Fix README

`nrows` may change if you restart the server; documented why this is
the case in the design.md file.  It's not a problem.

.gitignore

@@ -2,3 +2,6 @@ db/
 tests/*testdb/
 .coverage
 *.pyc
+design.html
+timeit*out
+

Makefile

@@ -8,11 +8,14 @@ tool:
 lint:
 	pylint -f parseable nilmdb
 
+%.html: %.md
+	pandoc -s $< > $@
+
 test:
-	nosetests
+	python runtests.py
 
 profile:
-	nosetests --with-profile 
+	python runtests.py --with-profile
 
 clean::
 	find . -name '*pyc' | xargs rm -f

README.txt

@@ -1,4 +1,3 @@
-sudo apt-get install python-nose python-coverage
-sudo apt-get install python-tables python-cherrypy3
+sudo apt-get install python2.7 python-cherrypy3 python-decorator python-nose python-coverage
 sudo apt-get install cython # 0.17.1-1 or newer
 

TODO

@@ -1 +1,5 @@
-- Merge adjacent intervals on insert (maybe with client help?)
+-- Clean up error responses.  Specifically I'd like to be able to add
+   json-formatted data to OverflowError and DB parsing errors.  It
+   seems like subclassing cherrypy.HTTPError and overriding
+   set_response is the best thing to do -- it would let me get rid
+   of the _be_ie_unfriendly and other hacks in the server.

design.md

@@ -1,11 +1,12 @@
 Structure
 ---------
-nilmdb.nilmdb is the NILM database interface.  It tracks a PyTables
-database holds actual rows of data, and a SQL database tracks metadata
-and ranges.
+nilmdb.nilmdb is the NILM database interface.  A nilmdb.BulkData
+interface stores data in flat files, and a SQL database tracks
+metadata and ranges.
 
 Access to the nilmdb must be single-threaded.  This is handled with
-the nilmdb.serializer class.
+the nilmdb.serializer class.  In the future this could probably
+be turned into a per-path serialization.
 
 nilmdb.server is a HTTP server that provides an interface to talk,
 thorugh the serialization layer, to the nilmdb object.
@@ -18,13 +19,13 @@ Sqlite performance
 Committing a transaction in the default sync mode (PRAGMA synchronous=FULL)
 takes about 125msec.  sqlite3 will commit transactions at 3 times:
 
-  1: explicit con.commit()
+1. explicit con.commit()
 
-  2: between a series of DML commands and non-DML commands, e.g.
+2. between a series of DML commands and non-DML commands, e.g.
    after a series of INSERT, SELECT, but before a CREATE TABLE or
    PRAGMA.
 
-3: at the end of an explicit transaction, e.g. "with self.con as con:"
+3. at the end of an explicit transaction, e.g. "with self.con as con:"
 
 To speed up testing, or if this transaction speed becomes an issue,
 the sync=False option to NilmDB will set PRAGMA synchronous=OFF.
@@ -47,6 +48,7 @@ transfer?
   everything still gets buffered.  Just a tradeoff of buffer size.
 
 Before timestamps are added:
+
 - Raw data is about 440 kB/s    (9 channels)
 - Prep data is about 12.5 kB/s  (1 phase)
 - How do we know how much data to send?
@@ -62,6 +64,7 @@ Before timestamps are added:
     - Should those numbers come from the server?
 
 Converting from ASCII to PyTables:
+
 - For each row getting added, we need to set attributes on a PyTables
   Row object and call table.append().  This means that there isn't a
   particularly efficient way of converting from ascii.
@@ -138,10 +141,19 @@ Speed
 - Next slowdown target is nilmdb.layout.Parser.parse().
     - Rewrote parsers using cython and sscanf
     - Stats (rev 10831), with _add_interval disabled
+
         layout.pyx.Parser.parse:128        6303 sec, 262k calls
          layout.pyx.parse:63               13913 sec, 5.1g calls
         numpy:records.py.fromrecords:569   7410 sec, 262k calls
-  - Probably OK for now.
+
+- Probably OK for now.
+
+- After all updates, now takes about 8.5 minutes to insert an hour of
+  data, constant after adding 171 hours (4.9 billion data points)
+
+- Data set size: 98 gigs = 20 bytes per data point.
+  6 uint16 data + 1 uint32 timestamp = 16 bytes per point
+  So compression must be off -- will retry with compression forced on.
 
 IntervalSet speed
 -----------------
@@ -191,3 +203,66 @@ handlers.  For compatibility:
     "RawData" == "uint16_6"
     "RawNotchedData" == "uint16_9"
     "PrepData" == "float32_8"
+
+
+BulkData design
+---------------
+
+BulkData is a custom bulk data storage system that was written to
+replace PyTables.  The general structure is a `data` subdirectory in
+the main NilmDB directory.  Within `data`, paths are created for each
+created stream.  These locations are called tables.  For example,
+tables might be located at
+
+    nilmdb/data/newton/raw/
+    nilmdb/data/newton/prep/
+    nilmdb/data/cottage/raw/
+
+Each table contains:
+
+- An unchanging `_format` file (Python pickle format) that describes
+  parameters of how the data is broken up, like files per directory,
+  rows per file, and the binary data format
+
+- Hex named subdirectories `("%04x", although more than 65536 can exist)`
+
+- Hex named files within those subdirectories, like:
+
+        /nilmdb/data/newton/raw/000b/010a
+
+    The data format of these files is raw binary, interpreted by the
+    Python `struct` module according to the format string in the
+    `_format` file.
+
+- Same as above, with `.removed` suffix, is an optional file (Python
+  pickle format) containing a list of row numbers that have been
+  logically removed from the file.  If this range covers the entire
+  file, the entire file will be removed.
+
+- Note that the `bulkdata.nrows` variable is calculated once in
+  `BulkData.__init__()`, and only ever incremented during use.  Thus,
+  even if all data is removed, `nrows` can remain high.  However, if
+  the server is restarted, the newly calculated `nrows` may be lower
+  than in a previous run due to deleted data.  To be specific, this
+  sequence of events:
+
+    - insert data
+    - remove all data
+    - insert data
+
+    will result in having different row numbers in the database, and
+    differently numbered files on the filesystem, than the sequence:
+
+    - insert data
+    - remove all data
+    - restart server
+    - insert data
+
+    This is okay!  Everything should remain consistent both in the
+    `BulkData` and `NilmDB`.  Not attempting to readjust `nrows` during
+    deletion makes the code quite a bit simpler.
+
+- Similarly, data files are never truncated shorter.  Removing data
+  from the end of the file will not shorten it; it will only be
+  deleted when it has been fully filled and all of the data has been
+  subsequently removed.

nilmdb/RedBlackTree.cc

@@ -1,605 +0,0 @@
-
-
-
-// The RedBlackEntry class is an Abstract Base Class.  This means that no
-// instance of the RedBlackEntry class can exist.  Only classes which
-// inherit from the RedBlackEntry class can exist.  Furthermore any class
-// which inherits from the RedBlackEntry class must define the member
-// function GetKey().  The Print() member function does not have to
-// be defined because a default definition exists.
-//
-// The GetKey() function should return an integer key for that entry.
-// The key for an entry should never change otherwise bad things might occur.
-
-class RedBlackEntry {
-public:
-  RedBlackEntry();
-  virtual ~RedBlackEntry();
-  virtual int GetKey() const = 0;
-  virtual void Print() const;
-};
-
-class RedBlackTreeNode {
-  friend class RedBlackTree;
-public:
-  void Print(RedBlackTreeNode*,
-	     RedBlackTreeNode*) const;
-  RedBlackTreeNode();
-  RedBlackTreeNode(RedBlackEntry *);
-  RedBlackEntry * GetEntry() const;
-  ~RedBlackTreeNode();
-protected:
-  RedBlackEntry * storedEntry;
-  int key;
-  int red; /* if red=0 then the node is black */
-  RedBlackTreeNode * left;
-  RedBlackTreeNode * right;
-  RedBlackTreeNode * parent;
-};
-
-
-
-class RedBlackTree {
-public:
-  RedBlackTree();
-  ~RedBlackTree();
-  void Print() const;
-  RedBlackEntry * DeleteNode(RedBlackTreeNode *);
-  RedBlackTreeNode * Insert(RedBlackEntry *);
-  RedBlackTreeNode * GetPredecessorOf(RedBlackTreeNode *) const;
-  RedBlackTreeNode * GetSuccessorOf(RedBlackTreeNode *) const;
-  RedBlackTreeNode * Search(int key);
-  TemplateStack<RedBlackTreeNode *> * Enumerate(int low, int high) ;
-  void CheckAssumptions() const;
-protected:
-  /*  A sentinel is used for root and for nil.  These sentinels are */
-  /*  created when RedBlackTreeCreate is caled.  root->left should always */
-  /*  point to the node which is the root of the tree.  nil points to a */
-  /*  node which should always be black but has aribtrary children and */
-  /*  parent and no key or info.  The point of using these sentinels is so */
-  /*  that the root and nil nodes do not require special cases in the code */
-  RedBlackTreeNode * root;
-  RedBlackTreeNode * nil;
-  void LeftRotate(RedBlackTreeNode *);
-  void RightRotate(RedBlackTreeNode *);
-  void TreeInsertHelp(RedBlackTreeNode *);
-  void TreePrintHelper(RedBlackTreeNode *) const;
-  void FixUpMaxHigh(RedBlackTreeNode *);
-  void DeleteFixUp(RedBlackTreeNode *);
-};
-
-const int MIN_INT=-MAX_INT;
-
-RedBlackTreeNode::RedBlackTreeNode(){
-};
-
-RedBlackTreeNode::RedBlackTreeNode(RedBlackEntry * newEntry)
-  : storedEntry (newEntry) , key(newEntry->GetKey()) {
-};
-
-RedBlackTreeNode::~RedBlackTreeNode(){
-};
-
-RedBlackEntry * RedBlackTreeNode::GetEntry() const {return storedEntry;}
-
-RedBlackEntry::RedBlackEntry(){
-};
-RedBlackEntry::~RedBlackEntry(){
-};
-void RedBlackEntry::Print() const {
-  cout << "No Print Method defined. Using Default: " << GetKey() << endl;
-}
-
-RedBlackTree::RedBlackTree()
-{
-  nil = new RedBlackTreeNode;
-  nil->left = nil->right = nil->parent = nil;
-  nil->red = 0;
-  nil->key = MIN_INT;
-  nil->storedEntry = NULL;
-
-  root = new RedBlackTreeNode;
-  root->parent = root->left = root->right = nil;
-  root->key = MAX_INT;
-  root->red=0;
-  root->storedEntry = NULL;
-}
-
-/***********************************************************************/
-/*  FUNCTION:  LeftRotate */
-/**/
-/*  INPUTS:  the node to rotate on */
-/**/
-/*  OUTPUT:  None */
-/**/
-/*  Modifies Input: this, x */
-/**/
-/*  EFFECTS:  Rotates as described in _Introduction_To_Algorithms by */
-/*            Cormen, Leiserson, Rivest (Chapter 14).  Basically this */
-/*            makes the parent of x be to the left of x, x the parent of */
-/*            its parent before the rotation and fixes other pointers */
-/*            accordingly.  */
-/***********************************************************************/
-
-void RedBlackTree::LeftRotate(RedBlackTreeNode* x) {
-  RedBlackTreeNode* y;
-
-  /*  I originally wrote this function to use the sentinel for */
-  /*  nil to avoid checking for nil.  However this introduces a */
-  /*  very subtle bug because sometimes this function modifies */
-  /*  the parent pointer of nil.  This can be a problem if a */
-  /*  function which calls LeftRotate also uses the nil sentinel */
-  /*  and expects the nil sentinel's parent pointer to be unchanged */
-  /*  after calling this function.  For example, when DeleteFixUP */
-  /*  calls LeftRotate it expects the parent pointer of nil to be */
-  /*  unchanged. */
-
-  y=x->right;
-  x->right=y->left;
-
-  if (y->left != nil) y->left->parent=x; /* used to use sentinel here */
-  /* and do an unconditional assignment instead of testing for nil */
-
-  y->parent=x->parent;
-
-  /* instead of checking if x->parent is the root as in the book, we */
-  /* count on the root sentinel to implicitly take care of this case */
-  if( x == x->parent->left) {
-    x->parent->left=y;
-  } else {
-    x->parent->right=y;
-  }
-  y->left=x;
-  x->parent=y;
-}
-
-/***********************************************************************/
-/*  FUNCTION:  RighttRotate */
-/**/
-/*  INPUTS:  node to rotate on */
-/**/
-/*  OUTPUT:  None */
-/**/
-/*  Modifies Input?: this, y */
-/**/
-/*  EFFECTS:  Rotates as described in _Introduction_To_Algorithms by */
-/*            Cormen, Leiserson, Rivest (Chapter 14).  Basically this */
-/*            makes the parent of x be to the left of x, x the parent of */
-/*            its parent before the rotation and fixes other pointers */
-/*            accordingly.  */
-/***********************************************************************/
-
-void RedBlackTree::RightRotate(RedBlackTreeNode* y) {
-  RedBlackTreeNode* x;
-
-  /*  I originally wrote this function to use the sentinel for */
-  /*  nil to avoid checking for nil.  However this introduces a */
-  /*  very subtle bug because sometimes this function modifies */
-  /*  the parent pointer of nil.  This can be a problem if a */
-  /*  function which calls LeftRotate also uses the nil sentinel */
-  /*  and expects the nil sentinel's parent pointer to be unchanged */
-  /*  after calling this function.  For example, when DeleteFixUP */
-  /*  calls LeftRotate it expects the parent pointer of nil to be */
-  /*  unchanged. */
-
-  x=y->left;
-  y->left=x->right;
-
-  if (nil != x->right)  x->right->parent=y; /*used to use sentinel here */
-  /* and do an unconditional assignment instead of testing for nil */
-
-  /* instead of checking if x->parent is the root as in the book, we */
-  /* count on the root sentinel to implicitly take care of this case */
-  x->parent=y->parent;
-  if( y == y->parent->left) {
-    y->parent->left=x;
-  } else {
-    y->parent->right=x;
-  }
-  x->right=y;
-  y->parent=x;
-}
-
-/***********************************************************************/
-/*  FUNCTION:  TreeInsertHelp  */
-/**/
-/*  INPUTS:  z is the node to insert */
-/**/
-/*  OUTPUT:  none */
-/**/
-/*  Modifies Input:  this, z */
-/**/
-/*  EFFECTS:  Inserts z into the tree as if it were a regular binary tree */
-/*            using the algorithm described in _Introduction_To_Algorithms_ */
-/*            by Cormen et al.  This funciton is only intended to be called */
-/*            by the Insert function and not by the user */
-/***********************************************************************/
-
-void RedBlackTree::TreeInsertHelp(RedBlackTreeNode* z) {
-  /*  This function should only be called by RedBlackTree::Insert */
-  RedBlackTreeNode* x;
-  RedBlackTreeNode* y;
-
-  z->left=z->right=nil;
-  y=root;
-  x=root->left;
-  while( x != nil) {
-    y=x;
-    if ( x->key > z->key) {
-      x=x->left;
-    } else { /* x->key <= z->key */
-      x=x->right;
-    }
-  }
-  z->parent=y;
-  if ( (y == root) ||
-       (y->key > z->key) ) {
-    y->left=z;
-  } else {
-    y->right=z;
-  }
-}
-
-/*  Before calling InsertNode  the node x should have its key set */
-
-/***********************************************************************/
-/*  FUNCTION:  InsertNode */
-/**/
-/*  INPUTS:  newEntry is the entry to insert*/
-/**/
-/*  OUTPUT:  This function returns a pointer to the newly inserted node */
-/*           which is guarunteed to be valid until this node is deleted. */
-/*           What this means is if another data structure stores this */
-/*           pointer then the tree does not need to be searched when this */
-/*           is to be deleted. */
-/**/
-/*  Modifies Input: tree */
-/**/
-/*  EFFECTS:  Creates a node node which contains the appropriate key and */
-/*            info pointers and inserts it into the tree. */
-/***********************************************************************/
-/* jim */
-RedBlackTreeNode * RedBlackTree::Insert(RedBlackEntry * newEntry)
-{
-  RedBlackTreeNode * y;
-  RedBlackTreeNode * x;
-  RedBlackTreeNode * newNode;
-
-  x = new RedBlackTreeNode(newEntry);
-  TreeInsertHelp(x);
-  newNode = x;
-  x->red=1;
-  while(x->parent->red) { /* use sentinel instead of checking for root */
-    if (x->parent == x->parent->parent->left) {
-      y=x->parent->parent->right;
-      if (y->red) {
-	x->parent->red=0;
-	y->red=0;
-	x->parent->parent->red=1;
-	x=x->parent->parent;
-      } else {
-	if (x == x->parent->right) {
-	  x=x->parent;
-	  LeftRotate(x);
-	}
-	x->parent->red=0;
-	x->parent->parent->red=1;
-	RightRotate(x->parent->parent);
-      }
-    } else { /* case for x->parent == x->parent->parent->right */
-             /* this part is just like the section above with */
-             /* left and right interchanged */
-      y=x->parent->parent->left;
-      if (y->red) {
-	x->parent->red=0;
-	y->red=0;
-	x->parent->parent->red=1;
-	x=x->parent->parent;
-      } else {
-	if (x == x->parent->left) {
-	  x=x->parent;
-	  RightRotate(x);
-	}
-	x->parent->red=0;
-	x->parent->parent->red=1;
-	LeftRotate(x->parent->parent);
-      }
-    }
-  }
-  root->left->red=0;
-  return(newNode);
-}
-
-/***********************************************************************/
-/*  FUNCTION:  GetSuccessorOf  */
-/**/
-/*    INPUTS:  x is the node we want the succesor of */
-/**/
-/*    OUTPUT:  This function returns the successor of x or NULL if no */
-/*             successor exists. */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    Note:  uses the algorithm in _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-RedBlackTreeNode * RedBlackTree::GetSuccessorOf(RedBlackTreeNode * x) const
-{
-  RedBlackTreeNode* y;
-
-  if (nil != (y = x->right)) { /* assignment to y is intentional */
-    while(y->left != nil) { /* returns the minium of the right subtree of x */
-      y=y->left;
-    }
-    return(y);
-  } else {
-    y=x->parent;
-    while(x == y->right) { /* sentinel used instead of checking for nil */
-      x=y;
-      y=y->parent;
-    }
-    if (y == root) return(nil);
-    return(y);
-  }
-}
-
-/***********************************************************************/
-/*  FUNCTION:  GetPredecessorOf  */
-/**/
-/*    INPUTS:  x is the node to get predecessor of */
-/**/
-/*    OUTPUT:  This function returns the predecessor of x or NULL if no */
-/*             predecessor exists. */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    Note:  uses the algorithm in _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-RedBlackTreeNode * RedBlackTree::GetPredecessorOf(RedBlackTreeNode * x) const {
-  RedBlackTreeNode* y;
-
-  if (nil != (y = x->left)) { /* assignment to y is intentional */
-    while(y->right != nil) { /* returns the maximum of the left subtree of x */
-      y=y->right;
-    }
-    return(y);
-  } else {
-    y=x->parent;
-    while(x == y->left) {
-      if (y == root) return(nil);
-      x=y;
-      y=y->parent;
-    }
-    return(y);
-  }
-}
-
-/***********************************************************************/
-/*  FUNCTION:  Print */
-/**/
-/*    INPUTS:  none */
-/**/
-/*    OUTPUT:  none  */
-/**/
-/*    EFFECTS:  This function recursively prints the nodes of the tree */
-/*              inorder. */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    Note:    This function should only be called from ITTreePrint */
-/***********************************************************************/
-
-void RedBlackTreeNode::Print(RedBlackTreeNode * nil,
-			     RedBlackTreeNode * root) const {
-  storedEntry->Print();
-  printf(", key=%i ",key);
-  printf("  l->key=");
-  if( left == nil) printf("NULL"); else printf("%i",left->key);
-  printf("  r->key=");
-  if( right == nil) printf("NULL"); else printf("%i",right->key);
-  printf("  p->key=");
-  if( parent == root) printf("NULL"); else printf("%i",parent->key);
-  printf("  red=%i\n",red);
-}
-
-void RedBlackTree::TreePrintHelper( RedBlackTreeNode* x) const {
-
-  if (x != nil) {
-    TreePrintHelper(x->left);
-    x->Print(nil,root);
-    TreePrintHelper(x->right);
-  }
-}
-
-/***********************************************************************/
-/*  FUNCTION:  Print */
-/**/
-/*    INPUTS:  none */
-/**/
-/*    OUTPUT:  none */
-/**/
-/*    EFFECT:  This function recursively prints the nodes of the tree */
-/*             inorder. */
-/**/
-/*    Modifies Input: none */
-/**/
-/***********************************************************************/
-
-void RedBlackTree::Print() const {
-  TreePrintHelper(root->left);
-}
-
-/***********************************************************************/
-/*  FUNCTION:  DeleteFixUp */
-/**/
-/*    INPUTS:  x is the child of the spliced */
-/*             out node in DeleteNode. */
-/**/
-/*    OUTPUT:  none */
-/**/
-/*    EFFECT:  Performs rotations and changes colors to restore red-black */
-/*             properties after a node is deleted */
-/**/
-/*    Modifies Input: this, x */
-/**/
-/*    The algorithm from this function is from _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-void RedBlackTree::DeleteFixUp(RedBlackTreeNode* x) {
-  RedBlackTreeNode * w;
-  RedBlackTreeNode * rootLeft = root->left;
-
-  while( (!x->red) && (rootLeft != x)) {
-    if (x == x->parent->left) {
-
-//
-      w=x->parent->right;
-      if (w->red) {
-	w->red=0;
-	x->parent->red=1;
-	LeftRotate(x->parent);
-	w=x->parent->right;
-      }
-      if ( (!w->right->red) && (!w->left->red) ) {
-	w->red=1;
-	x=x->parent;
-      } else {
-	if (!w->right->red) {
-	  w->left->red=0;
-	  w->red=1;
-	  RightRotate(w);
-	  w=x->parent->right;
-	}
-	w->red=x->parent->red;
-	x->parent->red=0;
-	w->right->red=0;
-	LeftRotate(x->parent);
-	x=rootLeft; /* this is to exit while loop */
-      }
-//
-
-    } else { /* the code below is has left and right switched from above */
-      w=x->parent->left;
-      if (w->red) {
-	w->red=0;
-	x->parent->red=1;
-	RightRotate(x->parent);
-	w=x->parent->left;
-      }
-      if ( (!w->right->red) && (!w->left->red) ) {
-	w->red=1;
-	x=x->parent;
-      } else {
-	if (!w->left->red) {
-	  w->right->red=0;
-	  w->red=1;
-	  LeftRotate(w);
-	  w=x->parent->left;
-	}
-	w->red=x->parent->red;
-	x->parent->red=0;
-	w->left->red=0;
-	RightRotate(x->parent);
-	x=rootLeft; /* this is to exit while loop */
-      }
-    }
-  }
-  x->red=0;
-
-}
-
-
-/***********************************************************************/
-/*  FUNCTION:  DeleteNode */
-/**/
-/*    INPUTS:  tree is the tree to delete node z from */
-/**/
-/*    OUTPUT:  returns the RedBlackEntry stored at deleted node */
-/**/
-/*    EFFECT:  Deletes z from tree and but don't call destructor */
-/**/
-/*    Modifies Input:  z */
-/**/
-/*    The algorithm from this function is from _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-RedBlackEntry * RedBlackTree::DeleteNode(RedBlackTreeNode * z){
-  RedBlackTreeNode* y;
-  RedBlackTreeNode* x;
-  RedBlackEntry * returnValue = z->storedEntry;
-
-  y= ((z->left == nil) || (z->right == nil)) ? z : GetSuccessorOf(z);
-  x= (y->left == nil) ? y->right : y->left;
-  if (root == (x->parent = y->parent)) { /* assignment of y->p to x->p is intentional */
-    root->left=x;
-  } else {
-    if (y == y->parent->left) {
-      y->parent->left=x;
-    } else {
-      y->parent->right=x;
-    }
-  }
-  if (y != z) { /* y should not be nil in this case */
-
-    /* y is the node to splice out and x is its child */
-
-    y->left=z->left;
-    y->right=z->right;
-    y->parent=z->parent;
-    z->left->parent=z->right->parent=y;
-    if (z == z->parent->left) {
-      z->parent->left=y;
-    } else {
-      z->parent->right=y;
-    }
-    if (!(y->red)) {
-      y->red = z->red;
-      DeleteFixUp(x);
-    } else
-      y->red = z->red;
-    delete z;
-  } else {
-    if (!(y->red)) DeleteFixUp(x);
-    delete y;
-  }
-  return returnValue;
-}
-
-
-/***********************************************************************/
-/*  FUNCTION:  Enumerate */
-/**/
-/*    INPUTS:  tree is the tree to look for keys between [low,high] */
-/**/
-/*    OUTPUT:  stack containing pointers to the nodes between [low,high] */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    EFFECT:  Returns a stack containing pointers to nodes containing */
-/*             keys which in [low,high]/ */
-/**/
-/***********************************************************************/
-
-TemplateStack<RedBlackTreeNode *> * RedBlackTree::Enumerate(int low,
-							    int high)  {
-  TemplateStack<RedBlackTreeNode *> * enumResultStack =
-    new TemplateStack<RedBlackTreeNode *>(4);
-
-  RedBlackTreeNode* x=root->left;
-  RedBlackTreeNode* lastBest=NULL;
-
-  while(nil != x) {
-    if ( x->key > high ) {
-      x=x->left;
-    } else {
-      lastBest=x;
-      x=x->right;
-    }
-  }
-  while ( (lastBest) && (low <= lastBest->key) ) {
-    enumResultStack->Push(lastBest);
-    lastBest=GetPredecessorOf(lastBest);
-  }
-  return(enumResultStack);
-}

