Sign upLogin

KarrLab/datanator_query_python

View on GitHub
Star

Showing 190 of 190 total issues

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        for bucket_all in r_all['top_kos']['buckets']:
            ko_all.add(bucket_all['top_ko']['hits']['hits'][0]['_source'].get(agg_field))
Severity: Major
Found in datanator_query_python/query/full_text_search.py and 1 other location - About 1 hr to fix
datanator_query_python/query/full_text_search.py on lines 414..415

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 45.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        if op == "update":
            self.client[db][col].update_one(query,
                                            _update,
                                            upsert=True)
        else:
Severity: Major
Found in datanator_query_python/util/mongo_util.py and 1 other location - About 1 hr to fix
datanator_query_python/util/mongo_util.py on lines 128..133

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 45.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        for bucket_abundance in r['aggregations']['top_kos']['buckets']:
            ko_abundance.add(bucket_abundance['top_ko']['hits']['hits'][0]['_source'].get(agg_field))
Severity: Major
Found in datanator_query_python/query/full_text_search.py and 1 other location - About 1 hr to fix
datanator_query_python/query/full_text_search.py on lines 417..418

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 45.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

            if ko_str != None:
                # s['top_ko']['hits']['hits'][0]['_source']['abundances'] = True
                s['top_ko']['hits']['hits'][0]['_source'][agg_field] = [ko_str[i:i+6] for i in range(0, len(ko_str), 6)]
            else:
                # s['top_ko']['hits']['hits'][0]['_source']['abundances'] = False
Severity: Major
Found in datanator_query_python/query/full_text_search.py and 1 other location - About 1 hr to fix
datanator_query_python/query/full_text_search.py on lines 423..428

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 43.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

            if ko_str is None:
            #     # s['top_ko']['hits']['hits'][0]['_source']['abundances'] = True
            #     s['top_ko']['hits']['hits'][0]['_source'][agg_field] = [ko_str[i:i+6] for i in range(0, len(ko_str), 6)]
            # else:
                # s['top_ko']['hits']['hits'][0]['_source']['abundances'] = False
Severity: Major
Found in datanator_query_python/query/full_text_search.py and 1 other location - About 1 hr to fix
datanator_query_python/query/full_text_search.py on lines 310..315

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 43.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db='datanator',
Severity: Major
Found in datanator_query_python/query/query_pax.py - About 1 hr to fix

    Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,
    Severity: Major
    Found in datanator_query_python/query/query_metabolites_meta.py - About 1 hr to fix

      Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db='datanator',
      Severity: Major
      Found in datanator_query_python/query/query_sabiork_old.py - About 1 hr to fix

        Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def __init__(self, cache_dirname=None, collection_str='taxon_tree',
        Severity: Major
        Found in datanator_query_python/query/query_taxon_tree.py - About 1 hr to fix

          Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db='datanator',
          Severity: Major
          Found in datanator_query_python/query/query_sabio_reaction_entries.py - About 1 hr to fix

            Function inchi_to_inchikey has 34 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def inchi_to_inchikey(self, szINCHISource):
        '''
            fork from git@github.com:mnowotka/chembl_ikey.git
        '''
        flagstd = 'S'
            Severity: Minor
            Found in datanator_query_python/util/chem_util.py - About 1 hr to fix

              Similar blocks of code found in 2 locations. Consider refactoring.
              Open

                      bounded_s = {'$or': [{'substrates': {'$size': len(substrates)}}, {'substrates': {'$size': len(substrates) + 1}}]}
              Severity: Major
              Found in datanator_query_python/query/query_sabio_reaction_entries.py and 1 other location - About 1 hr to fix
              datanator_query_python/query/query_sabio_reaction_entries.py on lines 39..39

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 42.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Similar blocks of code found in 2 locations. Consider refactoring.
              Open

                      bounded_p = {'$or': [{'products': {'$size': len(products)}}, {'products': {'$size': len(products) + 1}}]}
              Severity: Major
              Found in datanator_query_python/query/query_sabio_reaction_entries.py and 1 other location - About 1 hr to fix
              datanator_query_python/query/query_sabio_reaction_entries.py on lines 38..38

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 42.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Function get_metabolite_synonyms has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
              Open

                  def get_metabolite_synonyms(self, compounds):
        ''' Find synonyms of a compound

            Args:
                compound (list): name(s) of the compound e.g. "ATP", ["ATP", "Oxygen", ...]
              Severity: Minor
              Found in datanator_query_python/query/query_metabolites_meta.py - About 1 hr to fix

              Cognitive Complexity

              Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

              A method's cognitive complexity is based on a few simple rules:

              • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
              • Code is considered more complex for each "break in the linear flow of the code"
              • Code is considered more complex when "flow breaking structures are nested"

              Further reading

              Identical blocks of code found in 3 locations. Consider refactoring.
              Open

                      return {str(org1): distance1, str(org2): distance2, str(org1)+'_canon_ancestors':canon_anc_1,
        str(org2)+'_canon_ancestors':canon_anc_2}
              Severity: Major
              Found in datanator_query_python/query/query_protein.py and 2 other locations - About 1 hr to fix
              datanator_query_python/query/query_taxon_tree.py on lines 403..404
              datanator_query_python/query/query_taxon_tree.py on lines 453..454

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 41.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db='test',
              Severity: Major
              Found in datanator_query_python/util/mongo_util.py - About 1 hr to fix

                Identical blocks of code found in 3 locations. Consider refactoring.
                Open

                        return {str(org1): distance1, str(org2): distance2, str(org1)+'_canon_ancestors':canon_anc_1,
        str(org2)+'_canon_ancestors':canon_anc_2}
                Severity: Major
                Found in datanator_query_python/query/query_taxon_tree.py and 2 other locations - About 1 hr to fix
                datanator_query_python/query/query_protein.py on lines 1023..1024
                datanator_query_python/query/query_taxon_tree.py on lines 403..404

                Duplicated Code

                Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                Tuning

                This issue has a mass of 41.

                We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                Refactorings

                Further Reading

                Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def __init__(self, username=None, password=None, server=None, authSource='admin',
                Severity: Major
                Found in datanator_query_python/query/query_intact_complex.py - About 1 hr to fix

                  Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def __init__(self, username=None, password=None, server=None, authSource='admin',
                  Severity: Major
                  Found in datanator_query_python/query/query_xmdb.py - About 1 hr to fix

                    Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                        def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db='datanator',
                    Severity: Major
                    Found in datanator_query_python/query/query_sabiork.py - About 1 hr to fix
                      Severity
                      Category
                      Status
                      Source
                      Language