Selected Practical Software Development Lessons From A Large Digital Library System. Tibor Šimko <tibor.simko@cern.ch> August 2011 / openlab talk

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1 Selected Practical Software Development Lessons From A Large System <tibor.simko@cern.ch> Department of Information CERN August 2011 / openlab talk

2 Outline 1 2 3

3 Outline 1 2 3

4 What is? library in which collections are stored in digital formats (as opposed to print, microform, or other media) and accessible by computers (1) institutional document repositories (2) world-wide subject-based information systems Example #1: CERN Document Server managing CERN and selected non-cern high-energy physics and related documents since 1993 more than 1,000,000 records articles, books, theses, photos, videos, and more powered by, free digital library software

5 What is? library in which collections are stored in digital formats (as opposed to print, microform, or other media) and accessible by computers (1) institutional document repositories (2) world-wide subject-based information systems Example #1: CERN Document Server managing CERN and selected non-cern high-energy physics and related documents since 1993 more than 1,000,000 records articles, books, theses, photos, videos, and more powered by, free digital library software

6 CDS: Collection Tree

7 CDS: Search for Books

8 CDS: Search for Photos

9 CDS Features: Commenting

10 Features: Reviewing

11 CDS: Create Personal Alert

12 CDS: Add to Personal Basket

13 CDS: Display Personal Basket

14 CDS: Organize and Share Your Baskets

15 CDS: Journals and Bulletins

16 What is digital library? Example #2: INSPIRE world-wide high-energy physics information system run by CERN, DESY, FNAL, SLAC metadata curation since 1960s, technology since 2007 citation analysis, author/affiliation analysis close partnership with arxiv and ADS

17 INSPIRE: full-text search

18 INSPIRE: cite summary

19 INSPIRE: citation history

20 INSPIRE: author pages

21 Outline 1 2 3

22 Key Features navigable collection tree (regular, virtual) powerful search engine Google-like speed for up to 5M records combined metadata, reference and fulltext search flexible metadata (MARC, OA) handling any kind of document (multimedia) customizable input, formatting and linking personalization and collaborative features: alerts, baskets, groups, reviews, comments internationalisation (28 languages) open source, GNU General Public License co-developed by CERN (2002 ), EPFL (2004 ), DESY/FNAL/SLAC (2008 ), CfA (2009 ) installed at 30 institutions world-wide

23 Architecture: Overview Author

24 Architecture: Overview Author Ingestion

25 Architecture: Overview Author Ingestion Database

26 Architecture: Overview Author Sources Ingestion Database

27 Architecture: Overview Author Sources Processing Ingestion Database

28 Architecture: Overview Author Sources Processing Ingestion Database Dissemination User

29 Architecture: Overview Author Sources Ingestion Librarian Processing Database Curation Dissemination User

30 Architecture: Overview Author Sources Ingestion Librarian Processing Database Curation Overview Dissemination User

31 Modules: Ingestion Author

32 Modules: Ingestion Author WebSubmit WebSession, WebAccess

33 Modules: Ingestion Author WebSubmit WebSession, WebAccess metadata full-text document Metadata Full-text

34 Modules: Ingestion Author WebSubmit WebSession, WebAccess metadata BibConvert MARCXML BibUpload BibSched Metadata full-text document Full-text

35 Modules: Ingestion OAI Data Source Author BibHarvest WebSubmit WebSession, WebAccess metadata BibConvert MARCXML BibUpload BibSched Metadata full-text document Full-text

36 Modules: Ingestion OAI Data Source Author Non-OAI Data Source BibHarvest WebSubmit WebSession, WebAccess metadata ElmSubmit BibConvert MARCXML full-text document BibUpload BibSched Metadata Full-text

37 Modules: Ingestion OAI Data Source Author Non-OAI Data Source BibHarvest WebSubmit WebSession, WebAccess metadata ElmSubmit BibConvert MARCXML full-text document BibUpload BibSched Ingestion Metadata Full-text

38 Modules: Processing Metadata Full-text

39 Modules: Processing Metadata RefExtract Full-text BibClassify

40 Modules: Processing Clusters BibIndex Metadata RefExtract Full-text BibClassify

41 Modules: Processing WebColl Clusters BibIndex Metadata RefExtract Full-text BibClassify

42 Modules: Processing WebColl Clusters BibIndex Metadata RefExtract Full-text BibRank BibClassify

43 Modules: Processing WebColl Clusters BibIndex Metadata RefExtract Full-text BibRank BibClassify BibFormat

44 Modules: Processing WebColl Clusters BibIndex Metadata RefExtract Full-text BibRank BibClassify BibFormat Processing

45 Modules: Dissemination Clusters Metadata Full-text

46 Modules: Dissemination Clusters Metadata Full-text WebSearch User

47 Modules: Dissemination Clusters Metadata Full-text WebBasket WebSearch User

48 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch User

49 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert User

50 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest User OAI Harvester

51 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester

52 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester WebMessage

53 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester WebJournal WebMessage