nilmdb/__init__.py

@@ -3,14 +3,10 @@
 from .nilmdb import NilmDB
 from .server import Server
 from .client import Client
-from .timer import Timer
-
-import cmdline
 
 import pyximport; pyximport.install()
 import layout
-
-import serializer
-import timestamper
 import interval
-import du
+
+import cmdline
+

nilmdb/bulkdata.py

@@ -0,0 +1,460 @@
+# Fixed record size bulk data storage
+
+from __future__ import absolute_import
+from __future__ import division
+import nilmdb
+from nilmdb.utils.printf import *
+
+import os
+import sys
+import cPickle as pickle
+import struct
+import fnmatch
+import mmap
+import re
+
+# Up to 256 open file descriptors at any given time.
+# These variables are global so they can be used in the decorator arguments.
+table_cache_size = 16
+fd_cache_size = 16
+
+@nilmdb.utils.must_close(wrap_verify = True)
+class BulkData(object):
+    def __init__(self, basepath, **kwargs):
+        self.basepath = basepath
+        self.root = os.path.join(self.basepath, "data")
+
+        # Tuneables
+        if "file_size" in kwargs:
+            self.file_size = kwargs["file_size"]
+        else:
+            # Default to approximately 128 MiB per file
+            self.file_size = 128 * 1024 * 1024
+
+        if "files_per_dir" in kwargs:
+            self.files_per_dir = kwargs["files_per_dir"]
+        else:
+            # 32768 files per dir should work even on FAT32
+            self.files_per_dir = 32768
+
+        # Make root path
+        if not os.path.isdir(self.root):
+            os.mkdir(self.root)
+
+    def close(self):
+        self.getnode.cache_remove_all()
+
+    def _encode_filename(self, path):
+        # Encode all paths to UTF-8, regardless of sys.getfilesystemencoding(),
+        # because we want to be able to represent all code points and the user
+        # will never be directly exposed to filenames.  We can then do path
+        # manipulations on the UTF-8 directly.
+        if isinstance(path, unicode):
+            return path.encode('utf-8')
+        return path
+
+    def create(self, unicodepath, layout_name):
+        """
+        unicodepath: path to the data (e.g. u'/newton/prep').
+        Paths must contain at least two elements, e.g.:
+           /newton/prep
+           /newton/raw
+           /newton/upstairs/prep
+           /newton/upstairs/raw
+
+        layout_name: string for nilmdb.layout.get_named(), e.g. 'float32_8'
+        """
+        path = self._encode_filename(unicodepath)
+
+        if path[0] != '/':
+            raise ValueError("paths must start with /")
+        [ group, node ] = path.rsplit("/", 1)
+        if group == '':
+            raise ValueError("invalid path; path must contain at least one "
+                             "folder")
+
+        # Get layout, and build format string for struct module
+        try:
+            layout = nilmdb.layout.get_named(layout_name)
+            struct_fmt = '<d'  # Little endian, double timestamp
+            struct_mapping = {
+                "int8": 'b',
+                "uint8": 'B',
+                "int16": 'h',
+                "uint16": 'H',
+                "int32": 'i',
+                "uint32": 'I',
+                "int64": 'q',
+                "uint64": 'Q',
+                "float32": 'f',
+                "float64": 'd',
+                }
+            for n in range(layout.count):
+                struct_fmt += struct_mapping[layout.datatype]
+        except KeyError:
+            raise ValueError("no such layout, or bad data types")
+
+        # Create the table.  Note that we make a distinction here
+        # between NilmDB paths (always Unix style, split apart
+        # manually) and OS paths (built up with os.path.join)
+
+        # Make directories leading up to this one
+        elements = path.lstrip('/').split('/')
+        for i in range(len(elements)):
+            ospath = os.path.join(self.root, *elements[0:i])
+            if Table.exists(ospath):
+                raise ValueError("path is subdir of existing node")
+            if not os.path.isdir(ospath):
+                os.mkdir(ospath)
+
+        # Make the final dir
+        ospath = os.path.join(self.root, *elements)
+        if os.path.isdir(ospath):
+            raise ValueError("subdirs of this path already exist")
+        os.mkdir(ospath)
+
+        # Write format string to file
+        Table.create(ospath, struct_fmt, self.file_size, self.files_per_dir)
+
+        # Open and cache it
+        self.getnode(unicodepath)
+
+        # Success
+        return
+
+    def destroy(self, unicodepath):
+        """Fully remove all data at a particular path.  No way to undo
+        it!  The group/path structure is removed, too."""
+        path = self._encode_filename(unicodepath)
+
+        # Get OS path
+        elements = path.lstrip('/').split('/')
+        ospath = os.path.join(self.root, *elements)
+
+        # Remove Table object from cache
+        self.getnode.cache_remove(self, unicodepath)
+
+        # Remove the contents of the target directory
+        if not Table.exists(ospath):
+            raise ValueError("nothing at that path")
+        for (root, dirs, files) in os.walk(ospath, topdown = False):
+            for name in files:
+                os.remove(os.path.join(root, name))
+            for name in dirs:
+                os.rmdir(os.path.join(root, name))
+
+        # Remove empty parent directories
+        for i in reversed(range(len(elements))):
+            ospath = os.path.join(self.root, *elements[0:i+1])
+            try:
+                os.rmdir(ospath)
+            except OSError:
+                break
+
+    # Cache open tables
+    @nilmdb.utils.lru_cache(size = table_cache_size,
+                            onremove = lambda x: x.close())
+    def getnode(self, unicodepath):
+        """Return a Table object corresponding to the given database
+        path, which must exist."""
+        path = self._encode_filename(unicodepath)
+        elements = path.lstrip('/').split('/')
+        ospath = os.path.join(self.root, *elements)
+        return Table(ospath)
+
+@nilmdb.utils.must_close(wrap_verify = True)
+class Table(object):
+    """Tools to help access a single table (data at a specific OS path)."""
+    # See design.md for design details
+
+    # Class methods, to help keep format details in this class.
+    @classmethod
+    def exists(cls, root):
+        """Return True if a table appears to exist at this OS path"""
+        return os.path.isfile(os.path.join(root, "_format"))
+
+    @classmethod
+    def create(cls, root, struct_fmt, file_size, files_per_dir):
+        """Initialize a table at the given OS path.
+        'struct_fmt' is a Struct module format description"""
+
+        # Calculate rows per file so that each file is approximately
+        # file_size bytes.
+        packer = struct.Struct(struct_fmt)
+        rows_per_file = max(file_size // packer.size, 1)
+
+        format = { "rows_per_file": rows_per_file,
+                   "files_per_dir": files_per_dir,
+                   "struct_fmt": struct_fmt,
+                   "version": 1 }
+        with open(os.path.join(root, "_format"), "wb") as f:
+            pickle.dump(format, f, 2)
+
+    # Normal methods
+    def __init__(self, root):
+        """'root' is the full OS path to the directory of this table"""
+        self.root = root
+
+        # Load the format and build packer
+        with open(os.path.join(self.root, "_format"), "rb") as f:
+            format = pickle.load(f)
+
+        if format["version"] != 1: # pragma: no cover (just future proofing)
+            raise NotImplementedError("version " + format["version"] +
+                                      " bulk data store not supported")
+
+        self.rows_per_file = format["rows_per_file"]
+        self.files_per_dir = format["files_per_dir"]
+        self.packer = struct.Struct(format["struct_fmt"])
+        self.file_size = self.packer.size * self.rows_per_file
+
+        # Find nrows
+        self.nrows = self._get_nrows()
+
+    def close(self):
+        self.mmap_open.cache_remove_all()
+
+    # Internal helpers
+    def _get_nrows(self):
+        """Find nrows by locating the lexicographically last filename
+        and using its size"""
+        # Note that this just finds a 'nrows' that is guaranteed to be
+        # greater than the row number of any piece of data that
+        # currently exists, not necessarily all data that _ever_
+        # existed.
+        regex = re.compile("^[0-9a-f]{4,}$")
+
+        # Find the last directory.  We sort and loop through all of them,
+        # starting with the numerically greatest, because the dirs could be
+        # empty if something was deleted.
+        subdirs = sorted(filter(regex.search, os.listdir(self.root)),
+                         key = lambda x: int(x, 16), reverse = True)
+
+        for subdir in subdirs:
+            # Now find the last file in that dir
+            path = os.path.join(self.root, subdir)
+            files = filter(regex.search, os.listdir(path))
+            if not files: # pragma: no cover (shouldn't occur)
+                # Empty dir: try the next one
+                continue
+
+            # Find the numerical max
+            filename = max(files, key = lambda x: int(x, 16))
+            offset = os.path.getsize(os.path.join(self.root, subdir, filename))
+
+            # Convert to row number
+            return self._row_from_offset(subdir, filename, offset)
+
+        # No files, so no data
+        return 0
+
+    def _offset_from_row(self, row):
+        """Return a (subdir, filename, offset, count) tuple:
+
+          subdir: subdirectory for the file
+        filename: the filename that contains the specified row
+          offset: byte offset of the specified row within the file
+           count: number of rows (starting at offset) that fit in the file
+        """
+        filenum = row // self.rows_per_file
+        # It's OK if these format specifiers are too short; the filenames
+        # will just get longer but will still sort correctly.
+        dirname = sprintf("%04x", filenum // self.files_per_dir)
+        filename = sprintf("%04x", filenum % self.files_per_dir)
+        offset = (row % self.rows_per_file) * self.packer.size
+        count = self.rows_per_file - (row % self.rows_per_file)
+        return (dirname, filename, offset, count)
+
+    def _row_from_offset(self, subdir, filename, offset):
+        """Return the row number that corresponds to the given
+        'subdir/filename' and byte-offset within that file."""
+        if (offset % self.packer.size) != 0: # pragma: no cover; shouldn't occur
+            raise ValueError("file offset is not a multiple of data size")
+        filenum = int(subdir, 16) * self.files_per_dir + int(filename, 16)
+        row = (filenum * self.rows_per_file) + (offset // self.packer.size)
+        return row
+
+    # Cache open files
+    @nilmdb.utils.lru_cache(size = fd_cache_size,
+                            keys = slice(0,3), # exclude newsize
+                            onremove = lambda x: x.close())
+    def mmap_open(self, subdir, filename, newsize = None):
+        """Open and map a given 'subdir/filename' (relative to self.root).
+        Will be automatically closed when evicted from the cache.
+
+        If 'newsize' is provided, the file is truncated to the given
+        size before the mapping is returned.  (Note that the LRU cache
+        on this function means the truncate will only happen if the
+        object isn't already cached; mmap.resize should be used too.)"""
+        try:
+            os.mkdir(os.path.join(self.root, subdir))
+        except OSError:
+            pass
+        f = open(os.path.join(self.root, subdir, filename), "a+", 0)
+        if newsize is not None:
+            # mmap can't map a zero-length file, so this allows the
+            # caller to set the filesize between file creation and
+            # mmap.
+            f.truncate(newsize)
+        mm = mmap.mmap(f.fileno(), 0)
+        return mm
+
+    def mmap_open_resize(self, subdir, filename, newsize):
+        """Open and map a given 'subdir/filename' (relative to self.root).
+        The file is resized to the given size."""
+        # Pass new size to mmap_open
+        mm = self.mmap_open(subdir, filename, newsize)
+        # In case we got a cached copy, need to call mm.resize too.
+        mm.resize(newsize)
+        return mm
+
+    def append(self, data):
+        """Append the data and flush it to disk.
+        data is a nested Python list [[row],[row],[...]]"""
+        remaining = len(data)
+        dataiter = iter(data)
+        while remaining:
+            # See how many rows we can fit into the current file, and open it
+            (subdir, fname, offset, count) = self._offset_from_row(self.nrows)
+            if count > remaining:
+                count = remaining
+            newsize = offset + count * self.packer.size
+            mm = self.mmap_open_resize(subdir, fname, newsize)
+            mm.seek(offset)
+
+            # Write the data
+            for i in xrange(count):
+                row = dataiter.next()
+                mm.write(self.packer.pack(*row))
+            remaining -= count
+            self.nrows += count
+
+    def __getitem__(self, key):
+        """Extract data and return it.  Supports simple indexing
+        (table[n]) and range slices (table[n:m]).  Returns a nested
+        Python list [[row],[row],[...]]"""
+
+        # Handle simple slices
+        if isinstance(key, slice):
+            # Fall back to brute force if the slice isn't simple
+            if ((key.step is not None and key.step != 1) or
+                key.start is None or
+                key.stop is None or
+                key.start >= key.stop or
+                key.start < 0 or
+                key.stop > self.nrows):
+                return [ self[x] for x in xrange(*key.indices(self.nrows)) ]
+
+            ret = []
+            row = key.start
+            remaining = key.stop - key.start
+            while remaining:
+                (subdir, filename, offset, count) = self._offset_from_row(row)
+                if count > remaining:
+                    count = remaining
+                mm = self.mmap_open(subdir, filename)
+                for i in xrange(count):
+                    ret.append(list(self.packer.unpack_from(mm, offset)))
+                    offset += self.packer.size
+                remaining -= count
+                row += count
+            return ret
+
+        # Handle single points
+        if key < 0 or key >= self.nrows:
+            raise IndexError("Index out of range")
+        (subdir, filename, offset, count) = self._offset_from_row(key)
+        mm = self.mmap_open(subdir, filename)
+        # unpack_from ignores the mmap object's current seek position
+        return list(self.packer.unpack_from(mm, offset))
+
+    def _remove_rows(self, subdir, filename, start, stop):
+        """Helper to mark specific rows as being removed from a
+        file, and potentially removing or truncating the file itself."""
+        # Import an existing list of deleted rows for this file
+        datafile = os.path.join(self.root, subdir, filename)
+        cachefile = datafile + ".removed"
+        try:
+            with open(cachefile, "rb") as f:
+                ranges = pickle.load(f)
+            cachefile_present = True
+        except:
+            ranges = []
+            cachefile_present = False
+
+        # Append our new range and sort
+        ranges.append((start, stop))
+        ranges.sort()
+
+        # Merge adjacent ranges into "out"
+        merged = []
+        prev = None
+        for new in ranges:
+            if prev is None:
+                # No previous range, so remember this one
+                prev = new
+            elif prev[1] == new[0]:
+                # Previous range connected to this new one; extend prev
+                prev = (prev[0], new[1])
+            else:
+                # Not connected; append previous and start again
+                merged.append(prev)
+                prev = new
+        if prev is not None:
+            merged.append(prev)
+
+        # If the range covered the whole file, we can delete it now.
+        # Note that the last file in a table may be only partially
+        # full (smaller than self.rows_per_file).  We purposely leave
+        # those files around rather than deleting them, because the
+        # remainder will be filled on a subsequent append(), and things
+        # are generally easier if we don't have to special-case that.
+        if (len(merged) == 1 and
+            merged[0][0] == 0 and merged[0][1] == self.rows_per_file):
+            # Close potentially open file in mmap_open LRU cache
+            self.mmap_open.cache_remove(self, subdir, filename)
+
+            # Delete files
+            os.remove(datafile)
+            if cachefile_present:
+                os.remove(cachefile)
+
+            # Try deleting subdir, too
+            try:
+                os.rmdir(os.path.join(self.root, subdir))
+            except:
+                pass
+        else:
+            # Update cache.  Try to do it atomically.
+            nilmdb.utils.atomic.replace_file(cachefile,
+                                             pickle.dumps(merged, 2))
+
+    def remove(self, start, stop):
+        """Remove specified rows [start, stop) from this table.
+
+        If a file is left empty, it is fully removed.  Otherwise, a
+        parallel data file is used to remember which rows have been
+        removed, and the file is otherwise untouched."""
+        if start < 0 or start > stop or stop > self.nrows:
+            raise IndexError("Index out of range")
+
+        row = start
+        remaining = stop - start
+        while remaining:
+            # Loop through each file that we need to touch
+            (subdir, filename, offset, count) = self._offset_from_row(row)
+            if count > remaining:
+                count = remaining
+            row_offset = offset // self.packer.size
+            # Mark the rows as being removed
+            self._remove_rows(subdir, filename, row_offset, row_offset + count)
+            remaining -= count
+            row += count
+
+class TimestampOnlyTable(object):
+    """Helper that lets us pass a Tables object into bisect, by
+    returning only the timestamp when a particular row is requested."""
+    def __init__(self, table):
+        self.table = table
+    def __getitem__(self, index):
+        return self.table[index][0]

