + stroke: #ccc; + stroke-width: 1.5px; +} + +.templink { + fill: none; + stroke: red; + stroke-width: 3px; +} + +.ghostCircle.show{ + display:block; +} + +.ghostCircle, .activeDrag .ghostCircle{ + display: none; +} diff --git a/clade/mirror/cmds/static/cmds/css/pid_graph_lazy.css b/clade/mirror/cmds/static/cmds/css/pid_graph_lazy.css new file mode 100644 index 0000000..8780ea3 --- /dev/null +++ b/clade/mirror/cmds/static/cmds/css/pid_graph_lazy.css @@ -0,0 +1,30 @@ +html,body { + padding:0; + margin:0; + overflow:hidden; +} + +.node { + cursor: pointer; +} + +.overlay{ + background-color:#EEE; +} + +.node circle { + fill: #fff; + stroke: steelblue; + stroke-width: 1.5px; +} + +.node text { + font-size:10px; + font-family:sans-serif; +} + +.link { + fill: none; + stroke: #ccc; + stroke-width: 1.5px; +} diff --git a/clade/mirror/cmds/static/cmds/css/table.css b/clade/mirror/cmds/static/cmds/css/table.css new file mode 100644 index 0000000..0bbd2f1 --- /dev/null +++ b/clade/mirror/cmds/static/cmds/css/table.css @@ -0,0 +1,45 @@ +/* https://colorhunt.co/palette/156759 = color palette*/ + +table { + border-collapse: collapse; + table-layout: fixed; +} + + +table, th, td { + border: 1px solid black; +} + +th, td { + padding: 5px; +} + +.parsed { + background-color: #d9eeec; +} + +.table_head, .table_head_cmd { + font-weight: bold; + /* font-size: 1.1em; */ + font-family: Arial; + background-color: #3c70a4; + color: white; +} + +.table_head_cmd { + font-weight: bold; + /* font-size: 1.1em; */ + font-family: Arial; + background-color: #3c70a4; + color: white; + width: 80px; + text-align: center; +} + +.table_head a:visited { + color: white; +} + +.table_head a { + color: white; +} diff --git a/clade/mirror/cmds/static/cmds/js/d3.v3.min.js b/clade/mirror/cmds/static/cmds/js/d3.v3.min.js new file mode 100644 index 0000000..1664873 --- /dev/null +++ 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0000000..8eaeadd --- /dev/null +++ b/clade/mirror/cmds/static/cmds/js/dndTree.js @@ -0,0 +1,553 @@ +/*Copyright (c) 2013-2016, Rob Schmuecker +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this +list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + +* The name Rob Schmuecker may not be used to endorse or promote products +derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL MICHAEL BOSTOCK BE LIABLE FOR ANY DIRECT, +INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, +BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY +OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, +EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.*/ + +// https://gist.github.com/robschmuecker/7880033 +// http://bl.ocks.org/robschmuecker/7880033 + +// modified into a function + +function drawGraph(error, treeData) { + // Calculate total nodes, max label length + var totalNodes = 0; + var maxLabelLength = 15; + // variables for drag/drop + var selectedNode = null; + var draggingNode = null; + // panning variables + var panSpeed = 200; + var panBoundary = 20; // Within 20px from edges will pan when dragging. + // Misc. variables + var i = 0; + var duration = 750; + var root; + + // size of the diagram + var viewerWidth = $(document).width(); + var viewerHeight = $(document).height(); + + var tree = d3.layout.tree() + .size([viewerHeight, viewerWidth]); + + // define a d3 diagonal projection for use by the node paths later on. + var diagonal = d3.svg.diagonal() + .projection(function(d) { + return [d.y, d.x]; + }); + + // A recursive helper function for performing some setup by walking through all nodes + + function visit(parent, visitFn, childrenFn) { + if (!parent) return; + + visitFn(parent); + + var children = childrenFn(parent); + if (children) { + var count = children.length; + for (var i = 0; i < count; i++) { + visit(children[i], visitFn, childrenFn); + } + } + } + + // TODO: remove? + // Call visit function to establish maxLabelLength + // visit(treeData, function(d) { + // totalNodes++; + // maxLabelLength = Math.max(d.name.length, maxLabelLength); + + // }, function(d) { + // return d.children && d.children.length > 0 ? d.children : null; + // }); + + + // sort the tree according to the node names + + function sortTree() { + tree.sort(function(a, b) { + return b.name.toLowerCase() < a.name.toLowerCase() ? 