54 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester WebJournal WebMessage BibCirculation

55 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester WebJournal WebMessage BibCirculation WebStat

56 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester WebJournal WebMessage BibCirculation WebStat WebHelp

57 Modules: Dissemination Clusters Metadata Full-text WebTag WebBasket WebSearch WebAlert BibHarvest WebComment User OAI Harvester WebJournal WebMessage BibCirculation WebStat Dissemination WebHelp

58 Modules: Curation Metadata Librarian Full-text

59 Modules: Curation Metadata BibEdit Librarian Full-text

60 Modules: Curation MultiEdit Metadata BibEdit Librarian Full-text

61 Modules: Curation MultiEdit Metadata BibEdit Librarian Full-text BatchUploader

62 Modules: Curation MultiEdit Metadata BibEdit Librarian Full-text BatchUploader BibCheck

63 Modules: Curation MultiEdit Metadata BibEdit Librarian Full-text BatchUploader BibCheck BibCirculation

64 Modules: Curation MultiEdit Metadata BibEdit Librarian BibDocFile Full-text BatchUploader BibCheck BibCirculation

65 Modules: Curation MultiEdit BibClassify Metadata BibEdit Librarian BibDocFile Full-text BatchUploader BibCheck BibCirculation

66 Modules: Curation MultiEdit BibClassify Metadata BibEdit Librarian BibDocFile Full-text BatchUploader RefExtract BibCheck BibCirculation

67 Modules: Curation MultiEdit BibClassify Metadata BibEdit Librarian BibDocFile Full-text BatchUploader RefExtract BibCheck BibCatalog Tasks BibCirculation

68 Modules: Curation MultiEdit BibClassify Metadata BibEdit Librarian BibDocFile Full-text BatchUploader BibKnowledge RefExtract BibCheck BibCatalog Knowledge Bases Tasks BibCirculation

69 Modules: Curation MultiEdit BibExport BibClassify Metadata BibEdit Librarian BibDocFile Full-text BatchUploader BibKnowledge RefExtract BibCheck BibCatalog Knowledge Bases Tasks BibCirculation

70 Modules: Curation BibMatch MultiEdit BibExport BibClassify Metadata BibEdit Librarian BibDocFile Full-text BatchUploader BibKnowledge RefExtract BibCheck BibCatalog Knowledge Bases Tasks BibCirculation

71 Modules: Curation BibMatch MultiEdit BibExport BibClassify Metadata BibEdit Librarian BibDocFile Full-text BibMerge BatchUploader BibKnowledge RefExtract BibCheck BibCatalog Knowledge Bases Tasks BibCirculation

72 Modules: Curation BibMatch MultiEdit BibExport BibClassify Metadata BibEdit Librarian BibDocFile Full-text BibMerge BatchUploader BibKnowledge RefExtract Curation BibCheck BibCatalog Knowledge Bases Tasks BibCirculation

73 Modules: Summary 33 modules codebase 290,000 lines of Python code 12,000 lines of JavaScript code 6,000 lines of XSL code 5,000 lines of autotools code 75 authors since inception 25 authors and contributors in 2010 many short-term students importance of informal coding standards 10 years of development started at CERN, first release in 2002 now co-developed world-wide (EU, US) lego programming... but no silver bullet

74 Outline 1 2 3

75 Why Python? easy to read and understand (good for many temporary developers) suitable for rapid prototyping (good for organic-growth software development model) write code to throw it away

76 Art of Ikebana Japanese art of flower arrangement way of flowers natural shapes, graceful lines minimalism disciplined art form in which nature and humanity are brought together

77 Art of Ikebana Programming Java? new Callable() { public Object call(object x) { return x.times(k) } } Python! lambda x: k * x

78 Art of Ikebana Programming Java? new Callable() { public Object call(object x) { return x.times(k) } } Python! lambda x: k * x

79 Speeding Up Python bytecode interpreted language: what about speed? Cython permits to write C extensions easily combining efficiency of C with high-levelness of Python Example: intbitset.pyx ctypedef unsigned long long int word_t ctypedef struct IntBitSet: int size int allocated word_t trailing_bits int tot word_t *bitset