nilmdb/bxintersect.pyx

@@ -1,495 +0,0 @@
-# cython: profile=False
-# This is from bx-python 554:07aca5a9f6fc (BSD licensed), modified to
-# store interval ranges as doubles rather than 32-bit integers.
-
-"""
-Data structure for performing intersect queries on a set of intervals which
-preserves all information about the intervals (unlike bitset projection methods).
-
-:Authors: James Taylor (james@jamestaylor.org),
-          Ian Schenk (ian.schenck@gmail.com),
-          Brent Pedersen (bpederse@gmail.com)
-"""
-
-# Historical note:
-#    This module original contained an implementation based on sorted endpoints
-#    and a binary search, using an idea from Scott Schwartz and Piotr Berman.
-#    Later an interval tree implementation was implemented by Ian for Galaxy's
-#    join tool (see `bx.intervals.operations.quicksect.py`). This was then
-#    converted to Cython by Brent, who also added support for
-#    upstream/downstream/neighbor queries. This was modified by James to
-#    handle half-open intervals strictly, to maintain sort order, and to
-#    implement the same interface as the original Intersecter.
-
-#cython: cdivision=True
-
-import operator
-
-cdef extern from "stdlib.h":
-    int ceil(float f)
-    float log(float f)
-    int RAND_MAX
-    int rand()
-    int strlen(char *)
-    int iabs(int)
-
-cdef inline double dmax2(double a, double b):
-    if b > a: return b
-    return a
-
-cdef inline double dmax3(double a, double b, double c):
-    if b > a:
-        if c > b:
-            return c
-        return b
-    if a > c:
-        return a
-    return c
-
-cdef inline double dmin3(double a, double b, double c):
-    if b < a:
-        if c < b:
-            return c
-        return b
-    if a < c:
-        return a
-    return c
-
-cdef inline double dmin2(double a, double b):
-    if b < a: return b
-    return a
-
-cdef float nlog = -1.0 / log(0.5)
-
-cdef class IntervalNode:
-    """
-    A single node of an `IntervalTree`.
-
-    NOTE: Unless you really know what you are doing, you probably should us
-          `IntervalTree` rather than using this directly.
-    """
-    cdef float priority
-    cdef public object interval
-    cdef public double start, end
-    cdef double minend, maxend, minstart
-    cdef IntervalNode cleft, cright, croot
-
-    property left_node:
-        def __get__(self):
-            return self.cleft if self.cleft is not EmptyNode else None
-    property right_node:
-        def __get__(self):
-            return self.cright if self.cright is not EmptyNode else None
-    property root_node:
-        def __get__(self):
-            return self.croot if self.croot is not EmptyNode else None
-
-    def __repr__(self):
-        return "IntervalNode(%g, %g)" % (self.start, self.end)
-
-    def __cinit__(IntervalNode self, double start, double end, object interval):
-        # Python lacks the binomial distribution, so we convert a
-        # uniform into a binomial because it naturally scales with
-        # tree size.  Also, python's uniform is perfect since the
-        # upper limit is not inclusive, which gives us undefined here.
-        self.priority = ceil(nlog * log(-1.0/(1.0 * rand()/RAND_MAX - 1)))
-        self.start    = start
-        self.end      = end
-        self.interval = interval
-        self.maxend   = end
-        self.minstart = start
-        self.minend   = end
-        self.cleft    = EmptyNode
-        self.cright   = EmptyNode
-        self.croot    = EmptyNode
-
-    cpdef IntervalNode insert(IntervalNode self, double start, double end, object interval):
-        """
-        Insert a new IntervalNode into the tree of which this node is
-        currently the root. The return value is the new root of the tree (which
-        may or may not be this node!)
-        """
-        cdef IntervalNode croot = self
-        # If starts are the same, decide which to add interval to based on
-        # end, thus maintaining sortedness relative to start/end
-        cdef double decision_endpoint = start
-        if start == self.start:
-            decision_endpoint = end
-
-        if decision_endpoint > self.start:
-            # insert to cright tree
-            if self.cright is not EmptyNode:
-                self.cright = self.cright.insert( start, end, interval )
-            else:
-                self.cright = IntervalNode( start, end, interval )
-            # rebalance tree
-            if self.priority < self.cright.priority:
-                croot = self.rotate_left()
-        else:
-            # insert to cleft tree
-            if self.cleft is not EmptyNode:
-                self.cleft = self.cleft.insert( start, end, interval)
-            else:
-                self.cleft = IntervalNode( start, end, interval)
-            # rebalance tree
-            if self.priority < self.cleft.priority:
-                croot = self.rotate_right()
-
-        croot.set_ends()
-        self.cleft.croot  = croot
-        self.cright.croot = croot
-        return croot
-
-    cdef IntervalNode rotate_right(IntervalNode self):
-        cdef IntervalNode croot = self.cleft
-        self.cleft  = self.cleft.cright
-        croot.cright = self
-        self.set_ends()
-        return croot
-
-    cdef IntervalNode rotate_left(IntervalNode self):
-        cdef IntervalNode croot = self.cright
-        self.cright = self.cright.cleft
-        croot.cleft  = self
-        self.set_ends()
-        return croot
-
-    cdef inline void set_ends(IntervalNode self):
-        if self.cright is not EmptyNode and self.cleft is not EmptyNode:
-            self.maxend = dmax3(self.end, self.cright.maxend, self.cleft.maxend)
-            self.minend = dmin3(self.end, self.cright.minend, self.cleft.minend)
-            self.minstart = dmin3(self.start, self.cright.minstart, self.cleft.minstart)
-        elif self.cright is not EmptyNode:
-            self.maxend = dmax2(self.end, self.cright.maxend)
-            self.minend = dmin2(self.end, self.cright.minend)
-            self.minstart = dmin2(self.start, self.cright.minstart)
-        elif self.cleft is not EmptyNode:
-            self.maxend = dmax2(self.end, self.cleft.maxend)
-            self.minend = dmin2(self.end, self.cleft.minend)
-            self.minstart = dmin2(self.start, self.cleft.minstart)
-
-
-    def intersect( self, double start, double end, sort=True ):
-        """
-        given a start and a end, return a list of features
-        falling within that range
-        """
-        cdef list results = []
-        self._intersect( start, end, results )
-        if sort:
-            results = sorted(results)
-        return results
-
-    find = intersect
-
-    cdef void _intersect( IntervalNode self, double start, double end, list results):
-        # Left subtree
-        if self.cleft is not EmptyNode and self.cleft.maxend > start:
-            self.cleft._intersect( start, end, results )
-        # This interval
-        if ( self.end > start ) and ( self.start < end ):
-            results.append( self.interval )
-        # Right subtree
-        if self.cright is not EmptyNode and self.start < end:
-            self.cright._intersect( start, end, results )
-
-
-    cdef void _seek_left(IntervalNode self, double position, list results, int n, double max_dist):
-        # we know we can bail in these 2 cases.
-        if self.maxend + max_dist < position:
-            return
-        if self.minstart > position:
-            return
-
-        # the ordering of these 3 blocks makes it so the results are
-        # ordered nearest to farest from the query position
-        if self.cright is not EmptyNode:
-            self.cright._seek_left(position, results, n, max_dist)
-
-        if -1 < position - self.end < max_dist:
-            results.append(self.interval)
-
-        # TODO: can these conditionals be more stringent?
-        if self.cleft is not EmptyNode:
-                self.cleft._seek_left(position, results, n, max_dist)
-
-
-
-    cdef void _seek_right(IntervalNode self, double position, list results, int n, double max_dist):
-        # we know we can bail in these 2 cases.
-        if self.maxend < position: return
-        if self.minstart - max_dist > position: return
-
-        #print "SEEK_RIGHT:",self, self.cleft, self.maxend, self.minstart, position
-
-        # the ordering of these 3 blocks makes it so the results are
-        # ordered nearest to farest from the query position
-        if self.cleft is not EmptyNode:
-                self.cleft._seek_right(position, results, n, max_dist)
-
-        if -1 < self.start - position < max_dist:
-            results.append(self.interval)
-
-        if self.cright is not EmptyNode:
-                self.cright._seek_right(position, results, n, max_dist)
-
-
-    cpdef left(self, position, int n=1, double max_dist=2500):
-        """
-        find n features with a start > than `position`
-        f: a Interval object (or anything with an `end` attribute)
-        n: the number of features to return
-        max_dist: the maximum distance to look before giving up.
-        """
-        cdef list results = []
-        # use start - 1 becuase .left() assumes strictly left-of
-        self._seek_left( position - 1, results, n, max_dist )
-        if len(results) == n: return results
-        r = results
-        r.sort(key=operator.attrgetter('end'), reverse=True)
-        return r[:n]
-
-    cpdef right(self, position, int n=1, double max_dist=2500):
-        """
-        find n features with a end < than position
-        f: a Interval object (or anything with a `start` attribute)
-        n: the number of features to return
-        max_dist: the maximum distance to look before giving up.
-        """
-        cdef list results = []
-        # use end + 1 becuase .right() assumes strictly right-of
-        self._seek_right(position + 1, results, n, max_dist)
-        if len(results) == n: return results
-        r = results
-        r.sort(key=operator.attrgetter('start'))
-        return r[:n]
-
-    def traverse(self):
-        if self.cleft is not EmptyNode:
-            for node in self.cleft.traverse():
-                yield node
-        yield self.interval
-        if self.cright is not EmptyNode:
-            for node in self.cright.traverse():
-                yield node
-
-cdef IntervalNode EmptyNode = IntervalNode( 0, 0, Interval(0, 0))
-
-## ---- Wrappers that retain the old interface -------------------------------
-
-cdef class Interval:
-    """
-    Basic feature, with required integer start and end properties.
-    Also accepts optional strand as +1 or -1 (used for up/downstream queries),
-    a name, and any arbitrary data is sent in on the info keyword argument
-
-    >>> from bx.intervals.intersection import Interval
-
-    >>> f1 = Interval(23, 36)
-    >>> f2 = Interval(34, 48, value={'chr':12, 'anno':'transposon'})
-    >>> f2
-    Interval(34, 48, value={'anno': 'transposon', 'chr': 12})
-
-    """
-    cdef public double start, end
-    cdef public object value, chrom, strand
-
-    def __init__(self, double start, double end, object value=None, object chrom=None, object strand=None ):
-        assert start <= end, "start must be less than end"
-        self.start  = start
-        self.end   = end
-        self.value = value
-        self.chrom = chrom
-        self.strand = strand
-
-    def __repr__(self):
-        fstr = "Interval(%g, %g" % (self.start, self.end)
-        if not self.value is None:
-            fstr += ", value=" + str(self.value)
-        fstr += ")"
-        return fstr
-
-    def __richcmp__(self, other, op):
-        if op == 0:
-            # <
-            return self.start < other.start or self.end < other.end
-        elif op == 1:
-            # <=
-            return self == other or self < other
-        elif op == 2:
-            # ==
-            return self.start == other.start and self.end == other.end
-        elif op == 3:
-            # !=
-            return self.start != other.start or self.end != other.end
-        elif op == 4:
-            # >
-            return self.start > other.start or self.end > other.end
-        elif op == 5:
-            # >=
-            return self == other or self > other
-
-cdef class IntervalTree:
-    """
-    Data structure for performing window intersect queries on a set of
-    of possibly overlapping 1d intervals.
-
-    Usage
-    =====
-
-    Create an empty IntervalTree
-
-    >>> from bx.intervals.intersection import Interval, IntervalTree
-    >>> intersecter = IntervalTree()
-
-    An interval is a start and end position and a value (possibly None).
-    You can add any object as an interval:
-
-    >>> intersecter.insert( 0, 10, "food" )
-    >>> intersecter.insert( 3, 7, dict(foo='bar') )
-
-    >>> intersecter.find( 2, 5 )
-    ['food', {'foo': 'bar'}]
-
-    If the object has start and end attributes (like the Interval class) there
-    is are some shortcuts:
-
-    >>> intersecter = IntervalTree()
-    >>> intersecter.insert_interval( Interval( 0, 10 ) )
-    >>> intersecter.insert_interval( Interval( 3, 7 ) )
-    >>> intersecter.insert_interval( Interval( 3, 40 ) )
-    >>> intersecter.insert_interval( Interval( 13, 50 ) )
-
-    >>> intersecter.find( 30, 50 )
-    [Interval(3, 40), Interval(13, 50)]
-    >>> intersecter.find( 100, 200 )
-    []
-
-    Before/after for intervals
-
-    >>> intersecter.before_interval( Interval( 10, 20 ) )
-    [Interval(3, 7)]
-    >>> intersecter.before_interval( Interval( 5, 20 ) )
-    []
-
-    Upstream/downstream
-
-    >>> intersecter.upstream_of_interval(Interval(11, 12))
-    [Interval(0, 10)]
-    >>> intersecter.upstream_of_interval(Interval(11, 12, strand="-"))
-    [Interval(13, 50)]
-
-    >>> intersecter.upstream_of_interval(Interval(1, 2, strand="-"), num_intervals=3)
-    [Interval(3, 7), Interval(3, 40), Interval(13, 50)]
-
-
-    """
-
-    cdef IntervalNode root
-
-    def __cinit__( self ):
-        root = None
-
-    # ---- Position based interfaces -----------------------------------------
-
-    def insert( self, double start, double end, object value=None ):
-        """
-        Insert the interval [start,end) associated with value `value`.
-        """
-        if self.root is None:
-            self.root = IntervalNode( start, end, value )
-        else:
-            self.root = self.root.insert( start, end, value )
-
-    add = insert
-
-
-    def find( self, start, end ):
-        """
-        Return a sorted list of all intervals overlapping [start,end).
-        """
-        if self.root is None:
-            return []
-        return self.root.find( start, end )
-
-    def before( self, position, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie before `position` and are no
-        further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.left( position, num_intervals, max_dist )
-
-    def after( self, position, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie after `position` and are no
-        further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.right( position, num_intervals, max_dist )
-
-    # ---- Interval-like object based interfaces -----------------------------
-
-    def insert_interval( self, interval ):
-        """
-        Insert an "interval" like object (one with at least start and end
-        attributes)
-        """
-        self.insert( interval.start, interval.end, interval )
-
-    add_interval = insert_interval
-
-    def before_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely before `interval`
-        and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.left( interval.start, num_intervals, max_dist )
-
-    def after_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely after `interval` and
-        are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.right( interval.end, num_intervals, max_dist )
-
-    def upstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely upstream of
-        `interval` and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        if interval.strand == -1 or interval.strand == "-":
-            return self.root.right( interval.end, num_intervals, max_dist )
-        else:
-            return self.root.left( interval.start, num_intervals, max_dist )
-
-    def downstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely downstream of
-        `interval` and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        if interval.strand == -1 or interval.strand == "-":
-            return self.root.left( interval.start, num_intervals, max_dist )
-        else:
-            return self.root.right( interval.end, num_intervals, max_dist )
-
-    def traverse(self):
-        """
-        iterator that traverses the tree
-        """
-        if self.root is None:
-            return iter([])
-        return self.root.traverse()
-
-# For backward compatibility
-Intersecter = IntervalTree

nilmdb/client.py

@@ -3,7 +3,7 @@
 """Class for performing HTTP client requests via libcurl"""
 
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 import time
 import sys
@@ -12,6 +12,7 @@ import os
 import simplejson as json
 import itertools
 
+import nilmdb.utils
 import nilmdb.httpclient
 
 # Other functions expect to see these in the nilmdb.client namespace
@@ -96,6 +97,17 @@ class Client(object):
         params = { "path": path }
         return self.http.get("stream/destroy", params)
 
+    def stream_remove(self, path, start = None, end = None):
+        """Remove data from the specified time range"""
+        params = {
+            "path": path
+        }
+        if start is not None:
+            params["start"] = float_to_string(start)
+        if end is not None:
+            params["end"] = float_to_string(end)
+        return self.http.get("stream/remove", params)
+
     def stream_insert(self, path, data, start = None, end = None):
         """Insert data into a stream.  data should be a file-like object
         that provides ASCII data that matches the database layout for path.
@@ -114,11 +126,6 @@ class Client(object):
         max_time = 30
         end_epsilon = 1e-6
 
-        def pairwise(iterable):
-            "s -> (s0,s1), (s1,s2), ..., (sn,None)"
-            a, b = itertools.tee(iterable)
-            next(b, None)
-            return itertools.izip_longest(a, b)
 
         def extract_timestamp(line):
             return float(line.split()[0])
@@ -148,7 +155,7 @@ class Client(object):
         block_data = ""
         block_start = start
         result = None
-        for (line, nextline) in pairwise(data):
+        for (line, nextline) in nilmdb.utils.misc.pairwise(data):
             # If we don't have a starting time, extract it from the first line
             if block_start is None:
                 block_start = extract_timestamp(line)

nilmdb/cmdline/cmdline.py

@@ -1,7 +1,7 @@
 """Command line client functionality"""
 
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.client
 
 import datetime_tz
@@ -11,12 +11,12 @@ import re
 import argparse
 from argparse import ArgumentDefaultsHelpFormatter as def_form
 
-version = "0.1"
+version = "1.0"
 
 # Valid subcommands.  Defined in separate files just to break
 # things up -- they're still called with Cmdline as self.
 subcommands = [ "info", "create", "list", "metadata", "insert", "extract",
-                "destroy" ]
+                "remove", "destroy" ]
 
 # Import the subcommand modules.  Equivalent way of doing this would be
 # from . import info as cmd_info
@@ -24,10 +24,16 @@ subcmd_mods = {}
 for cmd in subcommands:
     subcmd_mods[cmd] = __import__("nilmdb.cmdline." + cmd, fromlist = [ cmd ])
 
+class JimArgumentParser(argparse.ArgumentParser):
+    def error(self, message):
+        self.print_usage(sys.stderr)
+        self.exit(2, sprintf("error: %s\n", message))
+
 class Cmdline(object):
 
     def __init__(self, argv):
         self.argv = argv
+        self.client = None
 
     def arg_time(self, toparse):
         """Parse a time string argument"""
@@ -93,7 +99,7 @@ class Cmdline(object):
         version_string = sprintf("nilmtool %s, client library %s",
                                  version, nilmdb.Client.client_version)
 
-        self.parser = argparse.ArgumentParser(add_help = False,
+        self.parser = JimArgumentParser(add_help = False,
                                         formatter_class = def_form)
 
         group = self.parser.add_argument_group("General options")
@@ -119,6 +125,7 @@ class Cmdline(object):
 
     def die(self, formatstr, *args):
         fprintf(sys.stderr, formatstr + "\n", *args)
+        if self.client:
             self.client.close()
         sys.exit(-1)
 
@@ -131,13 +138,17 @@ class Cmdline(object):
         self.parser_setup()
         self.args = self.parser.parse_args(self.argv)
 
