*.ipynb: Use absolute URLs to link to the glossary

SWC has a single, global glossary [1], not per-subject glossaries.
Because this per-subject branch no longer contains the global
glossary, we need to adjust the links to point at an external
glossary.  Done automatically with:

  $ sed -i 's|\.\./\.\./gloss.html|https://github.com/swcarpentry/bc/blob/master/gloss.md|g' *.ipynb

[1]: https://github.com/swcarpentry/bc/blob/master/gloss.md

diff --git a/01-select.ipynb b/01-select.ipynb
index 85f074a482af1afb5c7abe95699cced60b2449d0..2c14b257aceae3aec545aef8cf2ee56522229cd0 100644 (file)
--- a/01-select.ipynb
+++ b/01-select.ipynb
@@ -72,18 +72,18 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
      "cell_type": "markdown",
      "metadata": {},
      "source": [

-      "A [relational database](../../gloss.html#relational-database)\n",
+      "A [relational database](https://github.com/swcarpentry/bc/blob/master/gloss.md#relational-database)\n",

       "is a way to store and manipulate information\n",
       "is a way to store and manipulate information\n",

-      "that is arranged as [tables](../../gloss.html#table-database).\n",
-      "Each table has columns (also known as [fields](../../gloss.html#field-database)) which describe the data,\n",
-      "and rows (also known as [records](../../gloss.html#record-database)) which contain the data.\n",
+      "that is arranged as [tables](https://github.com/swcarpentry/bc/blob/master/gloss.md#table-database).\n",
+      "Each table has columns (also known as [fields](https://github.com/swcarpentry/bc/blob/master/gloss.md#field-database)) which describe the data,\n",
+      "and rows (also known as [records](https://github.com/swcarpentry/bc/blob/master/gloss.md#record-database)) which contain the data.\n",

       "  \n",
       "When we are using a spreadsheet,\n",
       "we put formulas into cells to calculate new values based on old ones.\n",
       "When we are using a database,\n",
       "we send commands\n",
       "  \n",
       "When we are using a spreadsheet,\n",
       "we put formulas into cells to calculate new values based on old ones.\n",
       "When we are using a database,\n",
       "we send commands\n",

-      "(usually called [queries](../../gloss.html#query))\n",
-      "to a [database manager](../../gloss.html#database-manager):\n",
+      "(usually called [queries](https://github.com/swcarpentry/bc/blob/master/gloss.md#query))\n",
+      "to a [database manager](https://github.com/swcarpentry/bc/blob/master/gloss.md#database-manager):\n",

       "a program that manipulates the database for us.\n",
       "The database manager does whatever lookups and calculations the query specifies,\n",
       "returning the results in a tabular form\n",
       "a program that manipulates the database for us.\n",
       "The database manager does whatever lookups and calculations the query specifies,\n",
       "returning the results in a tabular form\n",


@@ -97,7 +97,7 @@
       "> every database manager can import and export data in a variety of formats,\n",
       "> so it *is* possible to move information from one to another.\n",
       "\n",
       "> every database manager can import and export data in a variety of formats,\n",
       "> so it *is* possible to move information from one to another.\n",
       "\n",

-      "Queries are written in a language called [SQL](../../gloss.html#sql),\n",
+      "Queries are written in a language called [SQL](https://github.com/swcarpentry/bc/blob/master/gloss.md#sql),\n",

       "which stands for \"Structured Query Language\".\n",
       "SQL provides hundreds of different ways to analyze and recombine data;\n",
       "we will only look at a handful,\n",
       "which stands for \"Structured Query Language\".\n",
       "SQL provides hundreds of different ways to analyze and recombine data;\n",
       "we will only look at a handful,\n",


@@ -244,7 +244,7 @@
       "and the table name in Title Case,\n",
       "but we don't have to:\n",
       "as the example below shows,\n",
       "and the table name in Title Case,\n",
       "but we don't have to:\n",
       "as the example below shows,\n",

-      "SQL is [case insensitive](../../gloss.html#case-insensitive)."
+      "SQL is [case insensitive](https://github.com/swcarpentry/bc/blob/master/gloss.md#case-insensitive)."

      ]
     },
     {
      ]
     },
     {

diff --git a/03-filter.ipynb b/03-filter.ipynb
index f06d40e586b3a655ea984e3572e5d3a062ad7de3..2b9ceda71c55bb5e1a113c58d852e2232b391e90 100644 (file)
--- a/03-filter.ipynb
+++ b/03-filter.ipynb
@@ -34,7 +34,7 @@
      "metadata": {},
      "source": [
       "One of the most powerful features of a database is\n",
      "metadata": {},
      "source": [
       "One of the most powerful features of a database is\n",

-      "the ability to [filter](../../gloss.html#filter) data,\n",
+      "the ability to [filter](https://github.com/swcarpentry/bc/blob/master/gloss.md#filter) data,\n",