1 : -1; + }); + } + // Sort the tree initially incase the JSON isn't in a sorted order. + sortTree(); + + // TODO: Pan function, can be better implemented. + + function pan(domNode, direction) { + var speed = panSpeed; + if (panTimer) { + clearTimeout(panTimer); + translateCoords = d3.transform(svgGroup.attr("transform")); + if (direction == 'left' || direction == 'right') { + translateX = direction == 'left' ? translateCoords.translate[0] + speed : translateCoords.translate[0] - speed; + translateY = translateCoords.translate[1]; + } else if (direction == 'up' || direction == 'down') { + translateX = translateCoords.translate[0]; + translateY = direction == 'up' ? translateCoords.translate[1] + speed : translateCoords.translate[1] - speed; + } + scaleX = translateCoords.scale[0]; + scaleY = translateCoords.scale[1]; + scale = zoomListener.scale(); + svgGroup.transition().attr("transform", "translate(" + translateX + "," + translateY + ")scale(" + scale + ")"); + d3.select(domNode).select('g.node').attr("transform", "translate(" + translateX + "," + translateY + ")"); + zoomListener.scale(zoomListener.scale()); + zoomListener.translate([translateX, translateY]); + panTimer = setTimeout(function() { + pan(domNode, speed, direction); + }, 50); + } + } + + // Define the zoom function for the zoomable tree + + function zoom() { + svgGroup.attr("transform", "translate(" + d3.event.translate + ")scale(" + d3.event.scale + ")"); + } + + + // define the zoomListener which calls the zoom function on the "zoom" event constrained within the scaleExtents + var zoomListener = d3.behavior.zoom().scaleExtent([0.1, 3]).on("zoom", zoom); + + function initiateDrag(d, domNode) { + draggingNode = d; + d3.select(domNode).select('.ghostCircle').attr('pointer-events', 'none'); + d3.selectAll('.ghostCircle').attr('class', 'ghostCircle show'); + d3.select(domNode).attr('class', 'node activeDrag'); + + svgGroup.selectAll("g.node").sort(function(a, b) { // select the parent and sort the path's + if (a.id != draggingNode.id) return 1; // a is not the hovered element, send "a" to the back + else return -1; // a is the hovered element, bring "a" to the front + }); + // if nodes has children, remove the links and nodes + if (nodes.length > 1) { + // remove link paths + links = tree.links(nodes); + nodePaths = svgGroup.selectAll("path.link") + .data(links, function(d) { + return d.target.id; + }).remove(); + // remove child nodes + nodesExit = svgGroup.selectAll("g.node") + .data(nodes, function(d) { + return d.id; + }).filter(function(d, i) { + if (d.id == draggingNode.id) { + return false; + } + return true; + }).remove(); + } + + // remove parent link + parentLink = tree.links(tree.nodes(draggingNode.parent)); + svgGroup.selectAll('path.link').filter(function(d, i) { + if (d.target.id == draggingNode.id) { + return true; + } + return false; + }).remove(); + + dragStarted = null; + } + + // define the baseSvg, attaching a class for styling and the zoomListener + var baseSvg = d3.select("#tree-container").append("svg") + .attr("width", viewerWidth) + .attr("height", viewerHeight) + .attr("class", "overlay") + .call(zoomListener); + + + // Define the drag listeners for drag/drop behaviour of nodes. + dragListener = d3.behavior.drag() + .on("dragstart", function(d) { + if (d == root) { + return; + } + dragStarted = true; + nodes = tree.nodes(d); + d3.event.sourceEvent.stopPropagation(); + // it's important that we suppress the mouseover event on the node being dragged. Otherwise it will absorb the mouseover event and the underlying node will not detect it d3.select(this).attr('pointer-events', 'none'); + }) + .on("drag", function(d) { + if (d == root) { + return; + } + if (dragStarted) { + domNode = this; + initiateDrag(d, domNode); + } + + // get coords of mouseEvent relative to svg container to allow for panning + relCoords = d3.mouse($('svg').get(0)); + if (relCoords[0] < panBoundary) { + panTimer = true; + pan(this, 'left'); + } else if (relCoords[0] > ($('svg').width() - panBoundary)) { + + panTimer = true; + pan(this, 'right'); + } else if (relCoords[1] < panBoundary) { + panTimer = true; + pan(this, 'up'); + } else if (relCoords[1] > ($('svg').height() - panBoundary)) { + panTimer = true; + pan(this, 'down'); + } else { + try { + clearTimeout(panTimer); + } catch (e) { + + } + } + + d.x0 += d3.event.dy; + d.y0 += d3.event.dx; + var node = d3.select(this); + node.attr("transform", "translate(" + d.y0 + "," + d.x0 + ")"); + updateTempConnector(); + }).on("dragend", function(d) { + if (d == root) { + return; + } + domNode = this; + if (selectedNode) { + // now remove the element from the parent, and insert it into the new elements children + var index = draggingNode.parent.children.indexOf(draggingNode); + if (index > -1) { + draggingNode.parent.children.splice(index, 1); + } + if (typeof selectedNode.children !