+        # Run arg verify handler if there is one
+        if "verify" in self.args:
+            self.args.verify(self)
+
         self.client = nilmdb.Client(self.args.url)
 
         # Make a test connection to make sure things work
         try:
             server_version = self.client.version()
         except nilmdb.client.Error as e:
-            self.die("Error connecting to server: %s", str(e))
+            self.die("error connecting to server: %s", str(e))
 
         # Now dispatch client request to appropriate function.  Parser
         # should have ensured that we don't have any unknown commands

nilmdb/cmdline/create.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.client
 
 from argparse import ArgumentDefaultsHelpFormatter as def_form
@@ -24,4 +24,4 @@ def cmd_create(self):
     try:
         self.client.stream_create(self.args.path, self.args.layout)
     except nilmdb.client.ClientError as e:
-        self.die("Error creating stream: %s", str(e))
+        self.die("error creating stream: %s", str(e))

nilmdb/cmdline/destroy.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.client
 
 from argparse import ArgumentDefaultsHelpFormatter as def_form
@@ -22,4 +22,4 @@ def cmd_destroy(self):
     try:
         self.client.stream_destroy(self.args.path)
     except nilmdb.client.ClientError as e:
-        self.die("Error deleting stream: %s", str(e))
+        self.die("error destroying stream: %s", str(e))

nilmdb/cmdline/extract.py

@@ -1,5 +1,6 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from __future__ import print_function
+from nilmdb.utils.printf import *
 import nilmdb.client
 import sys
 
@@ -8,17 +9,18 @@ def setup(self, sub):
                          description="""
                          Extract data from a stream.
                          """)
-    cmd.set_defaults(handler = cmd_extract)
+    cmd.set_defaults(verify = cmd_extract_verify,
+                     handler = cmd_extract)
 
     group = cmd.add_argument_group("Data selection")
     group.add_argument("path",
                        help="Path of stream, e.g. /foo/bar")
     group.add_argument("-s", "--start", required=True,
                        metavar="TIME", type=self.arg_time,
-                       help="Starting timestamp (free-form)")
+                       help="Starting timestamp (free-form, inclusive)")
     group.add_argument("-e", "--end", required=True,
                        metavar="TIME", type=self.arg_time,
-                       help="Ending timestamp (free-form)")
+                       help="Ending timestamp (free-form, noninclusive)")
 
     group = cmd.add_argument_group("Output format")
     group.add_argument("-b", "--bare", action="store_true",
@@ -29,10 +31,15 @@ def setup(self, sub):
     group.add_argument("-c", "--count", action="store_true",
                        help="Just output a count of matched data points")
 
+def cmd_extract_verify(self):
+    if self.args.start is not None and self.args.end is not None:
+        if self.args.start > self.args.end:
+            self.parser.error("start is after end")
+
 def cmd_extract(self):
     streams = self.client.stream_list(self.args.path)
     if len(streams) != 1:
-        self.die("Error getting stream info for path %s", self.args.path)
+        self.die("error getting stream info for path %s", self.args.path)
     layout = streams[0][1]
 
     if self.args.annotate:
@@ -50,7 +57,7 @@ def cmd_extract(self):
             # Strip timestamp (first element).  Doesn't make sense
             # if we are only returning a count.
             dataline = ' '.join(dataline.split(' ')[1:])
-        print dataline
+        print(dataline)
         printed = True
     if not printed:
         if self.args.annotate:

nilmdb/cmdline/info.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 from argparse import ArgumentDefaultsHelpFormatter as def_form
 

nilmdb/cmdline/insert.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.client
 import nilmdb.timestamper
 
@@ -51,12 +51,12 @@ def cmd_insert(self):
     # Find requested stream
     streams = self.client.stream_list(self.args.path)
     if len(streams) != 1:
-        self.die("Error getting stream info for path %s", self.args.path)
+        self.die("error getting stream info for path %s", self.args.path)
 
     layout = streams[0][1]
 
     if self.args.start and len(self.args.file) != 1:
-        self.die("--start can only be used with one input file, for now")
+        self.die("error: --start can only be used with one input file")
 
     for filename in self.args.file:
         if filename == '-':
@@ -65,7 +65,7 @@ def cmd_insert(self):
             try:
                 infile = open(filename, "r")
             except IOError:
-                self.die("Error opening input file %s", filename)
+                self.die("error opening input file %s", filename)
 
         # Build a timestamper for this file
         if self.args.none:
@@ -77,11 +77,11 @@ def cmd_insert(self):
                 try:
                     start = self.parse_time(filename)
                 except ValueError:
-                    self.die("Error extracting time from filename '%s'",
+                    self.die("error extracting time from filename '%s'",
                              filename)
 
             if not self.args.rate:
-                self.die("Need to specify --rate")
+                self.die("error: --rate is needed, but was not specified")
             rate = self.args.rate
 
             ts = nilmdb.timestamper.TimestamperRate(infile, start, rate)
@@ -100,6 +100,6 @@ def cmd_insert(self):
             # ugly bracketed ranges of 16-digit numbers and a mangled URL.
             # Need to consider adding something like e.prettyprint()
             # that is smarter about the contents of the error.
-            self.die("Error inserting data: %s", str(e))
+            self.die("error inserting data: %s", str(e))
 
     return

nilmdb/cmdline/list.py

@@ -1,8 +1,9 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.client
 
 import fnmatch
+import argparse
 from argparse import ArgumentDefaultsHelpFormatter as def_form
 
 def setup(self, sub):
@@ -13,23 +14,41 @@ def setup(self, sub):
                          optionally filtering by layout or path.  Wildcards
                          are accepted.
                          """)
-    cmd.set_defaults(handler = cmd_list)
+    cmd.set_defaults(verify = cmd_list_verify,
+                     handler = cmd_list)
 
     group = cmd.add_argument_group("Stream filtering")
+    group.add_argument("-p", "--path", metavar="PATH", default="*",
+                       help="Match only this path (-p can be omitted)")
+    group.add_argument("path_positional", default="*",
+                       nargs="?", help=argparse.SUPPRESS)
     group.add_argument("-l", "--layout", default="*",
                        help="Match only this stream layout")
-    group.add_argument("-p", "--path", default="*",
-                       help="Match only this path")
 
     group = cmd.add_argument_group("Interval details")
     group.add_argument("-d", "--detail", action="store_true",
                        help="Show available data time intervals")
     group.add_argument("-s", "--start",
                        metavar="TIME", type=self.arg_time,
-                       help="Starting timestamp (free-form)")
+                       help="Starting timestamp (free-form, inclusive)")
     group.add_argument("-e", "--end",
                        metavar="TIME", type=self.arg_time,
-                       help="Ending timestamp (free-form)")
+                       help="Ending timestamp (free-form, noninclusive)")
+
+def cmd_list_verify(self):
+    # A hidden "path_positional" argument lets the user leave off the
+    # "-p" when specifying the path.  Handle it here.
+    got_opt = self.args.path != "*"
+    got_pos = self.args.path_positional != "*"
+    if got_pos:
+        if got_opt:
+            self.parser.error("too many paths specified")
+        else:
+            self.args.path = self.args.path_positional
+
+    if self.args.start is not None and self.args.end is not None:
+        if self.args.start > self.args.end:
+            self.parser.error("start is after end")
 
 def cmd_list(self):
     """List available streams"""

nilmdb/cmdline/metadata.py

@@ -1,5 +1,5 @@
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.client
 
 def setup(self, sub):
@@ -43,21 +43,21 @@ def cmd_metadata(self):
         for keyval in keyvals:
             kv = keyval.split('=')
             if len(kv) != 2 or kv[0] == "":
-                self.die("Error parsing key=value argument '%s'", keyval)
+                self.die("error parsing key=value argument '%s'", keyval)
             data[kv[0]] = kv[1]
 
         # Make the call
         try:
             handler(self.args.path, data)
         except nilmdb.client.ClientError as e:
-            self.die("Error setting/updating metadata: %s", str(e))
+            self.die("error setting/updating metadata: %s", str(e))
     else:
         # Get (or unspecified)
         keys = self.args.get or None
         try:
             data = self.client.stream_get_metadata(self.args.path, keys)
         except nilmdb.client.ClientError as e:
-            self.die("Error getting metadata: %s", str(e))
+            self.die("error getting metadata: %s", str(e))
         for key, value in sorted(data.items()):
             # Omit nonexistant keys
             if value is None:

nilmdb/cmdline/remove.py

@@ -0,0 +1,45 @@
+from __future__ import absolute_import
+from __future__ import print_function
+from nilmdb.utils.printf import *
+import nilmdb.client
+import sys
+
+def setup(self, sub):
+    cmd = sub.add_parser("remove", help="Remove data",
+                         description="""
+                         Remove all data from a specified time range within a
+                         stream.
+                         """)
+    cmd.set_defaults(verify = cmd_remove_verify,
+                     handler = cmd_remove)
+
+    group = cmd.add_argument_group("Data selection")
+    group.add_argument("path",
+                       help="Path of stream, e.g. /foo/bar")
+    group.add_argument("-s", "--start", required=True,
+                       metavar="TIME", type=self.arg_time,
+                       help="Starting timestamp (free-form, inclusive)")
+    group.add_argument("-e", "--end", required=True,
+                       metavar="TIME", type=self.arg_time,
+                       help="Ending timestamp (free-form, noninclusive)")
+
+    group = cmd.add_argument_group("Output format")
+    group.add_argument("-c", "--count", action="store_true",
+                       help="Output number of data points removed")
+
+def cmd_remove_verify(self):
+    if self.args.start is not None and self.args.end is not None:
+        if self.args.start > self.args.end:
+            self.parser.error("start is after end")
+
+def cmd_remove(self):
+    try:
+        count = self.client.stream_remove(self.args.path,
+                                          self.args.start, self.args.end)
+    except nilmdb.client.ClientError as e:
+        self.die("error removing data: %s", str(e))
+
+    if self.args.count:
+        printf("%d\n", count)
+
+    return 0

nilmdb/httpclient.py

@@ -1,7 +1,8 @@
 """HTTP client library"""
 
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
+import nilmdb.utils
 
 import time
 import sys
@@ -9,12 +10,9 @@ import re
 import os
 import simplejson as json
 import urlparse
-import urllib
 import pycurl
 import cStringIO
 
-import nilmdb.iteratorizer
-
 class Error(Exception):
     """Base exception for both ClientError and ServerError responses"""
     def __init__(self,
@@ -28,12 +26,19 @@ class Error(Exception):
         self.url = url           # URL we were requesting
         self.traceback = traceback # server traceback, if available
     def __str__(self):
+        s = sprintf("[%s]", self.status)
+        if self.message:
+            s += sprintf(" %s", self.message)
+        if self.traceback: # pragma: no cover
+            s += sprintf("\nServer traceback:\n%s", self.traceback)
+        return s
+    def __repr__(self): # pragma: no cover
         s = sprintf("[%s]", self.status)
         if self.message:
             s += sprintf(" %s", self.message)
         if self.url:
             s += sprintf(" (%s)", self.url)
-        if self.traceback: # pragma: no cover
+        if self.traceback:
             s += sprintf("\nServer traceback:\n%s", self.traceback)
         return s
 class ClientError(Error):
@@ -60,7 +65,8 @@ class HTTPClient(object):
     def _setup_url(self, url = "", params = ""):
         url = urlparse.urljoin(self.baseurl, url)
         if params:
-            url = urlparse.urljoin(url, "?" + urllib.urlencode(params, True))
+            url = urlparse.urljoin(
+                url, "?" + nilmdb.utils.urllib.urlencode(params))
         self.curl.setopt(pycurl.URL, url)
         self.url = url
 
@@ -85,6 +91,10 @@ class HTTPClient(object):
             raise ClientError(**args)
         else: # pragma: no cover
             if code >= 500 and code <= 599:
+                if args["message"] is None:
+                    args["message"] = ("(no message; try disabling " +
+                                       "response.stream option in " +
+                                       "nilmdb.server for better debugging)")
                 raise ServerError(**args)
             else:
                 raise Error(**args)
@@ -109,7 +119,7 @@ class HTTPClient(object):
             self.curl.setopt(pycurl.WRITEFUNCTION, callback)
             self.curl.perform()
         try:
-            for i in nilmdb.iteratorizer.Iteratorizer(func):
+            for i in nilmdb.utils.Iteratorizer(func):
                 if self._status == 200:
                     # If we had a 200 response, yield the data to the caller.
                     yield i

nilmdb/interval.pyx

@@ -37,6 +37,7 @@ cdef class Interval:
         'start' and 'end' are arbitrary floats that represent time
         """
         if start > end:
+            # Explicitly disallow zero-width intervals (since they're half-open)
             raise IntervalError("start %s must precede end %s" % (start, end))
         self.start = float(start)
         self.end = float(end)
@@ -278,7 +279,7 @@ cdef class IntervalSet:
 
         return out
 
-    def intersection(self, Interval interval not None):
+    def intersection(self, Interval interval not None, orig = False):
         """
         Compute a sequence of intervals that correspond to the
         intersection between `self` and the provided interval.
@@ -287,6 +288,10 @@ cdef class IntervalSet:
 
         Output intervals are built as subsets of the intervals in the
         first argument (self).
+
+        If orig = True, also return the original interval that was
+        (potentially) subsetted to make the one that is being
+        returned.
         """
         if not isinstance(interval, Interval):
             raise TypeError("bad type")
@@ -294,10 +299,16 @@ cdef class IntervalSet:
             i = n.obj
             if i:
                 if i.start >= interval.start and i.end <= interval.end:
+                    if orig:
+                        yield (i, i)
+                    else:
                         yield i
                 else:
                     subset = i.subset(max(i.start, interval.start),
                                       min(i.end, interval.end))
+                    if orig:
+                        yield (subset, i)
+                    else:
                         yield subset
 
     cpdef intersects(self, Interval other):

nilmdb/layout.pyx

@@ -1,6 +1,5 @@
 # cython: profile=False
 
-import tables
 import time
 import sys
 import inspect
@@ -122,15 +121,6 @@ class Layout:
             s += " %d" % d[i+1]
         return s + "\n"
 
-    # PyTables description
-    def description(self):
-        """Return the PyTables description of this layout"""
-        desc = {}
-        desc['timestamp'] = tables.Col.from_type('float64', pos=0)
-        for n in range(self.count):
-            desc['c' + str(n+1)] = tables.Col.from_type(self.datatype, pos=n+1)
-        return tables.Description(desc)
-
 # Get a layout by name
 def get_named(typestring):
     try:

nilmdb/nilmdb.py

@@ -4,17 +4,16 @@
 
 Object that represents a NILM database file.
 
-Manages both the SQL database and the PyTables storage backend.
+Manages both the SQL database and the table storage backend.
 """
 
 # Need absolute_import so that "import nilmdb" won't pull in nilmdb.py,
 # but will pull the nilmdb module instead.
 from __future__ import absolute_import
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 import sqlite3
-import tables
 import time
 import sys
 import os
@@ -25,6 +24,8 @@ import pyximport
 pyximport.install()
 from nilmdb.interval import Interval, DBInterval, IntervalSet, IntervalError
 
+from . import bulkdata
+
 # Note about performance and transactions:
 #
 # Committing a transaction in the default sync mode (PRAGMA synchronous=FULL)
@@ -79,7 +80,7 @@ _sql_schema_updates = {
 class NilmDBError(Exception):
     """Base exception for NilmDB errors"""
     def __init__(self, message = "Unspecified error"):
-        Exception.__init__(self, self.__class__.__name__ + ": " + message)
+        Exception.__init__(self, message)
 
 class StreamError(NilmDBError):
     pass
@@ -87,19 +88,14 @@ class StreamError(NilmDBError):
 class OverlapError(NilmDBError):
     pass
 
-# Helper that lets us pass a Pytables table into bisect
-class BisectableTable(object):
-    def __init__(self, table):
-        self.table = table
-    def __getitem__(self, index):
-        return self.table[index][0]
-
+@nilmdb.utils.must_close()
 class NilmDB(object):
     verbose = 0
 
-    def __init__(self, basepath, sync=True, max_results=None):
+    def __init__(self, basepath, sync=True, max_results=None,
+                 bulkdata_args={}):
         # set up path
-        self.basepath = os.path.abspath(basepath.rstrip('/'))
+        self.basepath = os.path.abspath(basepath)
 
         # Create the database path if it doesn't exist
         try:
@@ -108,16 +104,16 @@ class NilmDB(object):
             if e.errno != errno.EEXIST:
                 raise IOError("can't create tree " + self.basepath)
 
-        # Our HD5 file goes inside it
-        h5filename = os.path.abspath(self.basepath + "/data.h5")
-        self.h5file = tables.openFile(h5filename, "a", "NILM Database")
+        # Our data goes inside it
+        self.data = bulkdata.BulkData(self.basepath, **bulkdata_args)
 
         # SQLite database too
-        sqlfilename = os.path.abspath(self.basepath + "/data.sql")
+        sqlfilename = os.path.join(self.basepath, "data.sql")
         # We use check_same_thread = False, assuming that the rest
         # of the code (e.g. Server) will be smart and not access this
-        # database from multiple threads simultaneously.  That requirement
-        # may be relaxed later.
+        # database from multiple threads simultaneously.  Otherwise
+        # false positives will occur when the database is only opened
+        # in one thread, and only accessed in another.
         self.con = sqlite3.connect(sqlfilename, check_same_thread = False)
         self._sql_schema_update()
 
@@ -134,17 +130,6 @@ class NilmDB(object):
         else:
             self.max_results = 16384
 
-        self.opened = True
-
-        # Cached intervals
-        self._cached_iset = {}
-
-    def __del__(self):
-        if "opened" in self.__dict__: # pragma: no cover
-            fprintf(sys.stderr,
-                    "error: NilmDB.close() wasn't called, path %s",
-                    self.basepath)
-
     def get_basepath(self):
         return self.basepath
 
@@ -152,8 +137,7 @@ class NilmDB(object):
         if self.con:
             self.con.commit()
             self.con.close()
-        self.h5file.close()
-        del self.opened
+        self.data.close()
 
     def _sql_schema_update(self):
         cur = self.con.cursor()
@@ -170,12 +154,11 @@ class NilmDB(object):
             with self.con:
                 cur.execute("PRAGMA user_version = {v:d}".format(v=version))
 
+    @nilmdb.utils.lru_cache(size = 16)
     def _get_intervals(self, stream_id):
         """
         Return a mutable IntervalSet corresponding to the given stream ID.
         """
-        # Load from database if not cached
-        if stream_id not in self._cached_iset:
         iset = IntervalSet()
         result = self.con.execute("SELECT start_time, end_time, "
                                   "start_pos, end_pos "
@@ -188,16 +171,29 @@ class NilmDB(object):
                                    start_pos, end_pos)
         except IntervalError as e: # pragma: no cover
             raise NilmDBError("unexpected overlap in ranges table!")
-            self._cached_iset[stream_id] = iset
-        # Return cached value
-        return self._cached_iset[stream_id]
+
+        return iset
+
+    def _sql_interval_insert(self, id, start, end, start_pos, end_pos):
+        """Helper that adds interval to the SQL database only"""
+        self.con.execute("INSERT INTO ranges "
+                         "(stream_id,start_time,end_time,start_pos,end_pos) "
+                         "VALUES (?,?,?,?,?)",
+                         (id, start, end, start_pos, end_pos))
+
+    def _sql_interval_delete(self, id, start, end, start_pos, end_pos):
+        """Helper that removes interval from the SQL database only"""
+        self.con.execute("DELETE FROM ranges WHERE "
+                         "stream_id=? AND start_time=? AND "
+                         "end_time=? AND start_pos=? AND end_pos=?",
+                         (id, start, end, start_pos, end_pos))
 
     def _add_interval(self, stream_id, interval, start_pos, end_pos):
         """
         Add interval to the internal interval cache, and to the database.
         Note: arguments must be ints (not numpy.int64, etc)
         """
-        # Ensure this stream's intervals are cached
+        # Load this stream's intervals
         iset = self._get_intervals(stream_id)
 