80 Outline 1 2 3

81 Why Git? good for distributed teams offline development possible pull on demand collaboration model (as opposed to shared push collaboration model) inherent,natural code review process commit early, commit often (to private repositories) rebase and clean (before pushing for public consumption) interplay with SVN

82 Git Branches C 1 master

83 Git Branches C 1 C 2 master

84 Git Branches v1.0.0 C 1 C 2 C 3 master

85 Git Branches v1.0.0 C 1 C 2 C 3 C 4 master

86 Git Branches v1.0.0 M 1 maintenance C 1 C 2 C 3 C 4 master

87 Git Branches v1.0.0 M 1 M 2 maintenance C 1 C 2 C 3 C 4 master

88 Git Branches v1.0.0 M 1 M 2 maintenance C 1 C 2 C 3 C 4 C 5 master

89 Git Branches v1.0.1 v1.0.0 M 1 M 2 M 3 maintenance C 1 C 2 C 3 C 4 C 5 master

90 Git Branches v1.0.1 M 4 v1.0.0 M 1 M 2 M 3 maintenance C 1 C 2 C 3 C 4 C 5 master

91 Git Branches v1.0.1 M 4 v1.0.0 M 1 M 2 M 3 maintenance C 1 C 2 C 3 C 4 C 5 master N 1 next

92 Git Branches v1.0.1 M 4 v1.0.0 M 1 M 2 M 3 maintenance C 1 C 2 C 3 C 4 C 5 C 6 master N 1 next

93 Git Branches v1.0.1 M 4 v1.0.0 M 1 M 2 M 3 maintenance C 1 C 2 C 3 C 4 C 5 C 6 master N 1 N 2 next

94 Git Branches v1.0.1 M 4 v1.0.0 M 1 M 2 M 3 maintenance v1.1.0 C 1 C 2 C 3 C 4 C 5 C 6 C 7 master N 1 N 2 next

95 Git Branches v1.0.2 v1.0.1 M 4 M 5 v1.0.0 M 1 M 2 M 3 maintenance v1.1.0 C 1 C 2 C 3 C 4 C 5 C 6 C 7 master N 1 N 2 next

96 Git Branches v1.0.2 v1.0.1 M 4 M 5 v1.0.0 M 1 M 2 M 3 maintenance v1.1.0 C 1 C 2 C 3 C 4 C 5 C 6 C 7 master N 1 N 2 next maint release maintenance branch master new feature branch next things not yet release-ready

97 Git Development M 1 C 1 N 1 maint master next

98 Git Development B 1 some-bugfix M 1 C 1 N 1 maint master next

99 Git Development B 1 some-bugfix M 1 M 2 maint C 1 C 2 master next N 1 N 2

100 Git Development B 1 B 2 some-bugfix M 1 M 2 maint C 1 C 2 master next N 1 N 2

101 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint C 1 C 2 master next N 1 N 2

102 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 master next N 1 N 2

103 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 master next N 1 N 2 F 1 some-new-feature

104 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 master next N 1 N 2 F 1 F 2 some-new-feature

105 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 C 4 master merge next N 1 N 2 F 1 F 2 some-new-feature

106 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 C 4 master merge merge next N 1 N 2 N 3 F 1 F 2 some-new-feature

107 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 C 4 master merge merge next N 1 N 2 N 3 F 1 F 2 some-new-feature E 1 some-experimental-feature

108 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 C 4 master merge merge next N 1 N 2 N 3 F 1 F 2 some-new-feature E 1 E 2 some-experimental-feature

109 Git Development B 1 B 2 merge some-bugfix M 1 M 2 M 3 maint merge C 1 C 2 C 3 C 4 master merge merge next N 1 N 2 N 3 N 4 F 1 F 2 merge some-new-feature E 1 E 2 some-experimental-feature

110 Git collaboration model

111 Outline 1 2 3

112 Unit testing test-driven development when appropriate e.g. before/while developing strip_accents(), write: Example: search_engine_tests.py class TestStripAccents(unittest.TestCase): """Test for handling of UTF-8 accents.""" def test_strip_accents(self): """search engine - stripping of accented letters""" self.assertequal("memememe", search_engine.strip_accents('mémêmëmè')) self.assertequal("memememe", search_engine.strip_accents('mémêmëmè'))