== 'undefined' || typeof selectedNode._children !== 'undefined') { + if (typeof selectedNode.children !== 'undefined') { + selectedNode.children.push(draggingNode); + } else { + selectedNode._children.push(draggingNode); + } + } else { + selectedNode.children = []; + selectedNode.children.push(draggingNode); + } + // Make sure that the node being added to is expanded so user can see added node is correctly moved + expand(selectedNode); + sortTree(); + endDrag(); + } else { + endDrag(); + } + }); + + function endDrag() { + selectedNode = null; + d3.selectAll('.ghostCircle').attr('class', 'ghostCircle'); + d3.select(domNode).attr('class', 'node'); + // now restore the mouseover event or we won't be able to drag a 2nd time + d3.select(domNode).select('.ghostCircle').attr('pointer-events', ''); + updateTempConnector(); + if (draggingNode !== null) { + update(root); + centerNode(draggingNode); + draggingNode = null; + } + } + + // Helper functions for collapsing and expanding nodes. + + function collapse(d) { + if (d.children) { + d._children = d.children; + d._children.forEach(collapse); + d.children = null; + } + } + + function expand(d) { + if (d._children) { + d.children = d._children; + d.children.forEach(expand); + d._children = null; + } + } + + var overCircle = function(d) { + selectedNode = d; + updateTempConnector(); + }; + var outCircle = function(d) { + selectedNode = null; + updateTempConnector(); + }; + + // Function to update the temporary connector indicating dragging affiliation + var updateTempConnector = function() { + var data = []; + if (draggingNode !== null && selectedNode !== null) { + // have to flip the source coordinates since we did this for the existing connectors on the original tree + data = [{ + source: { + x: selectedNode.y0, + y: selectedNode.x0 + }, + target: { + x: draggingNode.y0, + y: draggingNode.x0 + } + }]; + } + var link = svgGroup.selectAll(".templink").data(data); + + link.enter().append("path") + .attr("class", "templink") + .attr("d", d3.svg.diagonal()) + .attr('pointer-events', 'none'); + + link.attr("d", d3.svg.diagonal()); + + link.exit().remove(); + }; + + // Function to center node when clicked/dropped so node doesn't get lost when collapsing/moving with large amount of children. + + function centerNode(source) { + scale = zoomListener.scale(); + x = -source.y0; + y = -source.x0; + x = x * scale + viewerWidth / 2; + y = y * scale + viewerHeight / 2; + d3.select('g').transition() + .duration(duration) + .attr("transform", "translate(" + x + "," + y + ")scale(" + scale + ")"); + zoomListener.scale(scale); + zoomListener.translate([x, y]); + } + + // Toggle children function + + function toggleChildren(d) { + if (d.children) { + d._children = d.children; + d.children = null; + } else if (d._children) { + d.children = d._children; + d._children = null; + } + return d; + } + + // Toggle children on click. + + function click(d) { + if (d3.event.defaultPrevented) return; // click suppressed + d = toggleChildren(d); + update(d); + centerNode(d); + } + + function update(source) { + // Compute the new height, function counts total children of root node and sets tree height accordingly. + // This prevents the layout looking squashed when new nodes are made visible or looking sparse when nodes are removed + // This makes the layout more consistent. + var levelWidth = [1]; + var childCount = function(level, n) { + + if (n.children && n.children.length > 0) { + if (levelWidth.length <= level + 1) levelWidth.push(0); + + levelWidth[level + 1] += n.children.length; + n.children.forEach(function(d) { + childCount(level + 1, d); + }); + } + }; + childCount(0, root); + var newHeight = d3.max(levelWidth) * 25; // 25 pixels per line + tree = tree.size([newHeight, viewerWidth]); + + // Compute the new tree layout. + var nodes = tree.nodes(root).reverse(), + links = tree.links(nodes); + + // Set widths between levels based on maxLabelLength. + nodes.forEach(function(d) { + d.y = (d.depth * (maxLabelLength * 10)); //maxLabelLength * 10px + // alternatively to keep a fixed scale one can set a fixed depth per level + // Normalize for fixed-depth by commenting out below line + // d.y = (d.depth * 500); //500px per level. + }); + + // Update the nodes… + node = svgGroup.selectAll("g.node") + .data(nodes, function(d) { + return d.id || (d.id = ++i); + }); + + // Enter any new nodes at the parent's previous position. + var nodeEnter = node.enter().append("g") + .call(dragListener) + .attr("class", "node") + .attr("transform", function(d) { + return "translate(" + source.y0 + "," + source.x0 + ")"; + }) + .on('click', click); + + nodeEnter.append("circle") + .attr('class', 'nodeCircle') + .attr("r", 0) + .style("fill", function(d) { + return d._children ? "lightsteelblue" : "#fff"; + }); + + nodeEnter.append("text") + .attr("x", function(d) { + return d.children || d._children ? -10 : 10; + }) + .attr("dy", ".35em") + .attr('class', 'nodeText') + .attr("text-anchor", function(d) { + return d.children || d._children ? "end" : "start"; + }) + .text(function(d) { + return d.name; + }) + .style("fill-opacity", 0); + + // phantom node to give us mouseover in a radius around it + nodeEnter.append("circle") + .attr('class', 'ghostCircle') + .attr("r", 30) + .attr("opacity", 0.2) // change this to zero to hide the target area + .style("fill", "red") + .attr('pointer-events', 'mouseover') + .on("mouseover", function(node) { + overCircle(node); + }) + .on("mouseout", function(node) { + outCircle(node); + }); + + // Update the text to reflect whether node has children or not. + node.select('text') + .attr("x", function(d) { + return d.children || d._children ? -10 : 10; + }) + .attr("text-anchor", function(d) { + return d.children || d._children ? "end" : "start"; + }) + .text(function(d) { + return d.name; + }); + + // Change the circle fill depending on whether it has children and is collapsed + node.select("circle.nodeCircle") + .attr("r", 4.5) + .style("fill", function(d) { + return d._children ? "lightsteelblue" : "#fff"; + }); + + // Transition nodes to their new position. + var nodeUpdate = node.transition() + .duration(duration) + .attr("transform", function(d) { + return "translate(" + d.y + "," + d.x + ")"; + }); + + // Fade the text in + nodeUpdate.select("text") + .style("fill-opacity", 1); + + // Transition exiting nodes to the parent's new position. + var nodeExit = node.exit().transition() + .duration(duration) + .attr("transform", function(d) { + return "translate(" + source.y + "," + source.x + ")"; + }) + .remove(); + + nodeExit.select("circle") + .attr("r", 0); + + nodeExit.select("text") + .style("fill-opacity", 0); + + // Update the links… + var link = svgGroup.selectAll("path.link") + .data(links, function(d) { + return d.target.id; + }); + + // Enter any new links at the parent's previous position. + link.enter().insert("path", "g") + .attr("class", "link") + .attr("d", function(d) { + var o = { + x: source.x0, + y: source.y0 + }; + return diagonal({ + source: o, + target: o + }); + }); + + // Transition links to their new position. + link.transition() + .duration(duration) + .attr("d", diagonal); + + // Transition exiting nodes to the parent's new position. + link.exit().transition() + .duration(duration) + .attr("d", function(d) { + var o = { + x: source.x, + y: source.y + }; + return diagonal({ + source: o, + target: o + }); + }) + .remove(); + + // Stash the old positions for transition. + nodes.forEach(function(d) { + d.x0 = d.x; + d.y0 = d.y; + }); + } + + // Append a group which holds all nodes and which the zoom Listener can act upon. + var svgGroup = baseSvg.append("g"); + + // Define the root + root = treeData; + root.x0 = viewerHeight / 2; + root.y0 = 0; + + // Layout the tree initially and center on the root node. + update(root); + centerNode(root); +} diff --git a/clade/mirror/cmds/static/cmds/js/drawGraph.js b/clade/mirror/cmds/static/cmds/js/drawGraph.js new file mode 100644 index 0000000..407f18e --- /dev/null +++ b/clade/mirror/cmds/static/cmds/js/drawGraph.js @@ -0,0 +1,493 @@ +/*Copyright (c) 2013-2016, Rob Schmuecker +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this +list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + +* The name Rob Schmuecker may not be used to endorse or promote products +derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL MICHAEL BOSTOCK BE LIABLE FOR ANY DIRECT, +INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, +BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY +OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, +EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.