         # Check for overlap
@@ -210,42 +206,77 @@ class NilmDB(object):
         # time range [adjacent.start -> interval.end)
         # and database rows [ adjacent.start_pos -> end_pos ].
         # Only do this if the resulting interval isn't too large.
-        max_merged_rows = 30000000 # a bit more than 1 hour at 8 KHz
+        max_merged_rows = 8000 * 60 * 60 * 1.05 # 1.05 hours at 8 KHz
         adjacent = iset.find_end(interval.start)
         if (adjacent is not None and
             start_pos == adjacent.db_endpos and
             (end_pos - adjacent.db_startpos) < max_merged_rows):
-            # First delete the old one, both from our cache and the
+            # First delete the old one, both from our iset and the
             # database
             iset -= adjacent
-            self.con.execute("DELETE FROM ranges WHERE "
-                             "stream_id=? AND start_time=? AND "
-                             "end_time=? AND start_pos=? AND "
-                             "end_pos=?", (stream_id,
-                                           adjacent.db_start,
-                                           adjacent.db_end,
-                                           adjacent.db_startpos,
-                                           adjacent.db_endpos))
+            self._sql_interval_delete(stream_id,
+                                      adjacent.db_start, adjacent.db_end,
+                                      adjacent.db_startpos, adjacent.db_endpos)
 
             # Now update our interval so the fallthrough add is
             # correct.
             interval.start = adjacent.start
             start_pos = adjacent.db_startpos
 
-        # Add the new interval to the cache
+        # Add the new interval to the iset
         iset.iadd_nocheck(DBInterval(interval.start, interval.end,
                                      interval.start, interval.end,
                                      start_pos, end_pos))
 
         # Insert into the database
-        self.con.execute("INSERT INTO ranges "
-                         "(stream_id,start_time,end_time,start_pos,end_pos) "
-                         "VALUES (?,?,?,?,?)",
-                         (stream_id, interval.start, interval.end,
-                          int(start_pos), int(end_pos)))
+        self._sql_interval_insert(stream_id, interval.start, interval.end,
+                                  int(start_pos), int(end_pos))
 
         self.con.commit()
 
+    def _remove_interval(self, stream_id, original, remove):
+        """
+        Remove an interval from the internal cache and the database.
+
+        stream_id: id of stream
+         original: original DBInterval; must be already present in DB
+        to_remove: DBInterval to remove; must be subset of 'original'
+        """
+        # Just return if we have nothing to remove
+        if remove.start == remove.end: # pragma: no cover
+            return
+
+        # Load this stream's intervals
+        iset = self._get_intervals(stream_id)
+
+        # Remove existing interval from the cached set and the database
+        iset -= original
+        self._sql_interval_delete(stream_id,
+                                  original.db_start, original.db_end,
+                                  original.db_startpos, original.db_endpos)
+
+        # Add back the intervals that would be left over if the
+        # requested interval is removed.  There may be two of them, if
+        # the removed piece was in the middle.
+        def add(iset, start, end, start_pos, end_pos):
+            iset += DBInterval(start, end, start, end, start_pos, end_pos)
+            self._sql_interval_insert(stream_id, start, end, start_pos, end_pos)
+
+        if original.start != remove.start:
+            # Interval before the removed region
+            add(iset, original.start, remove.start,
+                original.db_startpos, remove.db_startpos)
+
+        if original.end != remove.end:
+            # Interval after the removed region
+            add(iset, remove.end, original.end,
+                remove.db_endpos, original.db_endpos)
+
+        # Commit SQL changes
+        self.con.commit()
+
+        return
+
     def stream_list(self, path = None, layout = None):
         """Return list of [path, layout] lists of all streams
         in the database.
@@ -307,34 +338,11 @@ class NilmDB(object):
 
         layout_name: string for nilmdb.layout.get_named(), e.g. 'float32_8'
         """
-        if path[0] != '/':
-            raise ValueError("paths must start with /")
-        [ group, node ] = path.rsplit("/", 1)
-        if group == '':
-            raise ValueError("invalid path")
+        # Create the bulk storage.  Raises ValueError on error, which we
+        # pass along.
+        self.data.create(path, layout_name)
 
-        # Get description
-        try:
-            desc = nilmdb.layout.get_named(layout_name).description()
-        except KeyError:
-            raise ValueError("no such layout")
-
-        # Estimated table size (for PyTables optimization purposes): assume
-        # 3 months worth of data at 8 KHz.  It's OK if this is wrong.
-        exp_rows = 8000 * 60*60*24*30*3
-
-        # Create the table
-        try:
-            table = self.h5file.createTable(group, node,
-                                            description = desc,
-                                            expectedrows = exp_rows,
-                                            createparents = True)
-        except AttributeError:
-            # Trying to create e.g. /foo/bar/baz when /foo/bar is already
-            # a table raises this error.
-            raise ValueError("error creating table at that path")
-
-        # Insert into SQL database once the PyTables is happy
+        # Insert into SQL database once the bulk storage is happy
         with self.con as con:
             con.execute("INSERT INTO streams (path, layout) VALUES (?,?)",
                         (path, layout_name))
@@ -380,24 +388,14 @@ class NilmDB(object):
 
     def stream_destroy(self, path):
         """Fully remove a table and all of its data from the database.
-        No way to undo it!  The group structure is removed, if there
-        are no other tables in it.  Metadata is removed."""
+        No way to undo it!  Metadata is removed."""
         stream_id = self._stream_id(path)
 
-        # Delete the cached interval data
-        if stream_id in self._cached_iset:
-            del self._cached_iset[stream_id]
+        # Delete the cached interval data (if it was cached)
+        self._get_intervals.cache_remove(self, stream_id)
 
-        # Delete the data node, and all parent nodes (if they have no
-        # remaining children)
-        split_path = path.lstrip('/').split("/")
-        while split_path:
-            name = split_path.pop()
-            where = "/" + "/".join(split_path)
-            try:
-                self.h5file.removeNode(where, name, recursive = False)
-            except tables.NodeError:
-                break
+        # Delete the data
+        self.data.destroy(path)
 
         # Delete metadata, stream, intervals
         with self.con as con:
@@ -421,21 +419,19 @@ class NilmDB(object):
             raise OverlapError("new data overlaps existing data at range: "
                                + str(iset & interval))
 
-        # Insert the data into pytables
-        table = self.h5file.getNode(path)
+        # Insert the data
+        table = self.data.getnode(path)
         row_start = table.nrows
         table.append(data)
         row_end = table.nrows
-        table.flush()
 
         # Insert the record into the sql database.
-        # Casts are to convert from numpy.int64.
-        self._add_interval(stream_id, interval, int(row_start), int(row_end))
+        self._add_interval(stream_id, interval, row_start, row_end)
 
         # And that's all
         return "ok"
 
-    def _find_start(self, table, interval):
+    def _find_start(self, table, dbinterval):
         """
         Given a DBInterval, find the row in the database that
         corresponds to the start time.  Return the first database
@@ -443,14 +439,14 @@ class NilmDB(object):
         equal to 'start'.
         """
         # Optimization for the common case where an interval wasn't truncated
-        if interval.start == interval.db_start:
-            return interval.db_startpos
-        return bisect.bisect_left(BisectableTable(table),
-                                  interval.start,
-                                  interval.db_startpos,
-                                  interval.db_endpos)
+        if dbinterval.start == dbinterval.db_start:
+            return dbinterval.db_startpos
+        return bisect.bisect_left(bulkdata.TimestampOnlyTable(table),
+                                  dbinterval.start,
+                                  dbinterval.db_startpos,
+                                  dbinterval.db_endpos)
 
-    def _find_end(self, table, interval):
+    def _find_end(self, table, dbinterval):
         """
         Given a DBInterval, find the row in the database that follows
         the end time.  Return the first database position after the
@@ -458,16 +454,16 @@ class NilmDB(object):
         to 'end'.
         """
         # Optimization for the common case where an interval wasn't truncated
-        if interval.end == interval.db_end:
-            return interval.db_endpos
+        if dbinterval.end == dbinterval.db_end:
+            return dbinterval.db_endpos
         # Note that we still use bisect_left here, because we don't
         # want to include the given timestamp in the results.  This is
         # so a queries like 1:00 -> 2:00 and 2:00 -> 3:00 return
         # non-overlapping data.
-        return bisect.bisect_left(BisectableTable(table),
-                                  interval.end,
-                                  interval.db_startpos,
-                                  interval.db_endpos)
+        return bisect.bisect_left(bulkdata.TimestampOnlyTable(table),
+                                  dbinterval.end,
+                                  dbinterval.db_startpos,
+                                  dbinterval.db_endpos)
 
     def stream_extract(self, path, start = None, end = None, count = False):
         """
@@ -488,8 +484,8 @@ class NilmDB(object):
         than actually fetching the data.  It is not limited by
         max_results.
         """
-        table = self.h5file.getNode(path)
         stream_id = self._stream_id(path)
+        table = self.data.getnode(path)
         intervals = self._get_intervals(stream_id)
         requested = Interval(start or 0, end or 1e12)
         result = []
@@ -526,3 +522,45 @@ class NilmDB(object):
         if count:
             return matched
         return (result, restart)
+
+    def stream_remove(self, path, start = None, end = None):
+        """
+        Remove data from the specified time interval within a stream.
+        Removes all data in the interval [start, end), and intervals
+        are truncated or split appropriately.  Returns the number of
+        data points removed.
+        """
+        stream_id = self._stream_id(path)
+        table = self.data.getnode(path)
+        intervals = self._get_intervals(stream_id)
+        to_remove = Interval(start or 0, end or 1e12)
+        removed = 0
+
+        if start == end:
+            return 0
+
+        # Can't remove intervals from within the iterator, so we need to
+        # remember what's currently in the intersection now.
+        all_candidates = list(intervals.intersection(to_remove, orig = True))
+
+        for (dbint, orig) in all_candidates:
+            # Find row start and end
+            row_start = self._find_start(table, dbint)
+            row_end = self._find_end(table, dbint)
+
+            # Adjust the DBInterval to match the newly found ends
+            dbint.db_start = dbint.start
+            dbint.db_end = dbint.end
+            dbint.db_startpos = row_start
+            dbint.db_endpos = row_end
+
+            # Remove interval from the database
+            self._remove_interval(stream_id, orig, dbint)
+
+            # Remove data from the underlying table storage
+            table.remove(row_start, row_end)
+
+            # Count how many were removed
+            removed += row_end - row_start
+
+        return removed

nilmdb/server.py

@@ -3,15 +3,18 @@
 # Need absolute_import so that "import nilmdb" won't pull in nilmdb.py,
 # but will pull the nilmdb module instead.
 from __future__ import absolute_import
+from nilmdb.utils.printf import *
 import nilmdb
 
-from nilmdb.printf import *
-
 import cherrypy
 import sys
 import time
 import os
 import simplejson as json
+import decorator
+import traceback
+
+from nilmdb.nilmdb import NilmDBError
 
 try:
     import cherrypy
@@ -24,8 +27,53 @@ class NilmApp(object):
     def __init__(self, db):
         self.db = db
 
-version = "1.1"
+version = "1.2"
 
+# Decorators
+def chunked_response(func):
+    """Decorator to enable chunked responses."""
+    # Set this to False to get better tracebacks from some requests
+    # (/stream/extract, /stream/intervals).
+    func._cp_config = { 'response.stream': True }
+    return func
+
+@decorator.decorator
+def workaround_cp_bug_1200(func, *args, **kwargs): # pragma: no cover
+    """Decorator to work around CherryPy bug #1200 in a response
+    generator.
+
+    Even if chunked responses are disabled, LookupError or
+    UnicodeError exceptions may still be swallowed by CherryPy due to
+    bug #1200.  This throws them as generic Exceptions instead so that
+    they make it through.
+    """
+    try:
+        for val in func(*args, **kwargs):
+            yield val
+    except (LookupError, UnicodeError) as e:
+        raise Exception("bug workaround; real exception is:\n" +
+                        traceback.format_exc())
+
+def exception_to_httperror(*expected):
+    """Return a decorator-generating function that catches expected
+    errors and throws a HTTPError describing it instead.
+
+        @exception_to_httperror(NilmDBError, ValueError)
+        def foo():
+            pass
+    """
+    def wrapper(func, *args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except expected as e:
+            message = sprintf("%s", str(e))
+            raise cherrypy.HTTPError("400 Bad Request", message)
+    # We need to preserve the function's argspecs for CherryPy to
+    # handle argument errors correctly.  Decorator.decorator takes
+    # care of that.
+    return decorator.decorator(wrapper)
+
+# CherryPy apps
 class Root(NilmApp):
     """Root application for NILM database"""
 
@@ -59,7 +107,7 @@ class Root(NilmApp):
     @cherrypy.expose
     @cherrypy.tools.json_out()
     def dbsize(self):
-        return nilmdb.du.du(self.db.get_basepath())
+        return nilmdb.utils.du(self.db.get_basepath())
 
 class Stream(NilmApp):
     """Stream-specific operations"""
@@ -78,26 +126,20 @@ class Stream(NilmApp):
     # /stream/create?path=/newton/prep&layout=PrepData
     @cherrypy.expose
     @cherrypy.tools.json_out()
+    @exception_to_httperror(NilmDBError, ValueError)
     def create(self, path, layout):
         """Create a new stream in the database.  Provide path
         and one of the nilmdb.layout.layouts keys.
         """
-        try:
         return self.db.stream_create(path, layout)
-        except Exception as e:
-            message = sprintf("%s: %s", type(e).__name__, e.message)
-            raise cherrypy.HTTPError("400 Bad Request", message)
 
     # /stream/destroy?path=/newton/prep
     @cherrypy.expose
     @cherrypy.tools.json_out()
+    @exception_to_httperror(NilmDBError)
     def destroy(self, path):
         """Delete a stream and its associated data."""
-        try:
         return self.db.stream_destroy(path)
-        except Exception as e:
-            message = sprintf("%s: %s", type(e).__name__, e.message)
-            raise cherrypy.HTTPError("400 Bad Request", message)
 
     # /stream/get_metadata?path=/newton/prep
     # /stream/get_metadata?path=/newton/prep&key=foo&key=bar
@@ -126,30 +168,24 @@ class Stream(NilmApp):
     # /stream/set_metadata?path=/newton/prep&data=<json>
     @cherrypy.expose
     @cherrypy.tools.json_out()
+    @exception_to_httperror(NilmDBError, LookupError, TypeError)
     def set_metadata(self, path, data):
         """Set metadata for the named stream, replacing any
         existing metadata.  Data should be a json-encoded
         dictionary"""
-        try:
         data_dict = json.loads(data)
         self.db.stream_set_metadata(path, data_dict)
-        except Exception as e:
-            message = sprintf("%s: %s", type(e).__name__, e.message)
-            raise cherrypy.HTTPError("400 Bad Request", message)
         return "ok"
 
     # /stream/update_metadata?path=/newton/prep&data=<json>
     @cherrypy.expose
     @cherrypy.tools.json_out()
+    @exception_to_httperror(NilmDBError, LookupError, TypeError)
     def update_metadata(self, path, data):
         """Update metadata for the named stream.  Data
         should be a json-encoded dictionary"""
-        try:
         data_dict = json.loads(data)
         self.db.stream_update_metadata(path, data_dict)
-        except Exception as e:
-            message = sprintf("%s: %s", type(e).__name__, e.message)
-            raise cherrypy.HTTPError("400 Bad Request", message)
         return "ok"
 
     # /stream/insert?path=/newton/prep
@@ -182,7 +218,7 @@ class Stream(NilmApp):
             parser.parse(body)
         except nilmdb.layout.ParserError as e:
             raise cherrypy.HTTPError("400 Bad Request",
-                                     "Error parsing input data: " +
+                                     "error parsing input data: " +
                                      e.message)
 
         if (not parser.min_timestamp or not parser.max_timestamp or
@@ -211,9 +247,31 @@ class Stream(NilmApp):
         # Done
         return "ok"
 
+    # /stream/remove?path=/newton/prep
+    # /stream/remove?path=/newton/prep&start=1234567890.0&end=1234567899.0
+    @cherrypy.expose
+    @cherrypy.tools.json_out()
+    @exception_to_httperror(NilmDBError)
+    def remove(self, path, start = None, end = None):
+        """
+        Remove data from the backend database.  Removes all data in
+        the interval [start, end).  Returns the number of data points
+        removed.
+        """
+        if start is not None:
+            start = float(start)
+        if end is not None:
+            end = float(end)
+        if start is not None and end is not None:
+            if end < start:
+                raise cherrypy.HTTPError("400 Bad Request",
+                                         "end before start")
+        return self.db.stream_remove(path, start, end)
+
     # /stream/intervals?path=/newton/prep
     # /stream/intervals?path=/newton/prep&start=1234567890.0&end=1234567899.0
     @cherrypy.expose
+    @chunked_response
     def intervals(self, path, start = None, end = None):
         """
         Get intervals from backend database.  Streams the resulting
@@ -235,9 +293,9 @@ class Stream(NilmApp):
         if len(streams) != 1:
             raise cherrypy.HTTPError("404 Not Found", "No such stream")
 
+        @workaround_cp_bug_1200
         def content(start, end):
-            # Note: disable response.stream below to get better debug info
-            # from tracebacks in this subfunction.
+            # Note: disable chunked responses to see tracebacks from here.
             while True:
                 (intervals, restart) = self.db.stream_intervals(path,start,end)
                 response = ''.join([ json.dumps(i) + "\n" for i in intervals ])
@@ -246,10 +304,10 @@ class Stream(NilmApp):
                     break
                 start = restart
         return content(start, end)
-    intervals._cp_config = { 'response.stream': True } # chunked HTTP response
 
     # /stream/extract?path=/newton/prep&start=1234567890.0&end=1234567899.0
     @cherrypy.expose
+    @chunked_response
     def extract(self, path, start = None, end = None, count = False):
         """
         Extract data from backend database.  Streams the resulting
@@ -279,9 +337,9 @@ class Stream(NilmApp):
         # Get formatter
         formatter = nilmdb.layout.Formatter(layout)
 
+        @workaround_cp_bug_1200
         def content(start, end, count):
-            # Note: disable response.stream below to get better debug info
-            # from tracebacks in this subfunction.
+            # Note: disable chunked responses to see tracebacks from here.
             if count:
                 matched = self.db.stream_extract(path, start, end, count)
                 yield sprintf("%d\n", matched)
@@ -297,8 +355,6 @@ class Stream(NilmApp):
                     return
                 start = restart
         return content(start, end, count)
-    extract._cp_config = { 'response.stream': True } # chunked HTTP response
-
 
 class Exiter(object):
     """App that exits the server, for testing"""
@@ -323,7 +379,7 @@ class Server(object):
         # Need to wrap DB object in a serializer because we'll call
         # into it from separate threads.
         self.embedded = embedded
-        self.db = nilmdb.serializer.WrapObject(db)
+        self.db = nilmdb.utils.Serializer(db)
         cherrypy.config.update({
             'server.socket_host': host,
             'server.socket_port': port,
@@ -339,6 +395,11 @@ class Server(object):
         cherrypy.config.update({ 'request.show_tracebacks' : True })
         self.force_traceback = force_traceback
 