       "i.e.,\n",
       "to select only those records that match certain criteria.\n",
       "For example,\n",
       "i.e.,\n",
       "to select only those records that match certain criteria.\n",
       "For example,\n",

diff --git a/05-null.ipynb b/05-null.ipynb
index 0b0f3c35fb76d20cc6153c5e4bf6dda70ed5f068..6d312a22c230bb577a563149ed668ed46d4a8bf1 100644 (file)
--- a/05-null.ipynb
+++ b/05-null.ipynb
@@ -425,7 +425,7 @@
       "    What does it actually produce?\n",
       "\n",
       "1.  Some database designers prefer to use\n",
       "    What does it actually produce?\n",
       "\n",
       "1.  Some database designers prefer to use\n",

-      "    a [sentinel value](../../gloss.html#sentinel-value)\n",
+      "    a [sentinel value](https://github.com/swcarpentry/bc/blob/master/gloss.md#sentinel-value)\n",

       "    to mark missing data rather than `null`.\n",
       "    For example,\n",
       "    they will use the date \"0000-00-00\" to mark a missing date,\n",
       "    to mark missing data rather than `null`.\n",
       "    For example,\n",
       "    they will use the date \"0000-00-00\" to mark a missing date,\n",

diff --git a/06-agg.ipynb b/06-agg.ipynb
index f54e01f3249893cae0076a8a5077af1496b0c0f2..76353999d6238e5b7840a5faf5441f7137519cfe 100644 (file)
--- a/06-agg.ipynb
+++ b/06-agg.ipynb
@@ -87,7 +87,7 @@
      "metadata": {},
      "source": [
       "but to combine them,\n",
      "metadata": {},
      "source": [
       "but to combine them,\n",

-      "wee must use an [aggregation function](../../gloss.html#aggregation-function)\n",
+      "wee must use an [aggregation function](https://github.com/swcarpentry/bc/blob/master/gloss.md#aggregation-function)\n",

       "such as `min` or `max`.\n",
       "Each of these functions takes a set of records as input,\n",
       "and produces a single record as output:"
       "such as `min` or `max`.\n",
       "Each of these functions takes a set of records as input,\n",
       "and produces a single record as output:"

diff --git a/07-join.ipynb b/07-join.ipynb
index 93761c51a1821a27219ee179f622e1642408ff25..ef816e96d89f0b6ed85af7fbac708e912aaa06da 100644 (file)
--- a/07-join.ipynb
+++ b/07-join.ipynb
@@ -115,7 +115,7 @@
      "metadata": {},
      "source": [
       "`join` creates\n",
      "metadata": {},
      "source": [
       "`join` creates\n",

-      "the [cross product](../../gloss.html#cross-product)\n",
+      "the [cross product](https://github.com/swcarpentry/bc/blob/master/gloss.md#cross-product)\n",

       "of two tables,\n",
       "i.e.,\n",
       "it joins each record of one with each record of the other\n",
       "of two tables,\n",
       "i.e.,\n",
       "it joins each record of one with each record of the other\n",


@@ -294,8 +294,8 @@
       "We can tell which records from `Site`, `Visited`, and `Survey`\n",
       "correspond with each other\n",
       "because those tables contain\n",
       "We can tell which records from `Site`, `Visited`, and `Survey`\n",
       "correspond with each other\n",
       "because those tables contain\n",

-      "[primary keys](../../gloss.html#primary-key)\n",
-      "and [foreign keys](../../gloss.html#foreign-key).\n",
+      "[primary keys](https://github.com/swcarpentry/bc/blob/master/gloss.md#primary-key)\n",
+      "and [foreign keys](https://github.com/swcarpentry/bc/blob/master/gloss.md#foreign-key).\n",

       "A primary key is a value,\n",
       "or combination of values,\n",
       "that uniquely identifies each record in a table.\n",
       "A primary key is a value,\n",
       "or combination of values,\n",
       "that uniquely identifies each record in a table.\n",


@@ -371,7 +371,7 @@
       "Now that we have seen how joins work,\n",
       "we can see why the relational model is so useful\n",
       "and how best to use it.\n",
       "Now that we have seen how joins work,\n",
       "we can see why the relational model is so useful\n",
       "and how best to use it.\n",

-      "The first rule is that every value should be [atomic](../../gloss.html#atomic-value),\n",
+      "The first rule is that every value should be [atomic](https://github.com/swcarpentry/bc/blob/master/gloss.md#atomic-value),\n",

       "i.e.,\n",
       "not contain parts that we might want to work with separately.\n",
       "We store personal and family names in separate columns instead of putting the entire name in one column\n",
       "i.e.,\n",
       "not contain parts that we might want to work with separately.\n",
       "We store personal and family names in separate columns instead of putting the entire name in one column\n",

diff --git a/08-create.ipynb b/08-create.ipynb
index 94da1e94996aa71e7e21155408e61a8cf51d6475..7ae8a58a7cff17234a8f13120aa45ac3a8deb2c1 100644 (file)
--- a/08-create.ipynb
+++ b/08-create.ipynb
@@ -145,14 +145,14 @@
       "and all our queries assume there will be a row in the latter\n",
       "matching every value in the former.\n",
       "  \n",
       "and all our queries assume there will be a row in the latter\n",
       "matching every value in the former.\n",
       "  \n",