113 Functional testing functional/acceptance/regression testing testbed site (Atlantis of Institute Fictive Science) e.g. Python mechanize module to emulate browser Example: websearch_regression_tests.py class WebSearchSearchEnginePythonAPITest(unittest.TestCase): "Check typical search engine Python API calls on the demo data." def test_search_engine_python_api_for_failed_query(self): "websearch - search engine Python API for failed query" self.assertequal([], perform_request_search(p='aoeuidhtns')) def test_search_engine_python_api_for_successful_query(self): "websearch - search engine Python API for successful query" self.assertequal([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 47], perform_request_search(p='ellis'))

114 Web testing sometimes we need to run tests in real browser e.g. pages with heavy JavaScript using Selenium IDE extension for Firefox record and replay browser actions test for text existence or non-existence on pages test for link labels and targets Example: test_search_ellis.html <tr><td>open</td> <td> <td></td> </tr> <tr><td>type</td> <td>p</td> <td>ellis</td> </tr> <tr><td>clickandwait</td> <td>action_search</td> <td></td> </tr> <tr><td>verifytextpresent</td> <td>1. Thermal conductivity of dense quark matter and cooling of stars</td> <td></td> </tr>

115 Outline 1 2 3

116 Designing A Search Engine performance-driven design assumptions: high number of selects, low number of updates fast searching, slow indexation cache everything cacheable search functionality: search for words, phrases, regular expressions search in any field, authors, titles, etc index design: forward indexes: word1 [rec1, rec2,... ] word2 [rec2, rec7,... ] reverse indexes: rec1 [word1, word8,... ] rec2 [word1, word2,... ] Zipf s law on word frequency: few words occur very often (e.g. the) most words are infrequent (even e.g. boson)

117 Search Engine Under Cover

118 Measuring the Performance three important speed factors to consider: speed of finding sets (DB Server) speed of demarshaling sets (DB Web App Server) speed of intersecting sets (Web App Server) Example: speed of various parts (2002, before optimization) action / query: "CERN 2002" "of the this" fetching 0.28 sec 0.34 sec demarshaling 0.78 sec 1.10 sec adding colls 0.37 sec 0.63 sec intersecting 0.64 sec 1.19 sec total search time 2.07 sec 3.22 sec

119 Optimizing Data Structures data structures tested: sorted (lists, Patricia trees) unsorted (hashed sets, binary vectors) fast prototyping: (Python, Lisp in 2002) throw-away coding to test ideas Example: lists vs dicts, 350K sets in 800K universe marshaling lists bytes in 1.33 sec demarshaling lists items in 0.10 sec merging lists items in 0.34 sec intersecting lists items in 0.35 sec marshaling dicts bytes in 0.87 sec demarshaling dicts items in 0.36 sec merging dicts items in 0.09 sec intersecting dicts items in 0.15 sec

120 ... and the winner is: binary vectors found the best compromise! using Numeric Python module (in 2002) typical search time gain: 4.0 sec 0.2 sec (in 2002) typical indexing time loss: 7 hours 4 days (in 2002) mostly spare data modelled via mostly dense data structure? free your mind, think critically further optimization: Numeric module not addressing real bits, only bytes so home-made intbitset C extension in 2007 addressing real bits (factor of 8 already) saving space, saving (indexing) time

121 Outline 1 2 3

122 Splitting Web App Server and DB Server load of CDS Web and DB servers at the split time: split leads to efficient use of OS resources by lone, non-competing Web and DB daemon processes

123 Load-Balanced Setup useful for LHC First Beam Day rush situations with many concurrent visitors Apache mod_proxy_balancer App Worker 1 User Load Balancer App Worker 2 DB Server App Worker 3

124 Measuring Scalability using siege to simulate concurrent users and to measure throughput on a sample of typical URLs Example: inspirebeta.net under gentle siege $ siege -d 1 -c 20 -t 1m -f inspirebeta_urls.txt Transactions: 1329 hits Availability: % Elapsed time: secs Data transferred: MB Response time: 0.41 secs Transaction rate: trans/sec Throughput: 0.62 MB/sec Concurrency: 8.96 Successful transactions: 1329 Failed transactions: 0 Longest transaction: 3.05 Shortest transaction: 0.01

125 selected lessons from building a digital library system 300,000 LOCs from 75 authors over 10 years value of rapid prototyping value of organic-growth software development model value of coding aesthetics and minimalism morale from selected anecdotes? Never Lose A Holy Curiosity (A. Einstein)

Outline. Selected Practical Software Development Lessons From A Large Digital Library System. Tibor Šimko <tibor.simko@cern.ch>

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