+        # Patch CherryPy error handler to never pad out error messages.
+        # This isn't necessary, but then again, neither is padding the
+        # error messages.
+        cherrypy._cperror._ie_friendly_error_sizes = {}
+
         cherrypy.tree.apps = {}
         cherrypy.tree.mount(Root(self.db, self.version), "/")
         cherrypy.tree.mount(Stream(self.db), "/stream")

nilmdb/timestamper.py

@@ -1,7 +1,7 @@
 """File-like objects that add timestamps to the input lines"""
 
 from __future__ import absolute_import
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 import time
 import os

nilmdb/utils/__init__.py

@@ -0,0 +1,11 @@
+"""NilmDB utilities"""
+
+from .timer import Timer
+from .iteratorizer import Iteratorizer
+from .serializer import Serializer
+from .lrucache import lru_cache
+from .diskusage import du
+from .mustclose import must_close
+from .urllib import urlencode
+from . import misc
+from . import atomic

nilmdb/utils/atomic.py

@@ -0,0 +1,26 @@
+# Atomic file writing helper.
+
+import os
+
+def replace_file(filename, content):
+    """Attempt to atomically and durably replace the filename with the
+    given contents.  This is intended to be 'pretty good on most
+    OSes', but not necessarily bulletproof."""
+
+    newfilename = filename + ".new"
+
+    # Write to new file, flush it
+    with open(newfilename, "wb") as f:
+        f.write(content)
+        f.flush()
+        os.fsync(f.fileno())
+
+    # Move new file over old one
+    try:
+        os.rename(newfilename, filename)
+    except OSError: # pragma: no cover
+        # Some OSes might not support renaming over an existing file.
+        # This is definitely NOT atomic!
+        os.remove(filename)
+        os.rename(newfilename, filename)
+

nilmdb/utils/lrucache.py

@@ -0,0 +1,77 @@
+# Memoize a function's return value with a least-recently-used cache
+# Based on:
+#   http://code.activestate.com/recipes/498245-lru-and-lfu-cache-decorators/
+# with added 'destructor' functionality.
+
+import collections
+import decorator
+import warnings
+
+def lru_cache(size = 10, onremove = None, keys = slice(None)):
+    """Least-recently-used cache decorator.
+
+    @lru_cache(size = 10, onevict = None)
+    def f(...):
+        pass
+
+    Given a function and arguments, memoize its return value.  Up to
+    'size' elements are cached.  'keys' is a slice object that
+    represents which arguments are used as the cache key.
+
+    When evicting a value from the cache, call the function
+    'onremove' with the value that's being evicted.
+
+    Call f.cache_remove(...) to evict the cache entry with the given
+    arguments.  Call f.cache_remove_all() to evict all entries.
+    f.cache_hits and f.cache_misses give statistics.
+    """
+
+    def decorate(func):
+        cache = collections.OrderedDict()	# order: least- to most-recent
+
+        def evict(value):
+            if onremove:
+                onremove(value)
+
+        def wrapper(orig, *args, **kwargs):
+            if kwargs:
+                raise NotImplementedError("kwargs not supported")
+            key = args[keys]
+            try:
+                value = cache.pop(key)
+                orig.cache_hits += 1
+            except KeyError:
+                value = orig(*args)
+                orig.cache_misses += 1
+                if len(cache) >= size:
+                    evict(cache.popitem(0)[1])	# evict LRU cache entry
+            cache[key] = value              	# (re-)insert this key at end
+            return value
+
+        def cache_remove(*args):
+            """Remove the described key from this cache, if present."""
+            key = args
+            if key in cache:
+                evict(cache.pop(key))
+            else:
+                if len(cache) > 0 and len(args) != len(cache.iterkeys().next()):
+                    raise KeyError("trying to remove from LRU cache, but "
+                                   "number of arguments doesn't match the "
+                                   "cache key length")
+
+        def cache_remove_all():
+            for key in cache:
+                evict(cache.pop(key))
+
+        def cache_info():
+            return (func.cache_hits, func.cache_misses)
+
+        new = decorator.decorator(wrapper, func)
+        func.cache_hits = 0
+        func.cache_misses = 0
+        new.cache_info = cache_info
+        new.cache_remove = cache_remove
+        new.cache_remove_all = cache_remove_all
+        return new
+
+    return decorate

nilmdb/utils/misc.py

@@ -0,0 +1,8 @@
+import itertools
+
+def pairwise(iterable):
+    "s -> (s0,s1), (s1,s2), ..., (sn,None)"
+    a, b = itertools.tee(iterable)
+    next(b, None)
+    return itertools.izip_longest(a, b)
+

nilmdb/utils/mustclose.py

@@ -0,0 +1,63 @@
+from nilmdb.utils.printf import *
+import sys
+import inspect
+import decorator
+
+def must_close(errorfile = sys.stderr, wrap_verify = False):
+    """Class decorator that warns on 'errorfile' at deletion time if
+    the class's close() member wasn't called.
+
+    If 'wrap_verify' is True, every class method is wrapped with a
+    verifier that will raise AssertionError if the .close() method has
+    already been called."""
+    def class_decorator(cls):
+
+        # Helper to replace a class method with a wrapper function,
+        # while maintaining argument specs etc.
+        def wrap_class_method(wrapper_func):
+            method = wrapper_func.__name__
+            if method in cls.__dict__:
+                orig = getattr(cls, method).im_func
+            else:
+                orig = lambda self: None
+            setattr(cls, method, decorator.decorator(wrapper_func, orig))
+
+        @wrap_class_method
+        def __init__(orig, self, *args, **kwargs):
+            ret = orig(self, *args, **kwargs)
+            self.__dict__["_must_close"] = True
+            self.__dict__["_must_close_initialized"] = True
+            return ret
+
+        @wrap_class_method
+        def __del__(orig, self, *args, **kwargs):
+            if "_must_close" in self.__dict__:
+                fprintf(errorfile, "error: %s.close() wasn't called!\n",
+                        self.__class__.__name__)
+            return orig(self, *args, **kwargs)
+
+        @wrap_class_method
+        def close(orig, self, *args, **kwargs):
+            del self._must_close
+            return orig(self, *args, **kwargs)
+
+        # Optionally wrap all other functions
+        def verifier(orig, self, *args, **kwargs):
+            if ("_must_close" not in self.__dict__ and
+                "_must_close_initialized" in self.__dict__):
+                raise AssertionError("called " + str(orig) + " after close")
+            return orig(self, *args, **kwargs)
+        if wrap_verify:
+            for (name, method) in inspect.getmembers(cls, inspect.ismethod):
+                # Skip class methods
+                if method.__self__ is not None:
+                    continue
+                # Skip some methods
+                if name in [ "__del__", "__init__" ]:
+                    continue
+                # Set up wrapper
+                setattr(cls, name, decorator.decorator(verifier,
+                                                       method.im_func))
+
+        return cls
+    return class_decorator

nilmdb/utils/serializer.py

@@ -67,3 +67,6 @@ class WrapObject(object):
     def __del__(self):
         self.__wrap_call_queue.put((None, None, None, None))
         self.__wrap_serializer.join()
+
+# Just an alias
+Serializer = WrapObject

nilmdb/utils/timer.py

@@ -5,6 +5,7 @@
 #   with nilmdb.Timer("flush"):
 #       foo.flush()
 
+from __future__ import print_function
 import contextlib
 import time
 
@@ -18,4 +19,4 @@ def Timer(name = None, tosyslog = False):
         import syslog
         syslog.syslog(msg)
     else:
-        print msg
+        print(msg)

nilmdb/utils/urllib.py

@@ -0,0 +1,40 @@
+from __future__ import absolute_import
+from urllib import quote_plus, _is_unicode
+
+# urllib.urlencode insists on encoding Unicode as ASCII.  This is based
+# on that function, except we always encode it as UTF-8 instead.
+
+def urlencode(query):
+    """Encode a dictionary into a URL query string.
+
+    If any values in the query arg are sequences, each sequence
+    element is converted to a separate parameter.
+    """
+
+    query = query.items()
+
+    l = []
+    for k, v in query:
+        k = quote_plus(str(k))
+        if isinstance(v, str):
+            v = quote_plus(v)
+            l.append(k + '=' + v)
+        elif _is_unicode(v):
+            # is there a reasonable way to convert to ASCII?
+            # encode generates a string, but "replace" or "ignore"
+            # lose information and "strict" can raise UnicodeError
+            v = quote_plus(v.encode("utf-8","strict"))
+            l.append(k + '=' + v)
+        else:
+            try:
+                # is this a sufficient test for sequence-ness?
+                len(v)
+            except TypeError:
+                # not a sequence
+                v = quote_plus(str(v))
+                l.append(k + '=' + v)
+            else:
+                # loop over the sequence
+                for elt in v:
+                    l.append(k + '=' + quote_plus(str(elt)))
+    return '&'.join(l)

runserver.py

@@ -3,14 +3,17 @@
 import nilmdb
 import argparse
 
-parser = argparse.ArgumentParser(description='Run the NILM server')
+formatter = argparse.ArgumentDefaultsHelpFormatter
+parser = argparse.ArgumentParser(description='Run the NILM server',
+                                 formatter_class = formatter)
 parser.add_argument('-p', '--port', help='Port number', type=int, default=12380)
+parser.add_argument('-d', '--database', help='Database directory', default="db")
 parser.add_argument('-y', '--yappi', help='Run with yappi profiler',
                     action='store_true')
 args = parser.parse_args()
 
 # Start web app on a custom port
-db = nilmdb.NilmDB("db")
+db = nilmdb.NilmDB(args.database)
 server = nilmdb.Server(db, host = "127.0.0.1",
                        port = args.port,
                        embedded = False)

runtests.py

@@ -0,0 +1,46 @@
+#!/usr/bin/python
+
+import nose
+import os
+import sys
+import glob
+from collections import OrderedDict
+
+class JimOrderPlugin(nose.plugins.Plugin):
+    """When searching for tests and encountering a directory that
+    contains a 'test.order' file, run tests listed in that file, in the
+    order that they're listed.  Globs are OK in that file and duplicates
+    are removed."""
+    name = 'jimorder'
+    score = 10000
+
+    def prepareTestLoader(self, loader):
+        def wrap(func):
+            def wrapper(name, *args, **kwargs):
+                addr = nose.selector.TestAddress(
+                    name, workingDir=loader.workingDir)
+                try:
+                    order = os.path.join(addr.filename, "test.order")
+                except:
+                    order = None
+                if order and os.path.exists(order):
+                    files = []
+                    for line in open(order):
+                        line = line.split('#')[0].strip()
+                        if not line:
+                            continue
+                        fn = os.path.join(addr.filename, line.strip())
+                        files.extend(sorted(glob.glob(fn)) or [fn])
+                    files = list(OrderedDict.fromkeys(files))
+                    tests = [ wrapper(fn, *args, **kwargs) for fn in files ]
+                    return loader.suiteClass(tests)
+                return func(name, *args, **kwargs)
+            return wrapper
+        loader.loadTestsFromName = wrap(loader.loadTestsFromName)
+        return loader
+
+# Use setup.cfg for most of the test configuration.  Adding
+# --with-jimorder here means that a normal "nosetests" run will
+# still work, it just won't support test.order.
+nose.main(addplugins = [ JimOrderPlugin() ],
+          argv = sys.argv + ["--with-jimorder"])

setup.cfg

@@ -8,8 +8,14 @@ cover-package=nilmdb
 cover-erase=
 ##cover-html=         # this works, puts html output in cover/ dir
 ##cover-branches=     # need nose 1.1.3 for this
+#debug=nose
+#debug-log=nose.log
 stop=
 verbosity=2
+tests=tests
+#tests=tests/test_bulkdata.py
+#tests=tests/test_mustclose.py
+#tests=tests/test_lrucache.py
 #tests=tests/test_cmdline.py
 #tests=tests/test_layout.py
 #tests=tests/test_rbtree.py
@@ -21,6 +27,7 @@ verbosity=2
 #tests=tests/test_serializer.py
 #tests=tests/test_iteratorizer.py
 #tests=tests/test_client.py:TestClient.test_client_nilmdb
+#tests=tests/test_nilmdb.py
 #with-profile=
 #profile-sort=time
 ##profile-restrict=10  # doesn't work right, treated as string or something

tests/data/prep-20120323T1002-first19lines

@@ -0,0 +1,19 @@
+2.56437e+05  2.24430e+05  4.01161e+03  3.47534e+03  7.49589e+03  3.38894e+03  2.61397e+02  3.73126e+03  
+2.53963e+05  2.24167e+05  5.62107e+03  1.54801e+03  9.16517e+03  3.52293e+03  1.05893e+03  2.99696e+03  
+2.58508e+05  2.24930e+05  6.01140e+03  8.18866e+02  9.03995e+03  4.48244e+03  2.49039e+03  2.67934e+03  
+2.59627e+05  2.26022e+05  4.47450e+03  2.42302e+03  7.41419e+03  5.07197e+03  2.43938e+03  2.96296e+03  
+2.55187e+05  2.24632e+05  4.73857e+03  3.39804e+03  7.39512e+03  4.72645e+03  1.83903e+03  3.39353e+03  
+2.57102e+05  2.21623e+05  6.14413e+03  1.44109e+03  8.75648e+03  3.49532e+03  1.86994e+03  3.75253e+03  
+2.63653e+05  2.21770e+05  6.22177e+03  7.38962e+02  9.54760e+03  2.66682e+03  1.46266e+03  3.33257e+03  
+2.63613e+05  2.25256e+05  4.47712e+03  2.43745e+03  8.51021e+03  3.85563e+03  9.59442e+02  2.38718e+03  
+2.55350e+05  2.26264e+05  4.28372e+03  3.92394e+03  7.91247e+03  5.46652e+03  1.28499e+03  2.09372e+03  
+2.52727e+05  2.24609e+05  5.85193e+03  2.49198e+03  8.54063e+03  5.62305e+03  2.33978e+03  3.00714e+03  
+2.58475e+05  2.23578e+05  5.92487e+03  1.39448e+03  8.77962e+03  4.54418e+03  2.13203e+03  3.84976e+03  
+2.61563e+05  2.24609e+05  4.33614e+03  2.45575e+03  8.05538e+03  3.46911e+03  6.27873e+02  3.66420e+03  
+2.56401e+05  2.24441e+05  4.18715e+03  3.45717e+03  7.90669e+03  3.53355e+03  -5.84482e+00  2.96687e+03  
+2.54745e+05  2.22644e+05  6.02005e+03  1.94721e+03  9.28939e+03  3.80020e+03  1.34820e+03  2.37785e+03  
+2.60723e+05  2.22660e+05  6.69719e+03  1.03048e+03  9.26124e+03  4.34917e+03  2.84530e+03  2.73619e+03  
+2.63089e+05  2.25711e+05  4.77887e+03  2.60417e+03  7.39660e+03  4.59811e+03  2.17472e+03  3.40729e+03  
+2.55843e+05  2.27128e+05  4.02413e+03  4.39323e+03  6.79336e+03  4.62535e+03  7.52009e+02  3.44647e+03  
+2.51904e+05  2.24868e+05  5.82289e+03  3.02127e+03  8.46160e+03  3.80298e+03  8.07212e+02  3.53468e+03  
+2.57670e+05  2.22974e+05  6.73436e+03  1.60956e+03  9.92960e+03  2.98028e+03  1.44168e+03  3.05351e+03  

tests/test.order

@@ -0,0 +1,18 @@
+test_printf.py
+test_lrucache.py
+test_mustclose.py
+
+test_serializer.py
+test_iteratorizer.py
+
+test_timestamper.py
+test_layout.py
+test_rbtree.py
+test_interval.py
+
+test_bulkdata.py
+test_nilmdb.py
+test_client.py
+test_cmdline.py
+
+test_*.py

tests/test_bulkdata.py

@@ -0,0 +1,103 @@
+# -*- coding: utf-8 -*-
+
+import nilmdb
+from nilmdb.utils.printf import *
+import nilmdb.bulkdata
+
+from nose.tools import *
+from nose.tools import assert_raises
+import itertools
+
+from testutil.helpers import *
+
+testdb = "tests/bulkdata-testdb"
+
+from nilmdb.bulkdata import BulkData
+
+class TestBulkData(object):
+
+    def test_bulkdata(self):
+        for (size, files, db) in [ ( 0, 0, testdb ),
+                                       ( 25, 1000, testdb ),
+                                       ( 1000, 3, testdb.decode("utf-8") ) ]:
+            recursive_unlink(db)
+            os.mkdir(db)
+            self.do_basic(db, size, files)
+
+    def do_basic(self, db, size, files):
+        """Do the basic test with variable file_size and files_per_dir"""
+        if not size or not files:
+            data = BulkData(db)
+        else:
+            data = BulkData(db, file_size = size, files_per_dir = files)
+
+        # create empty
+        with assert_raises(ValueError):
+            data.create("/foo", "uint16_8")
+        with assert_raises(ValueError):
+            data.create("foo/bar", "uint16_8")
+        with assert_raises(ValueError):
+            data.create("/foo/bar", "uint8_8")
+        data.create("/foo/bar", "uint16_8")
+        data.create(u"/foo/baz/quux", "float64_16")
+        with assert_raises(ValueError):
+            data.create("/foo/bar/baz", "uint16_8")
+        with assert_raises(ValueError):
+            data.create("/foo/baz", "float64_16")
+
+        # get node -- see if caching works
+        nodes = []
+        for i in range(5000):
+            nodes.append(data.getnode("/foo/bar"))
+            nodes.append(data.getnode("/foo/baz/quux"))
+        del nodes
+
+        # Test node
+        node = data.getnode("/foo/bar")
+        with assert_raises(IndexError):
+            x = node[0]
+        raw = []
+        for i in range(1000):
+            raw.append([10000+i, 1, 2, 3, 4, 5, 6, 7, 8 ])
+        node.append(raw[0:1])
+        node.append(raw[1:100])
+        node.append(raw[100:])
+
+        misc_slices = [ 0, 100, slice(None), slice(0), slice(10),
+                        slice(5,10), slice(3,None), slice(3,-3),
+                        slice(20,10), slice(200,100,-1), slice(None,0,-1),
+                        slice(100,500,5) ]
+        # Extract slices
+        for s in misc_slices:
+            eq_(node[s], raw[s])
+
+        # Get some coverage of remove; remove is more fully tested
+        # in cmdline
+        with assert_raises(IndexError):
+            node.remove(9999,9998)
+
+        # close, reopen
+        # reopen
+        data.close()
+        if not size or not files:
+            data = BulkData(db)
+        else:
+            data = BulkData(db, file_size = size, files_per_dir = files)
+        node = data.getnode("/foo/bar")
+
+        # Extract slices
+        for s in misc_slices:
+            eq_(node[s], raw[s])
+
+        # destroy
+        with assert_raises(ValueError):
+            data.destroy("/foo")
+        with assert_raises(ValueError):
+            data.destroy("/foo/baz")
+        with assert_raises(ValueError):
+            data.destroy("/foo/qwerty")
+        data.destroy("/foo/baz/quux")
+        data.destroy("/foo/bar")
+
+        # close
+        data.close()

tests/test_client.py

@@ -1,5 +1,7 @@
+# -*- coding: utf-8 -*-
+
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 from nilmdb.client import ClientError, ServerError
 
 import datetime_tz
@@ -15,8 +17,9 @@ import cStringIO
 import simplejson as json
 import unittest
 import warnings
+import resource
 
-from test_helpers import *
+from testutil.helpers import *
 
 testdb = "tests/client-testdb"
 
@@ -67,7 +70,11 @@ class TestClient(object):
         eq_(distutils.version.StrictVersion(version),
             distutils.version.StrictVersion(test_server.version))
 
-    def test_client_2_nilmdb(self):
+        # Bad URLs should give 404, not 500
+        with assert_raises(ClientError):
+            client.http.get("/stream/create")
+
+    def test_client_2_createlist(self):
         # Basic stream tests, like those in test_nilmdb:test_stream
         client = nilmdb.Client(url = "http://localhost:12380/")
 
@@ -82,6 +89,8 @@ class TestClient(object):
         # Bad layout type
         with assert_raises(ClientError):
             client.stream_create("/newton/prep", "NoSuchLayout")
+
+        # Create three streams
         client.stream_create("/newton/prep", "PrepData")
         client.stream_create("/newton/raw", "RawData")
         client.stream_create("/newton/zzz/rawnotch", "RawNotchedData")
@@ -95,6 +104,20 @@ class TestClient(object):
         eq_(client.stream_list(layout="RawData"), [ ["/newton/raw", "RawData"] ])
         eq_(client.stream_list(path="/newton/raw"), [ ["/newton/raw", "RawData"] ])
 
+        # Try messing with resource limits to trigger errors and get
+        # more coverage.  Here, make it so we can only create files 1
+        # byte in size, which will trigger an IOError in the server when
+        # we create a table.
+        limit = resource.getrlimit(resource.RLIMIT_FSIZE)
+        resource.setrlimit(resource.RLIMIT_FSIZE, (1, limit[1]))
+        with assert_raises(ServerError) as e:
+            client.stream_create("/newton/hello", "RawData")
+        resource.setrlimit(resource.RLIMIT_FSIZE, limit)
+
+
+    def test_client_3_metadata(self):
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
         # Set / get metadata
         eq_(client.stream_get_metadata("/newton/prep"), {})
         eq_(client.stream_get_metadata("/newton/raw"), {})
@@ -124,7 +147,7 @@ class TestClient(object):
         with assert_raises(ClientError):
             client.stream_update_metadata("/newton/prep", [1,2,3])
 
-    def test_client_3_insert(self):
+    def test_client_4_insert(self):
         client = nilmdb.Client(url = "http://localhost:12380/")
 
         datetime_tz.localtz_set("America/New_York")
@@ -197,16 +220,19 @@ class TestClient(object):
         with assert_raises(ClientError) as e:
             result = client.stream_insert("/newton/prep", data)
         in_("400 Bad Request", str(e.exception))
-        in_("OverlapError", str(e.exception))
+        in_("verlap", str(e.exception))
 