*/ +// modified into a function +function drawGraph(error, treeData) { + // Calculate total nodes, max label length + var totalNodes = 0; + var maxLabelLength = 15; + // variables for drag/drop + var selectedNode = null; + var draggingNode = null; + // panning variables + var panSpeed = 200; + var panBoundary = 20; // Within 20px from edges will pan when dragging. + // Misc. variables + var i = 0; + var duration = 750; + var root; + // size of the diagram + var viewerWidth = $(document).width(); + var viewerHeight = $(document).height(); + var tree = d3.layout.tree() + .size([viewerHeight, viewerWidth]); + // define a d3 diagonal projection for use by the node paths later on. + var diagonal = d3.svg.diagonal() + .projection(function (d) { + return [d.y, d.x]; + }); + // A recursive helper function for performing some setup by walking through all nodes + function visit(parent, visitFn, childrenFn) { + if (!parent) + return; + visitFn(parent); + var children = childrenFn(parent); + if (children) { + var count = children.length; + for (var i = 0; i < count; i++) { + visit(children[i], visitFn, childrenFn); + } + } + } + // TODO: remove? + // Call visit function to establish maxLabelLength + // visit(treeData, function(d) { + // totalNodes++; + // maxLabelLength = Math.max(d.name.length, maxLabelLength); + // }, function(d) { + // return d.children && d.children.length > 0 ? d.children : null; + // }); + // sort the tree according to the node names + function sortTree() { + tree.sort(function (a, b) { + return b.name.toLowerCase() < a.name.toLowerCase() ? 1 : -1; + }); + } + // Sort the tree initially incase the JSON isn't in a sorted order. + sortTree(); + // TODO: Pan function, can be better implemented. + function pan(domNode, direction) { + var speed = panSpeed; + if (panTimer) { + clearTimeout(panTimer); + translateCoords = d3.transform(svgGroup.attr("transform")); + if (direction == 'left' || direction == 'right') { + translateX = direction == 'left' ? translateCoords.translate[0] + speed : translateCoords.translate[0] - speed; + translateY = translateCoords.translate[1]; + } + else if (direction == 'up' || direction == 'down') { + translateX = translateCoords.translate[0]; + translateY = direction == 'up' ? translateCoords.translate[1] + speed : translateCoords.translate[1] - speed; + } + scaleX = translateCoords.scale[0]; + scaleY = translateCoords.scale[1]; + scale = zoomListener.scale(); + svgGroup.transition().attr("transform", "translate(" + translateX + "," + translateY + ")scale(" + scale + ")"); + d3.select(domNode).select('g.node').attr("transform", "translate(" + translateX + "," + translateY + ")"); + zoomListener.scale(zoomListener.scale()); + zoomListener.translate([translateX, translateY]); + panTimer = setTimeout(function () { + pan(domNode, speed, direction); + }, 50); + } + } + // Define the zoom function for the zoomable tree + function zoom() { + svgGroup.attr("transform", "translate(" + d3.event.translate + ")scale(" + d3.event.scale + ")"); + } + // define the zoomListener which calls the zoom function on the "zoom" event constrained within the scaleExtents + var zoomListener = d3.behavior.zoom().scaleExtent([0.1, 3]).on("zoom", zoom); + function initiateDrag(d, domNode) { + draggingNode = d; + d3.select(domNode).select('.ghostCircle').attr('pointer-events', 'none'); + d3.selectAll('.ghostCircle').attr('class', 'ghostCircle show'); + d3.select(domNode).attr('class', 'node activeDrag'); + svgGroup.selectAll("g.node").sort(function (a, b) { + if (a.id != draggingNode.id) + return 1; // a is not the hovered element, send "a" to the back + else + return -1; // a is the hovered element, bring "a" to the front + }); + // if nodes has children, remove the links and nodes + if (nodes.length > 1) { + // remove link paths + links = tree.links(nodes); + nodePaths = svgGroup.selectAll("path.link") + .data(links, function (d) { + return d.target.id; + }).remove(); + // remove child nodes + nodesExit = svgGroup.selectAll("g.node") + .data(nodes, function (d) { + return d.id; + }).filter(function (d, i) { + if (d.id == draggingNode.id) { + return false; + } + return true; + }).remove(); + } + // remove parent link + parentLink = tree.links(tree.nodes(draggingNode.parent)); + svgGroup.selectAll('path.link').filter(function (d, i) { + if (d.target.id == draggingNode.id) { + return true; + } + return false; + }).remove(); + dragStarted = null; + } + // define the baseSvg, attaching a class for styling and the zoomListener + var baseSvg = d3.select("#tree-container").append("svg") + .attr("width", viewerWidth) + .attr("height", viewerHeight) + .attr("class", "overlay") + .call(zoomListener); + // Define the drag listeners for drag/drop behaviour of nodes. + dragListener = d3.behavior.drag() + .on("dragstart", function (d) { + if (d == root) { + return; + } + dragStarted = true; + nodes = tree.nodes(d); + d3.event.sourceEvent.stopPropagation(); + // it's important that we suppress the mouseover event on the node being dragged. Otherwise it will absorb the mouseover event and the underlying node will not detect it d3.select(this).attr('pointer-events', 'none'); + }) + .on("drag", function (d) { + if (d == root) { + return; + } + if (dragStarted) { + domNode = this; + initiateDrag(d, domNode); + } + // get coords of mouseEvent relative to svg container to allow for panning + relCoords = d3.mouse($('svg').get(0)); + if (relCoords[0] < panBoundary) { + panTimer = true; + pan(this, 'left'); + } + else if (relCoords[0] > ($('svg').width() - panBoundary)) { + panTimer = true; + pan(this, 'right'); + } + else if (relCoords[1] < panBoundary) { + panTimer = true; + pan(this, 'up'); + } + else if (relCoords[1] > ($('svg').height() - panBoundary)) { + panTimer = true; + pan(this, 'down'); + } + else { + try { + clearTimeout(panTimer); + } + catch (e) { + } + } + d.x0 += d3.event.dy; + d.y0 += d3.event.dx; + var node = d3.select(this); + node.attr("transform", "translate(" + d.y0 + "," + d.x0 + ")"); + updateTempConnector(); + }).on("dragend", function (d) { + if (d == root) { + return; + } + domNode = this; + if (selectedNode) { + // now remove the element from the parent, and insert it into the new elements children + var index = draggingNode.parent.children.indexOf(draggingNode); + if (index > -1) { + draggingNode.parent.children.splice(index, 1); + } + if (typeof selectedNode.children !== 'undefined' || typeof selectedNode._children !== 'undefined') { + if (typeof selectedNode.children !== 'undefined') { + selectedNode.children.push(draggingNode); + } + else { + selectedNode._children.push(draggingNode); + } + } + else { + selectedNode.children = []; + selectedNode.children.push(draggingNode); + } + // Make sure that the node being added to is expanded so user can see added node is correctly moved + expand(selectedNode); + sortTree(); + endDrag(); + } + else { + endDrag(); + } + }); + function endDrag() { + selectedNode = null; + d3.selectAll('.ghostCircle').attr('class', 'ghostCircle'); + d3.select(domNode).attr('class', 'node'); + // now restore the mouseover event or we won't be able to drag a 2nd time + d3.select(domNode).select('.ghostCircle').attr('pointer-events', ''); + updateTempConnector(); + if (draggingNode !== null) { + update(root); + centerNode(draggingNode); + draggingNode = null; + } + } + // Helper functions for collapsing and expanding nodes. + function collapse(d) { + if (d.children) { + d._children = d.children; + d._children.forEach(collapse); + d.children = null; + } + } + function expand(d) { + if (d._children) { + d.children = d._children; + d.children.forEach(expand); + d._children = null; + } + } + var overCircle = function (d) { + selectedNode = d; + updateTempConnector(); + }; + var outCircle = function (d) { + selectedNode = null; + updateTempConnector(); + }; + // Function to update the temporary connector indicating dragging affiliation + var updateTempConnector = function () { + var data = []; + if (draggingNode !== null && selectedNode !