-      "This problem is called [referential integrity](../../gloss.html#referential-integrity):\n",
+      "This problem is called [referential integrity](https://github.com/swcarpentry/bc/blob/master/gloss.md#referential-integrity):\n",

       "we need to ensure that all references between tables can always be resolved correctly.\n",
       "One way to do this is to delete all the records\n",
       "that use `'lake'` as a foreign key\n",
       "before deleting the record that uses it as a primary key.\n",
       "If our database manager supports it,\n",
       "we can automate this\n",
       "we need to ensure that all references between tables can always be resolved correctly.\n",
       "One way to do this is to delete all the records\n",
       "that use `'lake'` as a foreign key\n",
       "before deleting the record that uses it as a primary key.\n",
       "If our database manager supports it,\n",
       "we can automate this\n",

-      "using [cascading delete](../../gloss.html#cascading-delete).\n",
+      "using [cascading delete](https://github.com/swcarpentry/bc/blob/master/gloss.md#cascading-delete).\n",

       "However,\n",
       "this technique is outside the scope of this chapter.\n",
       "\n",
       "However,\n",
       "this technique is outside the scope of this chapter.\n",
       "\n",


@@ -179,7 +179,7 @@
       "    in `Survey.person`\n",
       "    with the string `'unknown'`.\n",
       "\n",
       "    in `Survey.person`\n",
       "    with the string `'unknown'`.\n",
       "\n",

-      "2.  One of our colleagues has sent us a [CSV](../../gloss.html#csv) file\n",
+      "2.  One of our colleagues has sent us a [CSV](https://github.com/swcarpentry/bc/blob/master/gloss.md#csv) file\n",

       "    containing temperature readings by Robert Olmstead,\n",
       "    which is formatted like this:\n",
       "\n",
       "    containing temperature readings by Robert Olmstead,\n",
       "    which is formatted like this:\n",
       "\n",

diff --git a/09-prog.ipynb b/09-prog.ipynb
index 63461bae5271a9292a030ba84c68049a309a9ecc..4d143683672715eed420717b44c3f352748f9ad5 100644 (file)
--- a/09-prog.ipynb
+++ b/09-prog.ipynb
@@ -91,7 +91,7 @@
       "all we need to specify is the name of the database file.\n",
       "Other systems may require us to provide a username and password as well.\n",
       "Line 3 then uses this connection to create\n",
       "all we need to specify is the name of the database file.\n",
       "Other systems may require us to provide a username and password as well.\n",
       "Line 3 then uses this connection to create\n",

-      "a [cursor](../../gloss.html#cursor);\n",
+      "a [cursor](https://github.com/swcarpentry/bc/blob/master/gloss.md#cursor);\n",

       "just like the cursor in an editor,\n",
       "its role is to keep track of where we are in the database.\n",
       "\n",
       "just like the cursor in an editor,\n",
       "its role is to keep track of where we are in the database.\n",
       "\n",


@@ -187,7 +187,7 @@
       "If we execute this,\n",
       "it will erase one of the tables in our database.\n",
       "  \n",
       "If we execute this,\n",
       "it will erase one of the tables in our database.\n",
       "  \n",

-      "This is called an [SQL injection attack](../../gloss.html#sql-injection-attack),\n",
+      "This is called an [SQL injection attack](https://github.com/swcarpentry/bc/blob/master/gloss.md#sql-injection-attack),\n",

       "and it has been used to attack thousands of programs over the years.\n",
       "In particular,\n",
       "many web sites that take data from users insert values directly into queries\n",
       "and it has been used to attack thousands of programs over the years.\n",
       "In particular,\n",
       "many web sites that take data from users insert values directly into queries\n",


@@ -197,7 +197,7 @@
       "the safest way to deal with this threat is\n",
       "to replace characters like quotes with their escaped equivalents,\n",
       "so that we can safely put whatever the user gives us inside a string.\n",
       "the safest way to deal with this threat is\n",
       "to replace characters like quotes with their escaped equivalents,\n",
       "so that we can safely put whatever the user gives us inside a string.\n",

-      "We can do this by using a [prepared statement](../../gloss.html#prepared-statement)\n",
+      "We can do this by using a [prepared statement](https://github.com/swcarpentry/bc/blob/master/gloss.md#prepared-statement)\n",

       "instead of formatting our statements as strings.\n",
       "Here's what our example program looks like if we do this:"
      ]
       "instead of formatting our statements as strings.\n",
       "Here's what our example program looks like if we do this:"
      ]