-    def test_client_4_extract(self):
-        # Misc tests for extract.  Most of them are in test_cmdline.
+    def test_client_5_extractremove(self):
+        # Misc tests for extract and remove.  Most of them are in test_cmdline.
         client = nilmdb.Client(url = "http://localhost:12380/")
 
         for x in client.stream_extract("/newton/prep", 123, 123):
             raise Exception("shouldn't be any data for this request")
 
-    def test_client_5_generators(self):
+        with assert_raises(ClientError) as e:
+            client.stream_remove("/newton/prep", 123, 120)
+
+    def test_client_6_generators(self):
         # A lot of the client functionality is already tested by test_cmdline,
         # but this gets a bit more coverage that cmdline misses.
         client = nilmdb.Client(url = "http://localhost:12380/")
@@ -255,7 +281,7 @@ class TestClient(object):
             in_("404 Not Found", str(e.exception))
             in_("No such stream", str(e.exception))
 
-    def test_client_6_chunked(self):
+    def test_client_7_chunked(self):
         # Make sure that /stream/intervals and /stream/extract
         # properly return streaming, chunked response.  Pokes around
         # in client.http internals a bit to look at the response
@@ -277,3 +303,40 @@ class TestClient(object):
                               "end": "123" }, retjson=False)
         if "transfer-encoding: chunked" not in client.http._headers.lower():
             warnings.warn("Non-chunked HTTP response for /stream/extract")
+
+    def test_client_8_unicode(self):
+        # Basic Unicode tests
+        client = nilmdb.Client(url = "http://localhost:12380/")
+
+        # Delete streams that exist
+        for stream in client.stream_list():
+            client.stream_destroy(stream[0])
+
+        # Database is empty
+        eq_(client.stream_list(), [])
+
+        # Create Unicode stream, match it
+        raw = [ u"/düsseldorf/raw", u"uint16_6" ]
+        prep = [ u"/düsseldorf/prep", u"uint16_6" ]
+        client.stream_create(*raw)
+        eq_(client.stream_list(), [raw])
+        eq_(client.stream_list(layout=raw[1]), [raw])
+        eq_(client.stream_list(path=raw[0]), [raw])
+        client.stream_create(*prep)
+        eq_(client.stream_list(), [prep, raw])
+
+        # Set / get metadata with Unicode keys and values
+        eq_(client.stream_get_metadata(raw[0]), {})
+        eq_(client.stream_get_metadata(prep[0]), {})
+        meta1 = { u"alpha": u"α",
+                  u"β": u"beta" }
+        meta2 = { u"alpha": u"α" }
+        meta3 = { u"β": u"beta" }
+        client.stream_set_metadata(prep[0], meta1)
+        client.stream_update_metadata(prep[0], {})
+        client.stream_update_metadata(raw[0], meta2)
+        client.stream_update_metadata(raw[0], meta3)
+        eq_(client.stream_get_metadata(prep[0]), meta1)
+        eq_(client.stream_get_metadata(raw[0]), meta1)
+        eq_(client.stream_get_metadata(raw[0], [ "alpha" ]), meta2)
+        eq_(client.stream_get_metadata(raw[0], [ "alpha", "β" ]), meta1)

tests/test_cmdline.py

@@ -1,29 +1,35 @@
+# -*- coding: utf-8 -*-
+
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import nilmdb.cmdline
 
+import unittest
 from nose.tools import *
 from nose.tools import assert_raises
 import itertools
 import datetime_tz
 import os
+import re
 import shutil
 import sys
 import threading
 import urllib2
 from urllib2 import urlopen, HTTPError
 import Queue
-import cStringIO
+import StringIO
 import shlex
 
-from test_helpers import *
+from testutil.helpers import *
 
 testdb = "tests/cmdline-testdb"
 
-def server_start(max_results = None):
+def server_start(max_results = None, bulkdata_args = {}):
     global test_server, test_db
     # Start web app on a custom port
-    test_db = nilmdb.NilmDB(testdb, sync = False, max_results = max_results)
+    test_db = nilmdb.NilmDB(testdb, sync = False,
+                            max_results = max_results,
+                            bulkdata_args = bulkdata_args)
     test_server = nilmdb.Server(test_db, host = "127.0.0.1",
                                 port = 12380, stoppable = False,
                                 fast_shutdown = True,
@@ -45,12 +51,18 @@ def setup_module():
 def teardown_module():
     server_stop()
 
+# Add an encoding property to StringIO so Python will convert Unicode
+# properly when writing or reading.
+class UTF8StringIO(StringIO.StringIO):
+    encoding = 'utf-8'
+
 class TestCmdline(object):
 
     def run(self, arg_string, infile=None, outfile=None):
         """Run a cmdline client with the specified argument string,
         passing the given input.  Returns a tuple with the output and
         exit code"""
+        # printf("TZ=UTC ./nilmtool.py %s\n", arg_string)
         class stdio_wrapper:
             def __init__(self, stdin, stdout, stderr):
                 self.io = (stdin, stdout, stderr)
@@ -61,15 +73,18 @@ class TestCmdline(object):
                 ( sys.stdin, sys.stdout, sys.stderr ) = self.saved
         # Empty input if none provided
         if infile is None:
-            infile = cStringIO.StringIO("")
+            infile = UTF8StringIO("")
         # Capture stderr
-        errfile = cStringIO.StringIO()
+        errfile = UTF8StringIO()
         if outfile is None:
             # If no output file, capture stdout with stderr
             outfile = errfile
         with stdio_wrapper(infile, outfile, errfile) as s:
             try:
-                nilmdb.cmdline.Cmdline(shlex.split(arg_string)).run()
+                # shlex doesn't support Unicode very well.  Encode the
+                # string as UTF-8 explicitly before splitting.
+                args = shlex.split(arg_string.encode('utf-8'))
+                nilmdb.cmdline.Cmdline(args).run()
                 sys.exit(0)
             except SystemExit as e:
                 exitcode = e.code
@@ -83,14 +98,24 @@ class TestCmdline(object):
             self.dump()
             eq_(self.exitcode, 0)
 
-    def fail(self, arg_string, infile = None, exitcode = None):
+    def fail(self, arg_string, infile = None,
+             exitcode = None, require_error = True):
         self.run(arg_string, infile)
         if exitcode is not None and self.exitcode != exitcode:
+            # Wrong exit code
             self.dump()
             eq_(self.exitcode, exitcode)
         if self.exitcode == 0:
+            # Success, when we wanted failure
             self.dump()
             ne_(self.exitcode, 0)
+        # Make sure the output contains the word "error" at the
+        # beginning of a line, but only if an exitcode wasn't
+        # specified.
+        if require_error and not re.search("^error",
+                                           self.captured, re.MULTILINE):
+            raise AssertionError("command failed, but output doesn't "
+                                 "contain the string 'error'")
 
     def contain(self, checkstring):
         in_(checkstring, self.captured)
@@ -120,7 +145,7 @@ class TestCmdline(object):
     def dump(self):
         printf("-----dump start-----\n%s-----dump end-----\n", self.captured)
 
-    def test_cmdline_01_basic(self):
+    def test_01_basic(self):
 
         # help
         self.ok("--help")
@@ -166,14 +191,14 @@ class TestCmdline(object):
             self.fail("extract --start 2000-01-01 --start 2001-01-02")
             self.contain("duplicated argument")
 
-    def test_cmdline_02_info(self):
+    def test_02_info(self):
         self.ok("info")
         self.contain("Server URL: http://localhost:12380/")
         self.contain("Server version: " + test_server.version)
         self.contain("Server database path")
         self.contain("Server database size")
 
-    def test_cmdline_03_createlist(self):
+    def test_03_createlist(self):
         # Basic stream tests, like those in test_client.
 
         # No streams
@@ -190,6 +215,10 @@ class TestCmdline(object):
         # Bad layout type
         self.fail("create /newton/prep NoSuchLayout")
         self.contain("no such layout")
+        self.fail("create /newton/prep float32_0")
+        self.contain("no such layout")
+        self.fail("create /newton/prep float33_1")
+        self.contain("no such layout")
 
         # Create a few streams
         self.ok("create /newton/zzz/rawnotch RawNotchedData")
@@ -199,7 +228,12 @@ class TestCmdline(object):
         # Should not be able to create a stream with another stream as
         # its parent
         self.fail("create /newton/prep/blah PrepData")
-        self.contain("error creating table at that path")
+        self.contain("path is subdir of existing node")
+
+        # Should not be able to create a stream at a location that
+        # has other nodes as children
+        self.fail("create /newton/zzz PrepData")
+        self.contain("subdirs of this path already exist")
 
         # Verify we got those 3 streams and they're returned in
         # alphabetical order.
@@ -208,10 +242,17 @@ class TestCmdline(object):
                    "/newton/raw RawData\n"
                    "/newton/zzz/rawnotch RawNotchedData\n")
 
-        # Match just one type or one path
+        # Match just one type or one path.  Also check
+        # that --path is optional
         self.ok("list --path /newton/raw")
         self.match("/newton/raw RawData\n")
 
+        self.ok("list /newton/raw")
+        self.match("/newton/raw RawData\n")
+
+        self.fail("list -p /newton/raw /newton/raw")
+        self.contain("too many paths")
+
         self.ok("list --layout RawData")
         self.match("/newton/raw RawData\n")
 
@@ -223,10 +264,17 @@ class TestCmdline(object):
         self.ok("list --path *zzz* --layout Raw*")
         self.match("/newton/zzz/rawnotch RawNotchedData\n")
 
+        self.ok("list *zzz* --layout Raw*")
+        self.match("/newton/zzz/rawnotch RawNotchedData\n")
+
         self.ok("list --path *zzz* --layout Prep*")
         self.match("")
 
-    def test_cmdline_04_metadata(self):
+        # reversed range
+        self.fail("list /newton/prep --start 2020-01-01 --end 2000-01-01")
+        self.contain("start is after end")
+
+    def test_04_metadata(self):
         # Set / get metadata
         self.fail("metadata")
         self.fail("metadata --get")
@@ -283,7 +331,7 @@ class TestCmdline(object):
         self.fail("metadata /newton/nosuchpath")
         self.contain("No stream at path /newton/nosuchpath")
 
-    def test_cmdline_05_parsetime(self):
+    def test_05_parsetime(self):
         os.environ['TZ'] = "America/New_York"
         cmd = nilmdb.cmdline.Cmdline(None)
         test = datetime_tz.datetime_tz.now()
@@ -292,30 +340,23 @@ class TestCmdline(object):
         eq_(cmd.parse_time("hi there 20120405 1400-0400 testing! 123"), test)
         eq_(cmd.parse_time("20120405 1800 UTC"), test)
         eq_(cmd.parse_time("20120405 1400-0400 UTC"), test)
+        for badtime in [ "20120405 1400-9999", "hello", "-", "", "14:00" ]:
             with assert_raises(ValueError):
-            print cmd.parse_time("20120405 1400-9999")
-        with assert_raises(ValueError):
-            print cmd.parse_time("hello")
-        with assert_raises(ValueError):
-            print cmd.parse_time("-")
-        with assert_raises(ValueError):
-            print cmd.parse_time("")
-        with assert_raises(ValueError):
-            print cmd.parse_time("14:00")
+                x = cmd.parse_time(badtime)
         eq_(cmd.parse_time("snapshot-20120405-140000.raw.gz"), test)
         eq_(cmd.parse_time("prep-20120405T1400"), test)
 
-    def test_cmdline_06_insert(self):
+    def test_06_insert(self):
         self.ok("insert --help")
 
         self.fail("insert /foo/bar baz qwer")
-        self.contain("Error getting stream info")
+        self.contain("error getting stream info")
 
         self.fail("insert /newton/prep baz qwer")
-        self.match("Error opening input file baz\n")
+        self.match("error opening input file baz\n")
 
         self.fail("insert /newton/prep")
-        self.contain("Error extracting time")
+        self.contain("error extracting time")
 
         self.fail("insert --start 19801205 /newton/prep 1 2 3 4")
         self.contain("--start can only be used with one input file")
@@ -356,7 +397,7 @@ class TestCmdline(object):
         os.environ['TZ'] = "UTC"
         self.fail("insert --rate 120 /newton/raw "
                   "tests/data/prep-20120323T1004")
-        self.contain("Error parsing input data")
+        self.contain("error parsing input data")
 
         # empty data does nothing
         self.ok("insert --rate 120 --start '03/23/2012 06:05:00' /newton/prep "
@@ -365,7 +406,7 @@ class TestCmdline(object):
         # bad start time
         self.fail("insert --rate 120 --start 'whatever' /newton/prep /dev/null")
 
-    def test_cmdline_07_detail(self):
+    def test_07_detail(self):
         # Just count the number of lines, it's probably fine
         self.ok("list --detail")
         lines_(self.captured, 8)
@@ -399,23 +440,30 @@ class TestCmdline(object):
         self.ok("list --detail")
         lines_(self.captured, 8)
 
-    def test_cmdline_08_extract(self):
+    def test_08_extract(self):
         # nonexistent stream
         self.fail("extract /no/such/foo --start 2000-01-01 --end 2020-01-01")
-        self.contain("Error getting stream info")
+        self.contain("error getting stream info")
 
-        # empty ranges return an error
+        # reversed range
+        self.fail("extract -a /newton/prep --start 2020-01-01 --end 2000-01-01")
+        self.contain("start is after end")
+
+        # empty ranges return error 2
         self.fail("extract -a /newton/prep " +
                   "--start '23 Mar 2012 10:00:30' " +
-                  "--end '23 Mar 2012 10:00:30'", exitcode = 2)
+                  "--end '23 Mar 2012 10:00:30'",
+                  exitcode = 2, require_error = False)
         self.contain("no data")
         self.fail("extract -a /newton/prep " +
                   "--start '23 Mar 2012 10:00:30.000001' " +
-                  "--end '23 Mar 2012 10:00:30.000001'", exitcode = 2)
+                  "--end '23 Mar 2012 10:00:30.000001'",
+                  exitcode = 2, require_error = False)
         self.contain("no data")
         self.fail("extract -a /newton/prep " +
                   "--start '23 Mar 2022 10:00:30' " +
-                  "--end '23 Mar 2022 10:00:30'", exitcode = 2)
+                  "--end '23 Mar 2022 10:00:30'",
+                  exitcode = 2, require_error = False)
         self.contain("no data")
 
         # but are ok if we're just counting results
@@ -454,7 +502,7 @@ class TestCmdline(object):
         self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
         self.match("43200\n")
 
-    def test_cmdline_09_truncated(self):
+    def test_09_truncated(self):
         # Test truncated responses by overriding the nilmdb max_results
         server_stop()
         server_start(max_results = 2)
@@ -463,7 +511,102 @@ class TestCmdline(object):
         server_stop()
         server_start()
 
-    def test_cmdline_10_destroy(self):
+    def test_10_remove(self):
+        # Removing data
+
+        # Try nonexistent stream
+        self.fail("remove /no/such/foo --start 2000-01-01 --end 2020-01-01")
+        self.contain("No stream at path")
+
+        self.fail("remove /newton/prep --start 2020-01-01 --end 2000-01-01")
+        self.contain("start is after end")
+
+        # empty ranges return success, backwards ranges return error
+        self.ok("remove /newton/prep " +
+                "--start '23 Mar 2012 10:00:30' " +
+                "--end '23 Mar 2012 10:00:30'")
+        self.match("")
+        self.ok("remove /newton/prep " +
+                "--start '23 Mar 2012 10:00:30.000001' " +
+                "--end '23 Mar 2012 10:00:30.000001'")
+        self.match("")
+        self.ok("remove /newton/prep " +
+                "--start '23 Mar 2022 10:00:30' " +
+                "--end '23 Mar 2022 10:00:30'")
+        self.match("")
+
+        # Verbose
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:30' " +
+                "--end '23 Mar 2012 10:00:30'")
+        self.match("0\n")
+        self.ok("remove --count /newton/prep " +
+                "--start '23 Mar 2012 10:00:30' " +
+                "--end '23 Mar 2012 10:00:30'")
+        self.match("0\n")
+
+        # Make sure we have the data we expect
+        self.ok("list --detail /newton/prep")
+        self.match("/newton/prep PrepData\n" +
+                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:01:59.991668 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:02:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:03:59.991668 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:04:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:05:59.991668 +0000 ]\n")
+
+        # Remove various chunks of prep data and make sure
+        # they're gone.
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:30' " +
+                "--end '23 Mar 2012 10:00:40'")
+        self.match("1200\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:10' " +
+                "--end '23 Mar 2012 10:00:20'")
+        self.match("1200\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:05' " +
+                "--end '23 Mar 2012 10:00:25'")
+        self.match("1200\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:03:50' " +
+                "--end '23 Mar 2012 10:06:50'")
+        self.match("15600\n")
+
+        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
+        self.match("24000\n")
+
+        # See the missing chunks in list output
+        self.ok("list --detail /newton/prep")
+        self.match("/newton/prep PrepData\n" +
+                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:00:05.000000 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:00:25.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:00:30.000000 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:00:40.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:01:59.991668 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:02:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:03:50.000000 +0000 ]\n")
+
+        # Remove all data, verify it's missing
+        self.ok("remove /newton/prep --start 2000-01-01 --end 2020-01-01")
+        self.match("")  # no count requested this time
+        self.ok("list --detail /newton/prep")
+        self.match("/newton/prep PrepData\n" +
+                   "  (no intervals)\n")
+
+        # Reinsert some data, to verify that no overlaps with deleted
+        # data are reported
+        os.environ['TZ'] = "UTC"
+        self.ok("insert --rate 120 /newton/prep "
+                "tests/data/prep-20120323T1000 "
+                "tests/data/prep-20120323T1002")
+
+    def test_11_destroy(self):
         # Delete records
         self.ok("destroy --help")
 
@@ -484,7 +627,7 @@ class TestCmdline(object):
 
         # Notice how they're not empty
         self.ok("list --detail")
-        lines_(self.captured, 8)
+        lines_(self.captured, 7)
 