== null) { + // have to flip the source coordinates since we did this for the existing connectors on the original tree + data = [{ + source: { + x: selectedNode.y0, + y: selectedNode.x0 + }, + target: { + x: draggingNode.y0, + y: draggingNode.x0 + } + }]; + } + var link = svgGroup.selectAll(".templink").data(data); + link.enter().append("path") + .attr("class", "templink") + .attr("d", d3.svg.diagonal()) + .attr('pointer-events', 'none'); + link.attr("d", d3.svg.diagonal()); + link.exit().remove(); + }; + // Function to center node when clicked/dropped so node doesn't get lost when collapsing/moving with large amount of children. + function centerNode(source) { + scale = zoomListener.scale(); + x = -source.y0; + y = -source.x0; + x = x * scale + viewerWidth / 2; + y = y * scale + viewerHeight / 2; + d3.select('g').transition() + .duration(duration) + .attr("transform", "translate(" + x + "," + y + ")scale(" + scale + ")"); + zoomListener.scale(scale); + zoomListener.translate([x, y]); + } + // Toggle children function + function toggleChildren(d) { + if (d.children) { + d._children = d.children; + d.children = null; + } + else if (d._children) { + d.children = d._children; + d._children = null; + } + return d; + } + // Toggle children on click. + function click(d) { + if (d3.event.defaultPrevented) + return; // click suppressed + d = toggleChildren(d); + update(d); + centerNode(d); + } + function update(source) { + // Compute the new height, function counts total children of root node and sets tree height accordingly. + // This prevents the layout looking squashed when new nodes are made visible or looking sparse when nodes are removed + // This makes the layout more consistent. + var levelWidth = [1]; + var childCount = function (level, n) { + if (n.children && n.children.length > 0) { + if (levelWidth.length <= level + 1) + levelWidth.push(0); + levelWidth[level + 1] += n.children.length; + n.children.forEach(function (d) { + childCount(level + 1, d); + }); + } + }; + childCount(0, root); + var newHeight = d3.max(levelWidth) * 25; // 25 pixels per line + tree = tree.size([newHeight, viewerWidth]); + // Compute the new tree layout. + var nodes = tree.nodes(root).reverse(), links = tree.links(nodes); + // Set widths between levels based on maxLabelLength. + nodes.forEach(function (d) { + d.y = (d.depth * (maxLabelLength * 10)); 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"end" : "start"; + }) + .text(function (d) { + return d.name; + }) + .style("fill-opacity", 0); + // phantom node to give us mouseover in a radius around it + nodeEnter.append("circle") + .attr('class', 'ghostCircle') + .attr("r", 30) + .attr("opacity", 0.2) // change this to zero to hide the target area + .style("fill", "red") + .attr('pointer-events', 'mouseover') + .on("mouseover", function (node) { + overCircle(node); + }) + .on("mouseout", function (node) { + outCircle(node); + }); + // Update the text to reflect whether node has children or not. + node.select('text') + .attr("x", function (d) { + return d.children || d._children ? -10 : 10; + }) + .attr("text-anchor", function (d) { + return d.children || d._children ? "end" : "start"; + }) + .text(function (d) { + return d.name; + }); + // Change the circle fill depending on whether it has children and is collapsed + node.select("circle.nodeCircle") + .attr("r", 4.5) + .style("fill", function (d) { + return d._children ? "lightsteelblue" : "#fff"; + }); + // Transition nodes to their new position. + var nodeUpdate = node.transition() + .duration(duration) + .attr("transform", function (d) { + return "translate(" + d.y + "," + d.x + ")"; + }); + // Fade the text in + nodeUpdate.select("text") + .style("fill-opacity", 1); + // Transition exiting nodes to the parent's new position. + var nodeExit = node.exit().transition() + .duration(duration) + .attr("transform", function (d) { + return "translate(" + source.y + "," + source.x + ")"; + }) + .remove(); + nodeExit.select("circle") + .attr("r", 0); + nodeExit.select("text") + .style("fill-opacity", 0); + // Update the links… + var link = svgGroup.selectAll("path.link") + .data(links, function (d) { + return d.target.id; + }); + // Enter any new links at the parent's previous position. + link.enter().insert("path", "g") + .attr("class", "link") + .attr("d", function (d) { + var o = { + x: source.x0, + y: source.y0 + }; + return diagonal({ + source: o, + 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