         # Delete some
         self.ok("destroy /newton/prep")
@@ -513,3 +656,167 @@ class TestCmdline(object):
             # Make sure it was created empty
             self.ok("list --detail --path " + path)
             self.contain("(no intervals)")
+
+    def test_12_unicode(self):
+        # Unicode paths.
+        self.ok("destroy /newton/asdf/qwer")
+        self.ok("destroy /newton/prep")
+        self.ok("destroy /newton/raw")
+        self.ok("destroy /newton/zzz")
+
+        self.ok(u"create /düsseldorf/raw uint16_6")
+        self.ok("list --detail")
+        self.contain(u"/düsseldorf/raw uint16_6")
+        self.contain("(no intervals)")
+
+        # Unicode metadata
+        self.ok(u"metadata /düsseldorf/raw --set α=beta 'γ=δ'")
+        self.ok(u"metadata /düsseldorf/raw --update 'α=β ε τ α'")
+        self.ok(u"metadata /düsseldorf/raw")
+        self.match(u"α=β ε τ α\nγ=δ\n")
+
+        self.ok(u"destroy /düsseldorf/raw")
+
+    def test_13_files(self):
+        # Test BulkData's ability to split into multiple files,
+        # by forcing the file size to be really small.
+        server_stop()
+        server_start(bulkdata_args = { "file_size" : 920, # 23 rows per file
+                                       "files_per_dir" : 3 })
+
+        # Fill data
+        self.ok("create /newton/prep float32_8")
+        os.environ['TZ'] = "UTC"
+        with open("tests/data/prep-20120323T1004-timestamped") as input:
+            self.ok("insert --none /newton/prep", input)
+
+        # Extract it
+        self.ok("extract /newton/prep --start '2000-01-01' " +
+                "--end '2012-03-23 10:04:01'")
+        lines_(self.captured, 120)
+        self.ok("extract /newton/prep --start '2000-01-01' " +
+                "--end '2022-03-23 10:04:01'")
+        lines_(self.captured, 14400)
+
+        # Make sure there were lots of files generated in the database
+        # dir
+        nfiles = 0
+        for (dirpath, dirnames, filenames) in os.walk(testdb):
+            nfiles += len(filenames)
+        assert(nfiles > 500)
+
+        # Make sure we can restart the server with a different file
+        # size and have it still work
+        server_stop()
+        server_start()
+        self.ok("extract /newton/prep --start '2000-01-01' " +
+                "--end '2022-03-23 10:04:01'")
+        lines_(self.captured, 14400)
+
+        # Now recreate the data one more time and make sure there are
+        # fewer files.
+        self.ok("destroy /newton/prep")
+        self.fail("destroy /newton/prep") # already destroyed
+        self.ok("create /newton/prep float32_8")
+        os.environ['TZ'] = "UTC"
+        with open("tests/data/prep-20120323T1004-timestamped") as input:
+            self.ok("insert --none /newton/prep", input)
+        nfiles = 0
+        for (dirpath, dirnames, filenames) in os.walk(testdb):
+            nfiles += len(filenames)
+        lt_(nfiles, 50)
+        self.ok("destroy /newton/prep") # destroy again
+
+    def test_14_remove_files(self):
+        # Test BulkData's ability to remove when data is split into
+        # multiple files.  Should be a fairly comprehensive test of
+        # remove functionality.
+        server_stop()
+        server_start(bulkdata_args = { "file_size" : 920, # 23 rows per file
+                                       "files_per_dir" : 3 })
+
+        # Insert data.  Just for fun, insert out of order
+        self.ok("create /newton/prep PrepData")
+        os.environ['TZ'] = "UTC"
+        self.ok("insert --rate 120 /newton/prep "
+                "tests/data/prep-20120323T1002 "
+                "tests/data/prep-20120323T1000")
+
+        # Should take up about 2.8 MB here (including directory entries)
+        du_before = nilmdb.utils.diskusage.du_bytes(testdb)
+
+        # Make sure we have the data we expect
+        self.ok("list --detail")
+        self.match("/newton/prep PrepData\n" +
+                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:01:59.991668 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:02:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:03:59.991668 +0000 ]\n")
+
+        # Remove various chunks of prep data and make sure
+        # they're gone.
+        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
+        self.match("28800\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:30' " +
+                "--end '23 Mar 2012 10:03:30'")
+        self.match("21600\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:10' " +
+                "--end '23 Mar 2012 10:00:20'")
+        self.match("1200\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:00:05' " +
+                "--end '23 Mar 2012 10:00:25'")
+        self.match("1200\n")
+
+        self.ok("remove -c /newton/prep " +
+                "--start '23 Mar 2012 10:03:50' " +
+                "--end '23 Mar 2012 10:06:50'")
+        self.match("1200\n")
+
+        self.ok("extract -c /newton/prep --start 2000-01-01 --end 2020-01-01")
+        self.match("3600\n")
+
+        # See the missing chunks in list output
+        self.ok("list --detail")
+        self.match("/newton/prep PrepData\n" +
+                   "  [ Fri, 23 Mar 2012 10:00:00.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:00:05.000000 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:00:25.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:00:30.000000 +0000 ]\n"
+                   "  [ Fri, 23 Mar 2012 10:03:30.000000 +0000"
+                   " -> Fri, 23 Mar 2012 10:03:50.000000 +0000 ]\n")
+
+        # We have 1/8 of the data that we had before, so the file size
+        # should have dropped below 1/4 of what it used to be
+        du_after = nilmdb.utils.diskusage.du_bytes(testdb)
+        lt_(du_after, (du_before / 4))
+
+        # Remove anything that came from the 10:02 data file
+        self.ok("remove /newton/prep " +
+                "--start '23 Mar 2012 10:02:00' --end '2020-01-01'")
+
+        # Re-insert 19 lines from that file, then remove them again.
+        # With the specific file_size above, this will cause the last
+        # file in the bulk data storage to be exactly file_size large,
+        # so removing the data should also remove that last file.
+        self.ok("insert --rate 120 /newton/prep " +
+                "tests/data/prep-20120323T1002-first19lines")
+        self.ok("remove /newton/prep " +
+                "--start '23 Mar 2012 10:02:00' --end '2020-01-01'")
+
+        # Shut down and restart server, to force nrows to get refreshed.
+        server_stop()
+        server_start()
+
+        # Re-add the full 10:02 data file.  This tests adding new data once
+        # we removed data near the end.
+        self.ok("insert --rate 120 /newton/prep tests/data/prep-20120323T1002")
+
+        # See if we can extract it all
+        self.ok("extract /newton/prep --start 2000-01-01 --end 2020-01-01")
+        lines_(self.captured, 15600)

tests/test_interval.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 import datetime_tz
 
 from nose.tools import *
@@ -10,13 +10,13 @@ import itertools
 
 from nilmdb.interval import Interval, DBInterval, IntervalSet, IntervalError
 
-from test_helpers import *
+from testutil.helpers import *
 import unittest
 
 # set to False to skip live renders
 do_live_renders = False
 def render(iset, description = "", live = True):
-    import renderdot
+    import testutil.renderdot as renderdot
     r = renderdot.RBTreeRenderer(iset.tree)
     return r.render(description, live and do_live_renders)
 
@@ -345,14 +345,15 @@ class TestIntervalSpeed:
     def test_interval_speed(self):
         import yappi
         import time
-        import aplotter
+        import testutil.aplotter as aplotter
         import random
         import math
 
         print
         yappi.start()
         speeds = {}
-        for j in [ 2**x for x in range(5,20) ]:
+        limit = 10 # was 20
+        for j in [ 2**x for x in range(5,limit) ]:
             start = time.time()
             iset = IntervalSet()
             for i in random.sample(xrange(j),j):

tests/test_iteratorizer.py

@@ -1,5 +1,5 @@
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 import nose
 from nose.tools import *
@@ -7,9 +7,7 @@ from nose.tools import assert_raises
 import threading
 import time
 
-from test_helpers import *
-
-import nilmdb.iteratorizer
+from testutil.helpers import *
 
 def func_with_callback(a, b, callback):
     callback(a)
@@ -27,7 +25,8 @@ class TestIteratorizer(object):
         eq_(self.result, "123")
 
         # Now make it an iterator
-        it = nilmdb.iteratorizer.Iteratorizer(lambda x:
+        it = nilmdb.utils.Iteratorizer(
+            lambda x:
             func_with_callback(1, 2, x))
         result = ""
         for i in it:
@@ -35,7 +34,8 @@ class TestIteratorizer(object):
         eq_(result, "123")
 
         # Make sure things work when an exception occurs
-        it = nilmdb.iteratorizer.Iteratorizer(lambda x:
+        it = nilmdb.utils.Iteratorizer(
+            lambda x:
             func_with_callback(1, "a", x))
         result = ""
         with assert_raises(TypeError) as e:
@@ -48,7 +48,8 @@ class TestIteratorizer(object):
         # itself.  This doesn't have a particular result in the test,
         # but gains coverage.
         def foo():
-            it = nilmdb.iteratorizer.Iteratorizer(lambda x:
+            it = nilmdb.utils.Iteratorizer(
+                lambda x:
                 func_with_callback(1, 2, x))
             it.next()
         foo()

tests/test_layout.py

@@ -2,7 +2,7 @@
 
 import nilmdb
 
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 from nose.tools import *
 from nose.tools import assert_raises
@@ -20,7 +20,7 @@ import cStringIO
 import random
 import unittest
 
-from test_helpers import *
+from testutil.helpers import *
 
 from nilmdb.layout import *
 
@@ -28,9 +28,13 @@ class TestLayouts(object):
     # Some nilmdb.layout tests.  Not complete, just fills in missing
     # coverage.
     def test_layouts(self):
-        x = nilmdb.layout.get_named("PrepData").description()
-        y = nilmdb.layout.get_named("float32_8").description()
-        eq_(repr(x), repr(y))
+        x = nilmdb.layout.get_named("PrepData")
+        y = nilmdb.layout.get_named("float32_8")
+        eq_(x.count, y.count)
+        eq_(x.datatype, y.datatype)
+        y = nilmdb.layout.get_named("float32_7")
+        ne_(x.count, y.count)
+        eq_(x.datatype, y.datatype)
 
     def test_parsing(self):
         self.real_t_parsing("PrepData", "RawData", "RawNotchedData")

tests/test_lrucache.py

@@ -0,0 +1,83 @@
+import nilmdb
+from nilmdb.utils.printf import *
+
+import nose
+from nose.tools import *
+from nose.tools import assert_raises
+import threading
+import time
+import inspect
+
+from testutil.helpers import *
+
+@nilmdb.utils.lru_cache(size = 3)
+def foo1(n):
+    return n
+
+@nilmdb.utils.lru_cache(size = 5)
+def foo2(n):
+    return n
+
+def foo3d(n):
+    foo3d.destructed.append(n)
+foo3d.destructed = []
+@nilmdb.utils.lru_cache(size = 3, onremove = foo3d)
+def foo3(n):
+    return n
+
+class Foo:
+    def __init__(self):
+        self.calls = 0
+    @nilmdb.utils.lru_cache(size = 3, keys = slice(1, 2))
+    def foo(self, n, **kwargs):
+        self.calls += 1
+
+class TestLRUCache(object):
+    def test(self):
+
+        [ foo1(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
+        eq_(foo1.cache_info(), (6, 3))
+        [ foo1(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
+        eq_(foo1.cache_info(), (15, 3))
+        [ foo1(n) for n in [ 4, 2, 1, 1, 4 ] ]
+        eq_(foo1.cache_info(), (18, 5))
+
+        [ foo2(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
+        eq_(foo2.cache_info(), (6, 3))
+        [ foo2(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
+        eq_(foo2.cache_info(), (15, 3))
+        [ foo2(n) for n in [ 4, 2, 1, 1, 4 ] ]
+        eq_(foo2.cache_info(), (19, 4))
+
+        [ foo3(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
+        eq_(foo3.cache_info(), (6, 3))
+        [ foo3(n) for n in [ 1, 2, 3, 1, 2, 3, 1, 2, 3 ] ]
+        eq_(foo3.cache_info(), (15, 3))
+        [ foo3(n) for n in [ 4, 2, 1, 1, 4 ] ]
+        eq_(foo3.cache_info(), (18, 5))
+        eq_(foo3d.destructed, [1, 3])
+        with assert_raises(KeyError):
+            foo3.cache_remove(1,2,3)
+        foo3.cache_remove(1)
+        eq_(foo3d.destructed, [1, 3, 1])
+        foo3.cache_remove_all()
+        eq_(foo3d.destructed, [1, 3, 1, 2, 4 ])
+
+        foo = Foo()
+        foo.foo(5)
+        foo.foo(6)
+        foo.foo(7)
+        foo.foo(5)
+        eq_(foo.calls, 3)
+
+        # Can't handle keyword arguments right now
+        with assert_raises(NotImplementedError):
+            foo.foo(3, asdf = 7)
+
+        # Verify that argspecs were maintained
+        eq_(inspect.getargspec(foo1),
+            inspect.ArgSpec(args=['n'],
+                            varargs=None, keywords=None, defaults=None))
+        eq_(inspect.getargspec(foo.foo),
+            inspect.ArgSpec(args=['self', 'n'],
+                            varargs=None, keywords="kwargs", defaults=None))

tests/test_mustclose.py

@@ -0,0 +1,110 @@
+import nilmdb
+from nilmdb.utils.printf import *
+
+import nose
+from nose.tools import *
+from nose.tools import assert_raises
+
+from testutil.helpers import *
+
+import sys
+import cStringIO
+import gc
+
+import inspect
+
+err = cStringIO.StringIO()
+
+@nilmdb.utils.must_close(errorfile = err)
+class Foo:
+    def __init__(self, arg):
+        fprintf(err, "Init %s\n", arg)
+
+    def __del__(self):
+        fprintf(err, "Deleting\n")
+
+    def close(self):
+        fprintf(err, "Closing\n")
+
+@nilmdb.utils.must_close(errorfile = err, wrap_verify = True)
+class Bar:
+    def __init__(self):
+        fprintf(err, "Init\n")
+
+    def __del__(self):
+        fprintf(err, "Deleting\n")
+
+    def close(self):
+        fprintf(err, "Closing\n")
+
+    def blah(self, arg):
+        fprintf(err, "Blah %s\n", arg)
+
+@nilmdb.utils.must_close(errorfile = err)
+class Baz:
+    pass
+
+class TestMustClose(object):
+    def test(self):
+
+        # Note: this test might fail if the Python interpreter doesn't
+        # garbage collect the object (and call its __del__ function)
+        # right after a "del x".
+
+        # Trigger error
+        err.truncate()
+        x = Foo("hi")
+        # Verify that the arg spec was maintained
+        eq_(inspect.getargspec(x.__init__),
+            inspect.ArgSpec(args = ['self', 'arg'],
+                            varargs = None, keywords = None, defaults = None))
+        del x
+        gc.collect()
+        eq_(err.getvalue(),
+            "Init hi\n"
+            "error: Foo.close() wasn't called!\n"
+            "Deleting\n")
+
+        # No error
+        err.truncate(0)
+        y = Foo("bye")
+        y.close()
+        del y
+        gc.collect()
+        eq_(err.getvalue(),
+            "Init bye\n"
+            "Closing\n"
+            "Deleting\n")
+
+        # Verify function calls when wrap_verify is True
+        err.truncate(0)
+        z = Bar()
+        eq_(inspect.getargspec(z.blah),
+            inspect.ArgSpec(args = ['self', 'arg'],
+                            varargs = None, keywords = None, defaults = None))
+        z.blah("boo")
+        z.close()
+        with assert_raises(AssertionError) as e:
+            z.blah("hello")
+        in_("called <function blah at 0x", str(e.exception))
+        in_("> after close", str(e.exception))
+        # Since the most recent assertion references 'z',
+        # we need to raise another assertion here so that
+        # 'z' will get properly deleted.
+        with assert_raises(AssertionError):
+            raise AssertionError()
+        del z
+        gc.collect()
+        eq_(err.getvalue(),
+            "Init\n"
+            "Blah boo\n"
+            "Closing\n"
+            "Deleting\n")
+
+        # Class with missing methods
+        err.truncate(0)
+        w = Baz()
+        w.close()
+        del w
+        eq_(err.getvalue(), "")
+

tests/test_nilmdb.py

@@ -14,6 +14,7 @@ import urllib2
 from urllib2 import urlopen, HTTPError
 import Queue
 import cStringIO
+import time
 
 testdb = "tests/testdb"
 
@@ -21,7 +22,7 @@ testdb = "tests/testdb"
 #def cleanup():
 #    os.unlink(testdb)
 
-from test_helpers import *
+from testutil.helpers import *
 
 class Test00Nilmdb(object):  # named 00 so it runs first
     def test_NilmDB(self):
@@ -39,8 +40,8 @@ class Test00Nilmdb(object):  # named 00 so it runs first
         capture = cStringIO.StringIO()
         old = sys.stdout
         sys.stdout = capture
-        with nilmdb.Timer("test"):
-            nilmdb.timer.time.sleep(0.01)
+        with nilmdb.utils.Timer("test"):
+            time.sleep(0.01)
         sys.stdout = old
         in_("test: ", capture.getvalue())
 
@@ -69,12 +70,14 @@ class Test00Nilmdb(object):  # named 00 so it runs first
         eq_(db.stream_list(layout="RawData"), [ ["/newton/raw", "RawData"] ])
         eq_(db.stream_list(path="/newton/raw"), [ ["/newton/raw", "RawData"] ])
 
-        # Verify that columns were made right
-        eq_(len(db.h5file.getNode("/newton/prep").cols), 9)
-        eq_(len(db.h5file.getNode("/newton/raw").cols), 7)
-        eq_(len(db.h5file.getNode("/newton/zzz/rawnotch").cols), 10)
-        assert(not db.h5file.getNode("/newton/prep").colindexed["timestamp"])
-        assert(not db.h5file.getNode("/newton/prep").colindexed["c1"])
+        # Verify that columns were made right (pytables specific)
+        if "h5file" in db.data.__dict__:
+            h5file = db.data.h5file
+            eq_(len(h5file.getNode("/newton/prep").cols), 9)
+            eq_(len(h5file.getNode("/newton/raw").cols), 7)
+            eq_(len(h5file.getNode("/newton/zzz/rawnotch").cols), 10)
+            assert(not h5file.getNode("/newton/prep").colindexed["timestamp"])
+            assert(not h5file.getNode("/newton/prep").colindexed["c1"])
 
         # Set / get metadata
         eq_(db.stream_get_metadata("/newton/prep"), {})

tests/test_printf.py

@@ -1,12 +1,12 @@
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 from nose.tools import *
 from nose.tools import assert_raises
 from cStringIO import StringIO
 import sys
 
-from test_helpers import *
+from testutil.helpers import *
 
 class TestPrintf(object):
     def test_printf(self):

tests/test_rbtree.py

@@ -1,20 +1,20 @@
 # -*- coding: utf-8 -*-
 
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 from nose.tools import *
 from nose.tools import assert_raises
 
 from nilmdb.rbtree import RBTree, RBNode
 
-from test_helpers import *
+from testutil.helpers import *
 import unittest
 
 # set to False to skip live renders
 do_live_renders = False
 def render(tree, description = "", live = True):
-    import renderdot
+    import testutil.renderdot as renderdot
     r = renderdot.RBTreeRenderer(tree)
     return r.render(description, live and do_live_renders)
 

tests/test_serializer.py

@@ -1,5 +1,5 @@
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 import nose
 from nose.tools import *
@@ -7,7 +7,7 @@ from nose.tools import assert_raises
 import threading
 import time
 
-from test_helpers import *
+from testutil.helpers import *
 
 #raise nose.exc.SkipTest("Skip these")
 
@@ -57,7 +57,7 @@ class TestUnserialized(Base):
 class TestSerialized(Base):
     def setUp(self):
         self.realfoo = Foo()
-        self.foo = nilmdb.serializer.WrapObject(self.realfoo)
+        self.foo = nilmdb.utils.Serializer(self.realfoo)
 
     def tearDown(self):
         del self.foo

tests/test_timestamper.py

@@ -1,5 +1,5 @@
 import nilmdb
-from nilmdb.printf import *
+from nilmdb.utils.printf import *
 
 import datetime_tz
 
@@ -9,7 +9,7 @@ import os
 import sys
 import cStringIO
 
-from test_helpers import *
+from testutil.helpers import *
 
 class TestTimestamper(object):
 

tests/testutil/__init__.py

@@ -0,0 +1 @@
+# empty

tests/testutil/helpers.py

@@ -12,6 +12,10 @@ def eq_(a, b):
     if not a == b:
         raise AssertionError("%s != %s" % (myrepr(a), myrepr(b)))
 
+def lt_(a, b):
+    if not a < b:
+        raise AssertionError("%s is not less than %s" % (myrepr(a), myrepr(b)))
+
 def in_(a, b):
     if a not in b:
         raise AssertionError("%s not in %s" % (myrepr(a), myrepr(b)))
@@ -23,6 +27,8 @@ def ne_(a, b):
 def lines_(a, n):
     l = a.count('\n')
     if not l == n:
+        if len(a) > 5000:
+            a = a[0:5000] + " ... truncated"
         raise AssertionError("wanted %d lines, got %d in output: '%s'"
                              % (n, l, a))
 

tests/testutil/renderdot.py

@@ -13,7 +13,7 @@ class Renderer(object):
 
     # Rendering
     def __render_dot_node(self, node, max_depth = 20):
-        from nilmdb.printf import sprintf
+        from nilmdb.utils.printf import sprintf
         """Render a single node and its children into a dot graph fragment"""
         if max_depth == 0:
             return ""

timeit.sh

@@ -1,21 +1,22 @@
 ./nilmtool.py destroy /bpnilm/2/raw
 ./nilmtool.py create /bpnilm/2/raw RawData
 
-if true; then
+if false; then
     time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-110000 -r 8000 /bpnilm/2/raw
     time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s 20110513-120001 -r 8000 /bpnilm/2/raw
 else
-    for i in $(seq 2000 2050); do
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-010001 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-020002 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-030003 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-040004 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-050005 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-060006 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-070007 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-080008 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-090009 /bpnilm/2/raw
-	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-100010 /bpnilm/2/raw
+    # 170 hours, about 98 gigs uncompressed:
+    for i in $(seq 2000 2016); do
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-010001 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-020002 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-030003 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-040004 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-050005 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-060006 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-070007 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-080008 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-090009 -r 8000 /bpnilm/2/raw
+	time zcat /home/jim/bpnilm-data/snapshot-1-20110513-110002.raw.gz | ./nilmtool.py insert -s ${i}0101-100010 -r 8000 /bpnilm/2/raw
     done
 fi